Citrus Sinensis ID: 042645

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------
Protein Sequence
MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVRRREQEVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHcHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHccccccEEEEEccccccHHHHHHHHHcccccccccccEEEEEEEcccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHcccccEEEEEcccccccccccccccccccccccEEEEEcccHHHHHHccccccEEcccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccccHHHHHHHHHHHHccccccccccccHHHHHHHcccccccccHHHHHHHHccccccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHccHHHHHHHHHHHHHHHHHcccccEEEccccccccccccccccEEccHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHHccccHccccccEEEEEEEcccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHccccEEEEEEccccHccHHHHcccccccccccEEEEEEccHHHHHHccccccEEEccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcHHcccccccccHHHHEEcHcccccHHHHHHHHHHHcccccccEcHHHHHHHHc
Coil and Loop (DISEMBL)
mgnvcstslscddtisrCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVRRREQEVICLdglryrssiksykYGKRVVKSLKNVqglrkegdfkdvaqtvpenpvderplpptvvgmqSTLDRVWRClteepvgivglygmggvgkTTLLTQINnsflhtpndfdFVIWEVVSRDLQLGKIQESIAKKIGLYneswdnksfDEKAQEIFKTMRNRKIVLLLDDIWELFDlaqvglpvpsrasaskvvfTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGrdildshpdipELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFsydflpsnetrFCLLYcgffpedysisIEDLIDCWI
Flexible Loop (DISEMBL)
mgnvcstslscddTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRrlqqvqgwlsrvqdveeevrrreqevicldglryrssiksykygkrvVKSLknvqglrkegdfkdvaqtvpenpvderplpptvVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIglyneswdnksfDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGlpvpsrasaskVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLrssaskfsgMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI
Low Complexity Region (SEG)
MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSrvqdveeevrrreqevICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPvgivglygmggvgKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI
Disordered region (IsUnstruct)
*******SLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVRRREQEVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGL**************************VVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLR************ALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCW*
Disordered Region (DISOPRED)
**NVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVRRREQEVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLR****************************MQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL*************AQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSS*****G**KKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI
Disordered Region (DISEMBL)
**********CDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVRRREQEVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA********EWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI
Disordered Region (DISPRO)
*GNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVRRREQEVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQxxxxxxxxxxxxxxxxxxxxxVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI
Positional Conservation
no confident homologs detected

---

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	427	2.2.26 [Sep-21-2011]
Q8RXS5	888	Probable disease resistan	yes	no	0.997	0.479	0.459	1e-106
O82484	892	Putative disease resistan	no	no	0.995	0.476	0.454	1e-105
P60838	894	Probable disease resistan	no	no	0.997	0.476	0.453	1e-101
Q8L3R3	885	Disease resistance protei	no	no	0.997	0.481	0.453	1e-101
Q9LMP6	851	Probable disease resistan	no	no	0.995	0.499	0.448	1e-101
O64973	889	Disease resistance protei	no	no	1.0	0.480	0.463	1e-101
Q940K0	889	Probable disease resistan	no	no	0.992	0.476	0.454	1e-100
O22727	967	Probable disease resistan	no	no	0.995	0.439	0.452	1e-100
O64789	925	Probable disease resistan	no	no	0.988	0.456	0.454	3e-99
P60839	884	Probable disease resistan	no	no	1.0	0.483	0.429	1e-98

>sp|Q8RXS5|DRL40_ARATH Probable disease resistance protein At5g63020 OS=Arabidopsis thaliana GN=At5g63020 PE=2 SV=2

 Score =  386 bits (992), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 199/433 (45%), Positives = 277/433 (63%), Gaps = 7/433 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MG   S S+SCD        C+     YI  L++NL AL+   +++ + R D+L ++   
Sbjct: 1   MGGCVSVSISCDQLTKNVCSCLNRNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSE 60

Query: 61  EQRQMRRLQQVQGWLSRVQD----VEEEVRRREQEV--ICLDGLRYRSSIKSYKYGKRVV 114
           E+R ++RL  VQGW+S+V+     V E VR R  +V  +CL G   ++ + SY+YGKRV+
Sbjct: 61  ERRGLQRLSVVQGWVSKVEAIVPRVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVM 120

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
           K ++ V+ LR +GDF  VA+ V    V+ERP  P +V M   L+  W  L E+ +GI+GL
Sbjct: 121 KMIEEVEVLRYQGDFAVVAERVDAARVEERPTRP-MVAMDPMLESAWNRLMEDEIGILGL 179

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           +GMGGVGKTTLL+ INN F     +FD VIW VVS++LQ+ +IQ+ I +K+   NE W  
Sbjct: 180 HGMGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDNEKWKQ 239

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
           K+ D KA  I+  +++++ VLLLDDIW   DL +VG+P PSR +  K+VFTTR  E+CG 
Sbjct: 240 KTEDIKASNIYNVLKHKRFVLLLDDIWSKVDLTEVGVPFPSRENGCKIVFTTRLKEICGR 299

Query: 295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
           M      +V CL  +DAW LF +KVG   L SHP+IP +A TVA++C GLPLAL  +G  
Sbjct: 300 MGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALNVIGET 359

Query: 355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
           MA K+  +EW  AI+VL SSA++FSGME + L  LK+SYD L S + + C  YC  FPED
Sbjct: 360 MAYKRTVQEWRSAIDVLTSSAAEFSGMEDEILPILKYSYDNLKSEQLKLCFQYCALFPED 419

Query: 415 YSISIEDLIDCWI 427
           ++I   DL+D WI
Sbjct: 420 HNIEKNDLVDYWI 432

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

>sp|O82484|DRL23_ARATH Putative disease resistance protein At4g10780 OS=Arabidopsis thaliana GN=At4g10780 PE=2 SV=1

 Score =  382 bits (982), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 197/433 (45%), Positives = 263/433 (60%), Gaps = 8/433 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MG+  S  +SCD  ++R   C  S   YI  LKDN+ AL    + L   R+DVL RV + 
Sbjct: 1   MGSCISLQISCDQVLTRAYSCFFSLGNYIHKLKDNIVALEKAIEDLTATRDDVLRRVQME 60

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEE------VRRREQEVICLDGLRYRSSIKSYKYGKRVV 114
           E + + RLQQVQ WL RV+ +  +       R  E + +C       +   SY YG+RV 
Sbjct: 61  EGKGLERLQQVQVWLKRVEIIRNQFYDLLSARNIEIQRLCFYSNCSTNLSSSYTYGQRVF 120

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
             +K V+ L   G F+ VA   P+  ++ RP+ PT++G ++   R W  L ++ VG +GL
Sbjct: 121 LMIKEVENLNSNGFFEIVAAPAPK--LEMRPIQPTIMGRETIFQRAWNRLMDDGVGTMGL 178

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           YGMGGVGKTTLLTQI+N+   T N  D VIW VVS DLQ+ KIQE I +K+G   + W+ 
Sbjct: 179 YGMGGVGKTTLLTQIHNTLHDTKNGVDIVIWVVVSSDLQIHKIQEDIGEKLGFIGKEWNK 238

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
           K   +KA +I   +  ++ VLLLDDIW+  DL ++G+P  +R +  KVVFTTR  +VC  
Sbjct: 239 KQESQKAVDILNCLSKKRFVLLLDDIWKKVDLTKIGIPSQTRENKCKVVFTTRSLDVCAR 298

Query: 295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
           M  H   +V+CL   DAW LF+EKVG+  L SHPDI ELA+ VA +C GLPLAL  +G  
Sbjct: 299 MGVHDPMEVQCLSTNDAWELFQEKVGQISLGSHPDILELAKKVAGKCRGLPLALNVIGET 358

Query: 355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
           MA K+A +EW HA++VL S A++FSGM+   L  LK+SYD L     R C  YC  +PED
Sbjct: 359 MAGKRAVQEWHHAVDVLTSYAAEFSGMDDHILLILKYSYDNLNDKHVRSCFQYCALYPED 418

Query: 415 YSISIEDLIDCWI 427
           YSI    LID WI
Sbjct: 419 YSIKKYRLIDYWI 431

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P60838|DRL1_ARATH Probable disease resistance protein At1g12280 OS=Arabidopsis thaliana GN=At1g12280 PE=3 SV=1

 Score =  370 bits (949), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 197/434 (45%), Positives = 266/434 (61%), Gaps = 8/434 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MG   + S SCD+ +++    +    GYIC L  N+ A++ + + L + R+DV  RV + 
Sbjct: 1   MGACLTLSFSCDEVVNQISQGLCINVGYICELSKNVVAMKKDMEVLKKKRDDVKRRVDIE 60

Query: 61  E-QRQMRRLQQVQGWLSRVQDVEEEVRR------REQEVICLDGLRYRSSIKSYKYGKRV 113
           E  R+  RL QVQGWL+ V  VE +          E + +CL G   ++   SY YGKRV
Sbjct: 61  EFTRRRERLSQVQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRV 120

Query: 114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVG 173
           V  LK ++ L  +GDF  V    P   ++E P+ PT+VG ++ L+RVW  LTE+   IVG
Sbjct: 121 VLMLKEIESLSSQGDFDTVTLATPIARIEEMPIQPTIVGQETMLERVWTRLTEDGDEIVG 180

Query: 174 LYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
           LYGMGGVGKTTLLT+INN F    + F  VIW VVS+   + +IQ  I K++ L  E WD
Sbjct: 181 LYGMGGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEEWD 240

Query: 234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG 293
           N + +++A +I+  +  +K VLLLDDIWE  +L  +G+P PSR +  KVVFTTR  +VCG
Sbjct: 241 NVNENQRALDIYNVLGKQKFVLLLDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCG 300

Query: 294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
            M      +V CL   +AW LF+ KVG + L  HPDIPELA  VA +C GLPLAL  +G 
Sbjct: 301 RMRVDDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPELARKVAGKCCGLPLALNVIGE 360

Query: 354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
            MA K+  +EW +AI+VL S A++F GME + L  LK+SYD L   + + C LYC  FPE
Sbjct: 361 TMACKRMVQEWRNAIDVLSSYAAEFPGME-QILPILKYSYDNLNKEQVKPCFLYCSLFPE 419

Query: 414 DYSISIEDLIDCWI 427
           DY +  E LID WI
Sbjct: 420 DYRMEKERLIDYWI 433

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L3R3|RFL1_ARATH Disease resistance protein RFL1 OS=Arabidopsis thaliana GN=RFL1 PE=3 SV=2

 Score =  370 bits (949), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 197/434 (45%), Positives = 265/434 (61%), Gaps = 8/434 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MG   S SLSCD  +++    +     YI +L +NL +L+     L   R+DV  R+   
Sbjct: 1   MGGCVSVSLSCDREVNQFSQWLCVSGSYIQNLSENLASLQKAMGVLNAKRDDVQGRINRE 60

Query: 61  E-QRQMRRLQQVQGWLSRVQDVEEEVR------RREQEVICLDGLRYRSSIKSYKYGKRV 113
           E     RRL QVQ WL+R+Q +E +          E + +CL G   ++   SY YGKRV
Sbjct: 61  EFTGHRRRLAQVQVWLTRIQTIENQFNDLLSTCNAEIQRLCLCGFCSKNVKMSYLYGKRV 120

Query: 114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVG 173
           +  L+ V+GL  +G F  V +  P   V+E P+  T+VG  S LD+VW CL E+ V IVG
Sbjct: 121 IVLLREVEGLSSQGVFDIVTEAAPIAEVEELPIQSTIVGQDSMLDKVWNCLMEDKVWIVG 180

Query: 174 LYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
           LYGMGGVGKTTLLTQINN F      FD VIW VVS++  + KIQ+SI +K+GL  ++WD
Sbjct: 181 LYGMGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVGKNWD 240

Query: 234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG 293
            K+ +++A +I   +R +K VLLLDDIWE  +L  +G+P PS  +  KV FTT   EVCG
Sbjct: 241 EKNKNQRALDIHNVLRRKKFVLLLDDIWEKVELKVIGVPYPSGENGCKVAFTTHSKEVCG 300

Query: 294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
            M      ++ CL   +AW L ++KVG + L SHPDIP+LA  V+ +C GLPLAL  +G 
Sbjct: 301 RMGVDNPMEISCLDTGNAWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPLALNVIGE 360

Query: 354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
            M+ K+  +EW HA EVL +SA+ FSGME + L  LK+SYD L   + + C LYC  FPE
Sbjct: 361 TMSFKRTIQEWRHATEVL-TSATDFSGMEDEILPILKYSYDSLNGEDAKSCFLYCSLFPE 419

Query: 414 DYSISIEDLIDCWI 427
           D+ I  E LI+ WI
Sbjct: 420 DFEIRKEMLIEYWI 433

Disease resistance (R) protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LMP6|DRL3_ARATH Probable disease resistance protein At1g15890 OS=Arabidopsis thaliana GN=At1g15890 PE=3 SV=2

 Score =  369 bits (948), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 194/433 (44%), Positives = 270/433 (62%), Gaps = 8/433 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGN  +  +SCD T++    C+     YI  ++ NL+AL+   Q+L E R+D+L RV + 
Sbjct: 1   MGNCVALEISCDQTLNHACGCLFGDRNYILKMEANLEALQNTMQELEERRDDLLRRVVIE 60

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEEV------RRREQEVICLDGLRYRSSIKSYKYGKRVV 114
           E + ++RL QVQGWLSRV+DV  +V      +  + E +CL G   ++ I    YG  V+
Sbjct: 61  EDKGLQRLAQVQGWLSRVKDVCSQVNDLLKAKSIQTERLCLCGYCSKNFISGRNYGINVL 120

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
           K LK+V+GL  +G F+ VA+ +P   V+++ +  T VG+ + + R W  L ++    +GL
Sbjct: 121 KKLKHVEGLLAKGVFEVVAEKIPAPKVEKKHIQ-TTVGLDAMVGRAWNSLMKDERRTLGL 179

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           YGMGGVGKTTLL  INN FL   N FD VIW VVS+DLQ   IQE I  ++GL+   W  
Sbjct: 180 YGMGGVGKTTLLASINNKFLEGMNGFDLVIWVVVSKDLQNEGIQEQILGRLGLH-RGWKQ 238

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
            +  EKA  I   +  +K VLLLDD+W   DL ++G+P  +R + SK+VFTTR  +VC  
Sbjct: 239 VTEKEKASYICNILNVKKFVLLLDDLWSEVDLEKIGVPPLTRENGSKIVFTTRSKDVCRD 298

Query: 295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
           M+     KV+CL  ++AW LF++KVG   L SH DIP LA  VA +C GLPLAL  +G+A
Sbjct: 299 MEVDGEMKVDCLPPDEAWELFQKKVGPIPLQSHEDIPTLARKVAEKCCGLPLALSVIGKA 358

Query: 355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
           MAS++  +EW H I VL SS+ +F  ME+K L  LKFSYD L   + + C LYC  FPED
Sbjct: 359 MASRETVQEWQHVIHVLNSSSHEFPSMEEKILPVLKFSYDDLKDEKVKLCFLYCSLFPED 418

Query: 415 YSISIEDLIDCWI 427
           Y +  E+LI+ W+
Sbjct: 419 YEVRKEELIEYWM 431

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O64973|RPS5_ARATH Disease resistance protein RPS5 OS=Arabidopsis thaliana GN=RPS5 PE=1 SV=2

 Score =  368 bits (944), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 201/434 (46%), Positives = 263/434 (60%), Gaps = 7/434 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MG   S SL CD  +S+    +  +  YI +L  NL +L+   + L   + DV+ R+   
Sbjct: 1   MGGCFSVSLPCDQVVSQFSQLLCVRGSYIHNLSKNLASLQKAMRMLKARQYDVIRRLETE 60

Query: 61  E-QRQMRRLQQVQGWLSRVQDVEEE----VRRREQEV--ICLDGLRYRSSIKSYKYGKRV 113
           E   + +RL QVQ WL+ V  ++ +    +R  E E+  +CL G   +    SY+YGKRV
Sbjct: 61  EFTGRQQRLSQVQVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRV 120

Query: 114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVG 173
           +  LK V+ L  +G F  V++  P   VDE P  PT+VG +  L++ W  L E+  GI+G
Sbjct: 121 IMMLKEVESLSSQGFFDVVSEATPFADVDEIPFQPTIVGQEIMLEKAWNRLMEDGSGILG 180

Query: 174 LYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
           LYGMGGVGKTTLLT+INN F    + FD VIW VVSR   + KIQ  IA+K+GL    W 
Sbjct: 181 LYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWS 240

Query: 234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG 293
            K+ ++ A +I   +R RK VLLLDDIWE  +L  VG+P PS+ +  KV FTTR  +VCG
Sbjct: 241 EKNDNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCG 300

Query: 294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
            M      +V CL  E++W LF+ KVG++ L SHPDIP LA  VAR+C GLPLAL  +G 
Sbjct: 301 RMGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGE 360

Query: 354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
           AMA K+   EW HAI+VL SSA  FSGME + L  LK+SYD L     + C LYC  FPE
Sbjct: 361 AMACKRTVHEWCHAIDVLTSSAIDFSGMEDEILHVLKYSYDNLNGELMKSCFLYCSLFPE 420

Query: 414 DYSISIEDLIDCWI 427
           DY I  E L+D WI
Sbjct: 421 DYLIDKEGLVDYWI 434

Disease resistance (R) protein that specifically recognizes the avrPphB type III effector avirulence protein from Pseudomonas syringae. Also confers resistance against Hyaloperonospora parasitica (downy mildew). Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Requires PBS1 to trigger the defense reaction against avrPphB. Probably triggers the defense mechanism when PBS1 is cleaved by avrPphB, suggesting that it detects indirectly the protease activity of avrPphB, and possibly binds to the cleaved RPS5.

Arabidopsis thaliana (taxid: 3702)

>sp|Q940K0|DRL15_ARATH Probable disease resistance protein At1g61180 OS=Arabidopsis thaliana GN=At1g61180 PE=2 SV=2

 Score =  366 bits (940), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 197/433 (45%), Positives = 269/433 (62%), Gaps = 9/433 (2%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MG+  S  +S D T++R  +C++ ++ YI  L+ NL AL+ E + L   +++V  +V   
Sbjct: 1   MGSCFSLQVS-DQTLNRIFNCLIGKS-YIRTLEKNLRALQREMEDLRAIQHEVQNKVARD 58

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEE------VRRREQEVICLDGLRYRSSIKSYKYGKRVV 114
           E R  RRL+ VQ WL RV  V+ E      V   E + +CL GL  +    SYKYGK+V 
Sbjct: 59  EARHQRRLEAVQVWLDRVNSVDIECKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVF 118

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
             L+ V+ L  EG+F +V+Q  P + V+ERP  PT+ G +  L++ W  L E+ VGI+GL
Sbjct: 119 LLLEEVKKLNSEGNFDEVSQPPPRSEVEERPTQPTI-GQEDMLEKAWNRLMEDGVGIMGL 177

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           +GMGGVGKTTL  +I+N F      FD VIW VVS+ + + K+QE IA+K+ L ++ W N
Sbjct: 178 HGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDLWKN 237

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
           K+  +KA +I + ++ ++ VL+LDDIWE  DL  +G+P PS  +  KV FTTR  EVCG 
Sbjct: 238 KNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCGE 297

Query: 295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
           M  HK  +V CL  EDAW LF+ KVG + L S P I ELA  VA++C GLPLAL  +G  
Sbjct: 298 MGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVELAREVAQKCRGLPLALNVIGET 357

Query: 355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
           M+SK   +EW HAI V  +SA++FS M+ K L  LK+SYD L     + C LYC  FPED
Sbjct: 358 MSSKTMVQEWEHAIHVFNTSAAEFSDMQNKILPILKYSYDSLGDEHIKSCFLYCALFPED 417

Query: 415 YSISIEDLIDCWI 427
             I  E LID WI
Sbjct: 418 GEIYNEKLIDYWI 430

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O22727|DRL16_ARATH Probable disease resistance protein At1g61190 OS=Arabidopsis thaliana GN=At1g61190 PE=3 SV=1

 Score =  365 bits (937), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 196/433 (45%), Positives = 268/433 (61%), Gaps = 8/433 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGN     +S D  + R + C+  + GYI +L+ NL AL+ E + L   +++V  +V   
Sbjct: 1   MGNFVCIEISGDQMLDRIIRCLCGK-GYIRNLEKNLRALQREMEDLRATQHEVQNKVARE 59

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEE------VRRREQEVICLDGLRYRSSIKSYKYGKRVV 114
           E R  +RL+ VQ WL RV  ++ E      V   E + +CL GL  +    SYKYGKRV 
Sbjct: 60  ESRHQQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVF 119

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
             L+ V  L+ EG+F +V+Q  P + V+ERP  PT+ G +  L + W  L E+ VGI+GL
Sbjct: 120 LLLEEVTKLKSEGNFDEVSQPPPRSEVEERPTQPTI-GQEEMLKKAWNRLMEDGVGIMGL 178

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           +GMGGVGKTTL  +I+N F  T   FD VIW VVS+  +L K+QE IA+K+ L ++ W N
Sbjct: 179 HGMGGVGKTTLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKN 238

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
           K+  +KA +I + ++ ++ VL+LDDIWE  DL  +G+P PS  +  KV FTTR+ +VCG 
Sbjct: 239 KNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRDQKVCGQ 298

Query: 295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
           M  HK  +V+CL  EDAW LF+ KVG + L S P I  LA  VA++C GLPLAL  +G  
Sbjct: 299 MGDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSCIGET 358

Query: 355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
           MASK   +EW HAI+VL  SA++FS M+ K L  LK+SYD L     + C LYC  FPED
Sbjct: 359 MASKTMVQEWEHAIDVLTRSAAEFSDMQNKILPILKYSYDSLEDEHIKSCFLYCALFPED 418

Query: 415 YSISIEDLIDCWI 427
             I  + LI+ WI
Sbjct: 419 DKIDTKTLINKWI 431

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O64789|DRL18_ARATH Probable disease resistance protein At1g61310 OS=Arabidopsis thaliana GN=At1g61310 PE=2 SV=1

 Score =  362 bits (930), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 196/431 (45%), Positives = 269/431 (62%), Gaps = 9/431 (2%)

Query: 1   MGNVCSTSLSC-DDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTV 59
           MG+  S  ++  D T++R  DC++ ++ YI  L+ NL AL+ E + L   +++V  +V  
Sbjct: 1   MGSCFSFQIAVGDQTMNRIFDCLIGKS-YIRTLEKNLRALQREMEDLRATQHEVQNKVAR 59

Query: 60  AEQRQMRRLQQVQGWLSRVQDVEEE------VRRREQEVICLDGLRYRSSIKSYKYGKRV 113
            E R  +RL+ VQ WL RV  ++ E      V   E + +CL GL  +    SYKYGK+V
Sbjct: 60  EESRHQQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCTKYVCSSYKYGKKV 119

Query: 114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVG 173
              L+ V+ L+ EG+F +V+Q  P + V+ERP  PT+ G +  L++ W  L E+ VGI+G
Sbjct: 120 FLLLEEVKILKSEGNFDEVSQPPPRSEVEERPTQPTI-GQEEMLEKAWNRLMEDGVGIMG 178

Query: 174 LYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
           L+GMGGVGKTTL  +I+N F      FD VIW VVS+  +L K+QE IA+K+ L ++ W 
Sbjct: 179 LHGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWK 238

Query: 234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG 293
           NK+  +KA +I + ++ ++ VL+LDDIWE  DL  +G+P PS  +  KV FTTR  EVCG
Sbjct: 239 NKNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCG 298

Query: 294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
            M  HK  +V CL  EDAW LF+ KVG + L S P I  LA  VA++C GLPLAL  +G 
Sbjct: 299 EMGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVGLAREVAQKCRGLPLALNVIGE 358

Query: 354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
            MASK   +EW +AI+VL  SA++FSGME K L  LK+SYD L     + C LYC  FPE
Sbjct: 359 TMASKTMVQEWEYAIDVLTRSAAEFSGMENKILPILKYSYDSLGDEHIKSCFLYCALFPE 418

Query: 414 DYSISIEDLID 424
           D  I  E LID
Sbjct: 419 DGQIYTETLID 429

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P60839|DRL2_ARATH Probable disease resistance protein At1g12290 OS=Arabidopsis thaliana GN=At1g12290 PE=2 SV=1

 Score =  360 bits (925), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 186/433 (42%), Positives = 263/433 (60%), Gaps = 6/433 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MG   S  +SCD  ++    C   +  YI ++K+NL +L    + L   R+D+L +V  A
Sbjct: 1   MGGCVSVQVSCDQLLNHLGRCFCRKLYYIQNIKENLTSLEEAMEDLKALRDDLLRKVQTA 60

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEEV------RRREQEVICLDGLRYRSSIKSYKYGKRVV 114
           E+  ++RL Q++ WL RV+ +E +       R  E + +C  G+  R+   SY YG+RV 
Sbjct: 61  EEGGLQRLHQIKVWLKRVKTIESQFNDLDSSRTVELQRLCCCGVGSRNLRLSYDYGRRVF 120

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
             L  V+ L+ +G F++VA        +ERPL PT+VG ++ L++ W  L ++   I+GL
Sbjct: 121 LMLNIVEDLKSKGIFEEVAHPATRAVGEERPLQPTIVGQETILEKAWDHLMDDGTKIMGL 180

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           YGMGGVGKTTLLTQINN F  T +  + VIW VVS DLQ+ KIQ+ I +KIG     W+ 
Sbjct: 181 YGMGGVGKTTLLTQINNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGEKIGFIGVEWNQ 240

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
           KS ++KA +I   +  ++ VLLLDDIW+  +L ++G+P P+  +  K+ FTTR   VC  
Sbjct: 241 KSENQKAVDILNFLSKKRFVLLLDDIWKRVELTEIGIPNPTSENGCKIAFTTRCQSVCAS 300

Query: 295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
           M  H   +V CLG +DAW LF++KVG   L SHPDIPE+A  VA+ C GLPLAL  +G  
Sbjct: 301 MGVHDPMEVRCLGADDAWDLFKKKVGDITLSSHPDIPEIARKVAQACCGLPLALNVIGET 360

Query: 355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
           MA KK  +EW  A++V  + A+ F  ++++ L  LK+SYD L S   + C LYC  FPED
Sbjct: 361 MACKKTTQEWDRAVDVSTTYAANFGAVKERILPILKYSYDNLESESVKTCFLYCSLFPED 420

Query: 415 YSISIEDLIDCWI 427
             I  E LID WI
Sbjct: 421 DLIEKERLIDYWI 433

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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	427
24461861	890	NBS-LRR type disease resistance protein	1.0	0.479	0.579	1e-143
24461866	890	NBS-LRR type disease resistance protein	0.997	0.478	0.559	1e-136
224055915	880	cc-nbs-lrr resistance protein [Populus t	0.997	0.484	0.546	1e-130
24461864	899	NBS-LRR type disease resistance protein	0.997	0.473	0.556	1e-129
359482676	896	PREDICTED: probable disease resistance p	0.992	0.473	0.518	1e-123
24461865	892	NBS-LRR type disease resistance protein	0.995	0.476	0.534	1e-120
225443158	903	PREDICTED: probable disease resistance p	0.997	0.471	0.505	1e-120
24461863	889	NBS-LRR type disease resistance protein	0.974	0.467	0.532	1e-120
147787894	864	hypothetical protein VITISV_040594 [Viti	0.995	0.491	0.526	1e-119
255553135	894	Disease resistance protein RFL1, putativ	0.978	0.467	0.508	1e-119

>gi|24461861|gb|AAN62348.1|AF506028_15 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  513 bits (1320), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 252/435 (57%), Positives = 322/435 (74%), Gaps = 8/435 (1%)

Query: 1   MGNVCSTSLSCDDTI-SRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTV 59
           MGN+C  S+SCD    +RCLDC + +  YI +L+DNL AL TE +KLI A+ND++ RV  
Sbjct: 1   MGNICQISISCDGAFFNRCLDCFLGKAAYISNLQDNLVALDTELRKLIAAKNDLMRRVND 60

Query: 60  AEQRQMRRLQQVQGWLSRVQDVEEEVR------RREQEVICLDGLRYRSSIKSYKYGKRV 113
           AE++QMRRL QVQ W+SRV+ VE E         +E E +CL G   ++   SYK+GK+V
Sbjct: 61  AERQQMRRLDQVQVWVSRVETVETEADAFIGDGTQEIEKLCLGGYCSKNCKSSYKFGKQV 120

Query: 114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVG 173
            + L++++ L  EG F+ VA  VPE  VDERP  PTVVG+QS L+ VWRCL EEPVGIVG
Sbjct: 121 ARKLRDIKTLMGEGVFEVVADKVPEPAVDERPTEPTVVGLQSQLEEVWRCLVEEPVGIVG 180

Query: 174 LYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
           LYGMGGVGKTTLLT INN FL +P +FD VI  VVS+DL+L  IQE I +KIGL N++W 
Sbjct: 181 LYGMGGVGKTTLLTHINNKFLGSPTNFDLVILVVVSKDLRLESIQEVIGEKIGLLNDAWK 240

Query: 234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVP-SRASASKVVFTTREFEVC 292
           ++  ++KA +IF+ +R +  V+LLDDIW+  DLA+VG+P+P S+ SASKVVFTTR  EVC
Sbjct: 241 SRRIEQKALDIFRILRGKNFVVLLDDIWQRVDLAKVGIPLPNSQTSASKVVFTTRSEEVC 300

Query: 293 GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG 352
           GLM+AHK FKVECL   DAW LF +KVG + L+ H DI ELA+TV +ECGGLPLALIT+G
Sbjct: 301 GLMEAHKKFKVECLSGNDAWELFRQKVGEETLNCHHDILELAQTVTKECGGLPLALITIG 360

Query: 353 RAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFP 412
           RAMA KK P EW++AI+VLR+S+S+F G+  +    LKFSYD LP++  R CLLYC  +P
Sbjct: 361 RAMACKKTPEEWSYAIQVLRTSSSQFPGLGNEVYPLLKFSYDNLPNDTIRSCLLYCCLYP 420

Query: 413 EDYSISIEDLIDCWI 427
           ED  IS E+L+DCWI
Sbjct: 421 EDCCISKENLVDCWI 435

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461866|gb|AAN62353.1|AF506028_20 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  492 bits (1267), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 243/434 (55%), Positives = 317/434 (73%), Gaps = 8/434 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGNV    +   +   RCLD I+++  YI  L+DNLD L+T+ ++LIEA++DV+ RV +A
Sbjct: 1   MGNVFGVQIPWSNIFPRCLDWILNEAKYISQLEDNLDDLQTKLEQLIEAKDDVMNRVEIA 60

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEE------VRRREQEVICLDGLRYRSSIKSYKYGKRVV 114
           E++QM RL QVQGW+SRV+ V+ E      V  +E E +CL G   ++   SY +GK+V 
Sbjct: 61  ERQQMSRLNQVQGWVSRVEAVKAEADQLIRVGSQEIERLCLWGYCSKNCKSSYDFGKKVT 120

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
           K L+ V+ L  EG F+ VA+ VP     ERP  PTV+G+QS L++VWRCL EEP GIVGL
Sbjct: 121 KKLQLVETLMGEGIFEVVAEKVPGAAATERPTEPTVIGLQSQLEQVWRCLVEEPAGIVGL 180

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           YGMGGVGKTTLLT INN FL +  +F++VIW VVS+DL+L  IQE+I +KIGL N++W N
Sbjct: 181 YGMGGVGKTTLLTHINNKFLESTTNFNYVIWVVVSKDLRLENIQETIGEKIGLLNDTWKN 240

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPS-RASASKVVFTTREFEVCG 293
           +  ++KA +IFK ++ +K VLLLDD+W+  DL +VG+P+P  ++S SKVVFT+R  EVCG
Sbjct: 241 RRIEQKALDIFKILKEKKFVLLLDDLWQRVDLVEVGVPLPGPQSSTSKVVFTSRSEEVCG 300

Query: 294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
           LM+AHK FKV CL   DAW LF++KVG + L S PDI +LA+T A+ECGGLPLALIT+GR
Sbjct: 301 LMEAHKKFKVACLSDIDAWELFQQKVGEETLKS-PDIRQLAQTAAKECGGLPLALITIGR 359

Query: 354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
           AMA KK P EW +AIEVLR+S+S+F G+  +    LKFSYD LPS+  R CLLYC  +PE
Sbjct: 360 AMACKKTPEEWTYAIEVLRTSSSQFPGLGNEVYPLLKFSYDSLPSDTIRSCLLYCCLYPE 419

Query: 414 DYSISIEDLIDCWI 427
           DY IS E LIDCWI
Sbjct: 420 DYCISKEILIDCWI 433

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224055915|ref|XP_002298700.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222845958|gb|EEE83505.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  471 bits (1213), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 237/434 (54%), Positives = 302/434 (69%), Gaps = 8/434 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGN CS S+SCD  +S CLD    +  YI  LK+N+D L+   ++L +  NDV  RV V 
Sbjct: 1   MGNFCSISISCDKLLSGCLDFTFRKAVYISKLKENVDGLKIAVEELTDLHNDVTRRVKVD 60

Query: 61  EQRQMRRLQQVQGWLSR----VQDVEEEVRRREQEV--ICLDGLRYRSSIKSYKYGKRVV 114
           E++Q+++L QVQ W+SR    +    E +R   QE+  +CL G   ++   SY++ K V 
Sbjct: 61  EEQQLKQLDQVQRWISRAKAAIDKANELLREDSQEIERLCLRGYCSKNYKSSYRFAKEVD 120

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEP-VGIVG 173
           K L++V  L+  GDFK VA+ VP      RP  PTV G++ST ++VW CL EE  VGIVG
Sbjct: 121 KRLRDVADLKANGDFKVVAEKVPAASGVPRPSEPTV-GLESTFNQVWTCLREEKQVGIVG 179

Query: 174 LYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
           LYGMGGVGKTTLLTQINN  L TP+DFD VIW VVS+DL+L  +QESI + IG  ++ W 
Sbjct: 180 LYGMGGVGKTTLLTQINNESLKTPDDFDIVIWVVVSKDLKLNTVQESIGRNIGCSDDLWK 239

Query: 234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG 293
           NKS DEKA +IF  +R+++ V+LLDDIWE  DL ++G+P+P   + SKVVFTTR  E+CG
Sbjct: 240 NKSLDEKAVDIFNALRHKRFVMLLDDIWERVDLKKLGVPLPDMNNGSKVVFTTRSEEICG 299

Query: 294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
           LMDAHK+ KV+CL ++DAW LF++KVG   L  H DIP+LA  VA+ECGGLPLALIT+GR
Sbjct: 300 LMDAHKTMKVDCLAWDDAWDLFQKKVGDQTLCVHTDIPKLARNVAKECGGLPLALITIGR 359

Query: 354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
           AMA KK P+EW HAIEVLR SAS+FSGM  +    LKFSYD L   + R C LYC  FPE
Sbjct: 360 AMACKKTPQEWRHAIEVLRKSASEFSGMGDEVFPLLKFSYDNLSKQKIRTCFLYCSLFPE 419

Query: 414 DYSISIEDLIDCWI 427
           D+ I+  DLID WI
Sbjct: 420 DFLINKNDLIDYWI 433

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461864|gb|AAN62351.1|AF506028_18 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  469 bits (1207), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 243/437 (55%), Positives = 306/437 (70%), Gaps = 11/437 (2%)

Query: 1   MGNVCSTSLSCDDT-ISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTV 59
           MGN+   S+SCD T  +RCLDC + +  Y+ +L+ N++AL+ E  KLI  ++DV+ RV  
Sbjct: 1   MGNILQISISCDGTCFNRCLDCFLGKAAYVRNLQKNVEALKNELPKLIAKKDDVMARVVN 60

Query: 60  AEQRQM-RRLQQVQGWLSRVQDV----EEEVRRREQEV--ICLDGLRYRSSIKSYKYGKR 112
           AE++QM  RL +VQ WLSRV  V    +E +R   QE+  +CL G   ++   S K+GK+
Sbjct: 61  AERQQMMTRLNEVQLWLSRVDAVTAGADELIRIGSQEIEKLCLGGYCSKNCKSSKKFGKQ 120

Query: 113 VVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIV 172
           V K L +V+ L  EG F  VAQ  PE+  DERP+ P V G+QS L++VWRCL EEPVGIV
Sbjct: 121 VDKKLSDVKILLAEGSFAVVAQRAPESVADERPIEPAV-GIQSQLEQVWRCLVEEPVGIV 179

Query: 173 GLYGMGGVGKTTLLTQINNSFLHTPN-DFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES 231
           GLYGMGGVGKTTLLT +NN FL   +  FDF+IW VVS+DLQ+ KIQE I KK+GL+N+S
Sbjct: 180 GLYGMGGVGKTTLLTHLNNKFLGQRDFHFDFLIWVVVSKDLQIEKIQEIIGKKVGLFNDS 239

Query: 232 WDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSR-ASASKVVFTTREFE 290
           W  K+  E+A +I+  ++ +K VLLLDD+W+  D A VG+P+P R  SASKVVFTTR  E
Sbjct: 240 WMKKNLAERAVDIYNVLKEKKFVLLLDDVWQRVDFATVGVPIPPRDKSASKVVFTTRSTE 299

Query: 291 VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT 350
           VCG M AHK  +VECL   DAW LF + VG + L+  P I ELAE VA+ECG LPLALI 
Sbjct: 300 VCGRMGAHKKIEVECLSANDAWELFRQNVGEETLNGQPKILELAERVAKECGCLPLALIV 359

Query: 351 VGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGF 410
            GRAMA KK P EW  AI+VL++SAS+F G+E   L  LKFSYD LP + TR CLLYC  
Sbjct: 360 TGRAMACKKTPAEWRDAIKVLQTSASEFPGLENNVLRVLKFSYDSLPDDTTRSCLLYCCL 419

Query: 411 FPEDYSISIEDLIDCWI 427
           FPEDY I  E+LIDCWI
Sbjct: 420 FPEDYRIYKENLIDCWI 436

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482676|ref|XP_002281742.2| PREDICTED: probable disease resistance protein At5g63020-like [Vitis vinifera]

 Score =  446 bits (1148), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 226/436 (51%), Positives = 299/436 (68%), Gaps = 12/436 (2%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGNVCS S+S +D   RC DC  ++  YIC L++N   LRTE QKL E RNDV  +V VA
Sbjct: 1   MGNVCSVSISTEDIAGRCCDCTAARANYICKLQENRVTLRTELQKLRELRNDVKRKVDVA 60

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEEVRRR--------EQEVICLDGLRY-RSSIKSYKYGK 111
           E++QM+RL QVQGWLSRV+D+E EV +         E++  C  G  Y +  I SY  GK
Sbjct: 61  ERQQMKRLDQVQGWLSRVEDMETEVTQLIGDGAENIEEKRFC--GSCYPKHCISSYTLGK 118

Query: 112 RVVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGI 171
           +VV+ L+ V  L  +G F+ VA  VP   V+E P   T VG++ST DRVWRCL EE VG+
Sbjct: 119 KVVRKLQQVAALMSDGRFEVVADIVPPAAVEEIP-SGTTVGLESTFDRVWRCLGEEHVGM 177

Query: 172 VGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES 231
           +GLYG+GGVGKTTLLTQINN FL T ++FD VIW VVS+   L ++Q  I +K+G  ++ 
Sbjct: 178 IGLYGLGGVGKTTLLTQINNHFLKTSHNFDVVIWVVVSKTPNLDEVQNEIWEKVGFCDDK 237

Query: 232 WDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEV 291
           W +KS   KA++I+K +  ++ V+LLDD+WE  +L +VG+P P + + SK++FTTR  ++
Sbjct: 238 WKSKSRHLKAKDIWKALNEKRFVMLLDDLWEQMNLLEVGIPPPHQQNKSKLIFTTRSLDL 297

Query: 292 CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV 351
           CG M A K  +V+ L ++D+W LF++ VG D L+S P+IPE AE VAREC GLPL +IT+
Sbjct: 298 CGQMGAQKKIEVKSLAWKDSWDLFQKYVGEDTLNSDPEIPEQAEIVARECCGLPLVIITI 357

Query: 352 GRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFF 411
           GRAMASK  P++W HAI VL++SASKF GM      RLK+SYD LP+   + C LYC  F
Sbjct: 358 GRAMASKVTPQDWKHAIRVLQTSASKFPGMGDPVYPRLKYSYDSLPTKIVQSCFLYCSLF 417

Query: 412 PEDYSISIEDLIDCWI 427
           PED+SI  E LI  WI
Sbjct: 418 PEDFSIDKEALIWKWI 433

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461865|gb|AAN62352.1|AF506028_19 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  438 bits (1127), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 233/436 (53%), Positives = 311/436 (71%), Gaps = 11/436 (2%)

Query: 1   MGNVCSTSLSCDDTI-SRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTV 59
           MGN+    ++CD  + +RCLDC + +  YI +LK NL  L TE  KLI+A+ DV+ RV  
Sbjct: 1   MGNI--FQITCDGALFNRCLDCFLGKAAYIKNLKQNLADLETELGKLIDAKEDVMRRVNT 58

Query: 60  AEQR-QMRRLQQVQGWLSRVQ----DVEEEVRRREQEV--ICLDGLRYRSSIKSYKYGKR 112
           AE+   M+RL +VQGWLSRV+    D ++ +    QE+  +CL G   ++   SY++GK+
Sbjct: 59  AERHPMMKRLNKVQGWLSRVEAAKSDGDKLITCGSQEIKKLCLGGYCSKNCKSSYEFGKQ 118

Query: 113 VVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIV 172
           V + L +V+ L  E  F+ VA+ VP+  VDERP  PTVVG+QS  ++V  CL EE   IV
Sbjct: 119 VARKLGDVKTLMAEEAFEAVAEEVPQPAVDERPTEPTVVGLQSQFEQVCNCLEEESARIV 178

Query: 173 GLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW 232
           GLYGMGGVGKTTLLT I+N F+ +P +F++VIW V S+DL+L  IQE+I ++IGL N++W
Sbjct: 179 GLYGMGGVGKTTLLTHIHNKFIQSPTNFNYVIWVVASKDLRLENIQETIGEQIGLLNDTW 238

Query: 233 DNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPS-RASASKVVFTTREFEV 291
            NK  ++KAQ+IF+ ++ +K +LLLDD+W+  DL +VG+P+P  + +ASKVVFTTR  EV
Sbjct: 239 KNKRIEQKAQDIFRILKQKKFLLLLDDLWQRVDLTKVGVPLPGPQNNASKVVFTTRSEEV 298

Query: 292 CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV 351
           CGLM AH  FKV CL   DAW LF + VG + ++SHPDI +LA+T ARECGGLPLALIT+
Sbjct: 299 CGLMGAHTRFKVACLSNIDAWELFRQNVGEETMNSHPDILQLAQTAARECGGLPLALITI 358

Query: 352 GRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFF 411
           GRAMA KK P EW++AIEVLR+S+S+F G+  +    LKFSYD LPS+  R C LYC  +
Sbjct: 359 GRAMACKKTPEEWSYAIEVLRTSSSQFPGLGNEVYPLLKFSYDSLPSDTIRSCHLYCSLY 418

Query: 412 PEDYSISIEDLIDCWI 427
           PEDY IS E LIDCWI
Sbjct: 419 PEDYCISKEKLIDCWI 434

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443158|ref|XP_002263674.1| PREDICTED: probable disease resistance protein At5g63020-like [Vitis vinifera]

 Score =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 219/433 (50%), Positives = 289/433 (66%), Gaps = 7/433 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGN+ S S+S  D++  C      +  YIC  ++N+ AL+   + L + RND+  +V + 
Sbjct: 1   MGNLFSVSISMQDSLPGCKGGTALRAKYICEFEENIKALKEALEDLKDFRNDMKRKVEMG 60

Query: 61  EQRQMRRLQQVQGWLSRVQDVEEEVRR------REQEVICLDGLRYRSSIKSYKYGKRVV 114
           E + M +L QVQ W SR + +E EV +      RE +  CL G   ++ + SYK G+++V
Sbjct: 61  EGQPMEQLDQVQRWFSRAEAMELEVDQLIRDGTRETQKFCLGGCCSKNCLSSYKLGRKLV 120

Query: 115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGL 174
           K   +V  LR    F  +A  +P   VDERP  PTV G +ST+D VW CL EE V I+GL
Sbjct: 121 KKADDVATLRSTRLFDGLADRLPPPAVDERPSEPTV-GFESTIDEVWSCLREEQVQIIGL 179

Query: 175 YGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
           YGMGGVGKTTL+TQ+NN FL T + FD VIW VVSRD    K+Q+ I KK+G  ++ W +
Sbjct: 180 YGMGGVGKTTLMTQVNNEFLKTIHQFDIVIWVVVSRDPNPEKVQDEIWKKVGFCDDKWKS 239

Query: 235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
           KS DEKA  IF+ +  +K VL LDD+WE FDL +VG+P+P++ + SK+VFTTR  EVCG 
Sbjct: 240 KSQDEKAISIFRILGKKKFVLFLDDVWERFDLLKVGIPLPNQQNNSKLVFTTRSEEVCGR 299

Query: 295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
           M AH+  KVECL ++ AW LF+  VG D L+SHP+IP+LAET+ +EC GLPLAL+T GR 
Sbjct: 300 MGAHRRIKVECLAWKQAWDLFQNMVGEDTLNSHPEIPQLAETIVKECLGLPLALVTTGRT 359

Query: 355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
           MA KKAP+EW  AI++L+SS+S F GM  +  S LKFSYD LPS+  R C LYC  +PED
Sbjct: 360 MACKKAPQEWKFAIKMLQSSSSSFPGMRDEVFSLLKFSYDNLPSDTARSCFLYCSLYPED 419

Query: 415 YSISIEDLIDCWI 427
             I  EDLIDCWI
Sbjct: 420 NDIFKEDLIDCWI 432

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461863|gb|AAN62350.1|AF506028_17 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  436 bits (1122), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 232/436 (53%), Positives = 289/436 (66%), Gaps = 20/436 (4%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGN+   ++      +RC+DC + +  YI +L++N+ AL TE  KLIEA+NDV+ RV   
Sbjct: 1   MGNILQIAID-GAVFNRCMDCFLGKAAYIRNLQENVVALETELGKLIEAKNDVMARVVNT 59

Query: 61  E-QRQMRRLQQVQGWLSRVQDVEEE----VRRREQEV--ICLDGLRYRSSIKSYKYGKRV 113
           E Q  M RL +VQGWLS V  V+ E    +R   QE+  +CL G   ++   SYK+GK+V
Sbjct: 60  ERQPMMTRLNKVQGWLSGVDAVKAEADELIRHGSQEIEKLCLGGYCSKNWKSSYKFGKQV 119

Query: 114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVG 173
            K L++   L  EG F+ VA+  PE+           VGMQS L+ VWRCL EEPVGIVG
Sbjct: 120 AKKLRDAGTLMAEGVFEVVAERAPES---------AAVGMQSRLEPVWRCLVEEPVGIVG 170

Query: 174 LYGMGGVGKTTLLTQINNSFLHTPN-DFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW 232
           LYGMGGVGKTTLLT +NN FL   +  FDF+IW VVS+DLQ+ KIQE I KK+G +N+SW
Sbjct: 171 LYGMGGVGKTTLLTHLNNKFLGQRDFHFDFLIWVVVSKDLQIEKIQEIIGKKVGFFNDSW 230

Query: 233 DNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSR-ASASKVVFTTREFEV 291
             K+  E+A +I+  ++ +K VLLLDD+W+  D A VG+P+P R  SASKVVFTTR  EV
Sbjct: 231 MKKNLAERAVDIYNVLKEKKFVLLLDDVWQRVDFATVGVPIPPRDKSASKVVFTTRSAEV 290

Query: 292 CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV 351
           C  M AHK F V CL   DAW LF + VG + L S  DI ELA+ VA ECGGLPLALIT+
Sbjct: 291 CVWMGAHKKFGVGCLSANDAWELFRQNVGEETLTSDHDIAELAQIVAEECGGLPLALITI 350

Query: 352 GRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFF 411
           G+AMA KK   EW HAIEVLR SAS+F G +   L   KFSYD LP + TR C LYC  +
Sbjct: 351 GQAMAYKKTVEEWRHAIEVLRRSASEFPGFD-NVLRVFKFSYDSLPDDTTRSCFLYCCLY 409

Query: 412 PEDYSISIEDLIDCWI 427
           P+DY I   DLIDCWI
Sbjct: 410 PKDYGILKWDLIDCWI 425

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147787894|emb|CAN71751.1| hypothetical protein VITISV_040594 [Vitis vinifera]

 Score =  434 bits (1116), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 227/431 (52%), Positives = 286/431 (66%), Gaps = 6/431 (1%)

Query: 1   MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
           MGN+CS S+S +D ++    C      YIC L++N  ALR   +KLIE RNDV  +V +A
Sbjct: 1   MGNLCSISVSIEDIVASFWGCTXRPANYICKLEENQLALRIALRKLIELRNDVKRKVDLA 60

Query: 61  EQRQMRRLQQVQGWLSRVQDVE---EEVR-RREQEVICLDGLRYRSSIKSYKYGKRVVKS 116
           E++QM+ L QVQGWLSRV+ +E    E+R     E   L   R +  +  YK GK+V   
Sbjct: 61  ERQQMKPLDQVQGWLSRVEALETAXSEMRGSAAMEANRLGSYRIKGFMSRYKLGKKVATK 120

Query: 117 LKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYG 176
           L+ V  LR+EG F  VA   P  PV+ RP  PTV G++S  + VW CL E  V I+GLYG
Sbjct: 121 LEEVATLRREGRFDVVADRSPPTPVNLRPSGPTV-GLESKFEEVWGCLGEG-VWIIGLYG 178

Query: 177 MGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKS 236
           +GGVGKTTL+TQINN+   T +DFD VIW VVS D    K+Q+ I KKIG  ++ W NKS
Sbjct: 179 LGGVGKTTLMTQINNALYKTTHDFDVVIWAVVSSDPDPRKVQDEIWKKIGFCDDIWKNKS 238

Query: 237 FDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMD 296
            D+KA EIF+ +  +K VL LDDIW+ FDL +VG+P P + + SK+VFTTR  EVC  M 
Sbjct: 239 QDDKAIEIFQILNKKKFVLFLDDIWKWFDLLRVGVPFPDQENKSKIVFTTRSEEVCCSMG 298

Query: 297 AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMA 356
           A K  KVECL +  AW LF  KVG D ++ HPDIP+LA+TVA ECGGLPLALIT+GRAMA
Sbjct: 299 AQKIIKVECLAWGRAWDLFRSKVGEDTINFHPDIPQLAKTVANECGGLPLALITIGRAMA 358

Query: 357 SKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYS 416
            K+ PREW HAI+VL +SAS F GM +  L  LKFSYD LP++  R C LYC  +P+D  
Sbjct: 359 CKRTPREWNHAIKVLHNSASNFPGMPEDVLPLLKFSYDSLPNDIARTCFLYCSLYPDDRL 418

Query: 417 ISIEDLIDCWI 427
           I  E L+D WI
Sbjct: 419 IYKEXLVDNWI 429

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553135|ref|XP_002517610.1| Disease resistance protein RFL1, putative [Ricinus communis] gi|223543242|gb|EEF44774.1| Disease resistance protein RFL1, putative [Ricinus communis]

 Score =  433 bits (1114), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 217/427 (50%), Positives = 298/427 (69%), Gaps = 9/427 (2%)

Query: 4   VCSTSLSCDDTISR-CLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQ 62
           VC   + C D++ R CL C   Q  YIC L+DNL AL+T  ++L E ++DV+ ++++ E 
Sbjct: 2   VCPFQVQCGDSLIRQCLKCTAGQGAYICKLEDNLVALQTATEELRELKDDVIQKLSIEEG 61

Query: 63  RQMRRLQQVQGWLSRVQDVEEEVRRREQEVICLDGLRYRSSIKS-YKYGKRVVKSLKNVQ 121
           ++M+RL+QVQGW+SR      E +  E + +  +GL    + KS Y +G+ V K L++V 
Sbjct: 62  QRMKRLKQVQGWISRA-----EAKITEVDELIKEGLPKILNCKSRYIFGRSVAKKLEDVI 116

Query: 122 GLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVG 181
            ++++GDFK VA+      V ERP  PTV G++S L+RVW+CL EE VG+VG+YGMGGVG
Sbjct: 117 AMKRKGDFKVVAERAAGEAVVERPSEPTV-GLESILNRVWKCLVEEEVGVVGIYGMGGVG 175

Query: 182 KTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN-ESWDNKSFDEK 240
           KTT+LTQINN F+ +PNDF  VIW VVS+DL+L K+QE IAK+IGL + + W NK+F +K
Sbjct: 176 KTTILTQINNMFVTSPNDFVAVIWVVVSKDLRLDKVQEEIAKRIGLSDDQQWKNKNFSDK 235

Query: 241 AQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKS 300
           A++IF+ +  RK VLLLDDIW+  +L +VG+P+P R S SK+VFT R   VC  M+A K 
Sbjct: 236 AEDIFRVLHKRKFVLLLDDIWKRLELKEVGVPLPKRQSRSKIVFTARSEAVCSSMEAQKK 295

Query: 301 FKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKA 360
            KVE L + +AW LF+EKVG D L +HP+IP +AE VAR+CGGLPLAL+T+ RAMA ++ 
Sbjct: 296 IKVEPLEWLEAWELFQEKVGGDTLRAHPEIPLIAEAVARKCGGLPLALVTIARAMACRRT 355

Query: 361 PREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIE 420
            +EW +A+E LR SAS   GM  +    LKFSYD LP++  + C LYC  FPED  I  +
Sbjct: 356 LQEWKYAVETLRKSASNLQGMGDEVFPILKFSYDCLPNDTIKSCFLYCALFPEDVKILKD 415

Query: 421 DLIDCWI 427
           +LID WI
Sbjct: 416 NLIDYWI 422

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	427
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.997	0.479	0.420	5.9e-89
TAIR|locus:2132741	892	AT4G10780 [Arabidopsis thalian	0.995	0.476	0.424	7.7e-87
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.997	0.476	0.419	3.3e-86
TAIR|locus:2036214	851	AT1G15890 [Arabidopsis thalian	0.995	0.499	0.413	8.9e-86
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.997	0.479	0.429	6.2e-85
TAIR|locus:2008510	967	AT1G61190 "AT1G61190" [Arabido	0.995	0.439	0.415	7.2e-84
TAIR|locus:2008440	899	AT1G61180 [Arabidopsis thalian	0.992	0.471	0.415	9.1e-84
TAIR|locus:2201986	885	RFL1 "AT1G12210" [Arabidopsis	0.997	0.481	0.417	1.2e-83
TAIR|locus:2034765	884	AT1G12290 [Arabidopsis thalian	1.0	0.483	0.394	5.8e-82
TAIR|locus:2170892	848	AT5G43730 [Arabidopsis thalian	0.946	0.476	0.409	1.4e-78

TAIR|locus:2166320 AT5G63020 [Arabidopsis thaliana (taxid:3702)]

 Score = 888 (317.7 bits), Expect = 5.9e-89, P = 5.9e-89
 Identities = 182/433 (42%), Positives = 254/433 (58%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MG   S S+SCD        C+     YI  L++NL AL+   +++ + R D+L ++   
Sbjct:     1 MGGCVSVSISCDQLTKNVCSCLNRNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSE 60

Query:    61 EQRQMRRLQQVQGWLSXXXXXX------XXXXXXXXXXICLDGLRYRSSIKSYKYGKRVV 114
             E+R ++RL  VQGW+S                      +CL G   ++ + SY+YGKRV+
Sbjct:    61 ERRGLQRLSVVQGWVSKVEAIVPRVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVM 120

Query:   115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXXX 174
             K ++ V+ LR +GDF  VA+ V    V+ERP  P +V M   L+  W  L E+       
Sbjct:   121 KMIEEVEVLRYQGDFAVVAERVDAARVEERPTRP-MVAMDPMLESAWNRLMEDEIGILGL 179

Query:   175 XXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
                    KTTLL+ INN F     +FD VIW VVS++LQ+ +IQ+ I +K+   NE W  
Sbjct:   180 HGMGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDNEKWKQ 239

Query:   235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
             K+ D KA  I+  +++++ VLLLDDIW   DL +VG+P PSR +  K+VFTTR  E+CG 
Sbjct:   240 KTEDIKASNIYNVLKHKRFVLLLDDIWSKVDLTEVGVPFPSRENGCKIVFTTRLKEICGR 299

Query:   295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
             M      +V CL  +DAW LF +KVG   L SHP+IP +A TVA++C GLPLAL  +G  
Sbjct:   300 MGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALNVIGET 359

Query:   355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
             MA K+  +EW  AI+VL SSA++FSGME + L  LK+SYD L S + + C  YC  FPED
Sbjct:   360 MAYKRTVQEWRSAIDVLTSSAAEFSGMEDEILPILKYSYDNLKSEQLKLCFQYCALFPED 419

Query:   415 YSISIEDLIDCWI 427
             ++I   DL+D WI
Sbjct:   420 HNIEKNDLVDYWI 432

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2132741 AT4G10780 [Arabidopsis thaliana (taxid:3702)]

 Score = 868 (310.6 bits), Expect = 7.7e-87, P = 7.7e-87
 Identities = 184/433 (42%), Positives = 246/433 (56%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MG+  S  +SCD  ++R   C  S   YI  LKDN+ AL    + L   R+DVL RV + 
Sbjct:     1 MGSCISLQISCDQVLTRAYSCFFSLGNYIHKLKDNIVALEKAIEDLTATRDDVLRRVQME 60

Query:    61 EQRQMRRLQQVQGWLSXXXXXXXXXXXXXXXX-ICLDGLRYRSSIK-----SYKYGKRVV 114
             E + + RLQQVQ WL                  I +  L + S+       SY YG+RV 
Sbjct:    61 EGKGLERLQQVQVWLKRVEIIRNQFYDLLSARNIEIQRLCFYSNCSTNLSSSYTYGQRVF 120

Query:   115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXXX 174
               +K V+ L   G F+ VA   P+  ++ RP+ PT++G ++   R W  L ++       
Sbjct:   121 LMIKEVENLNSNGFFEIVAAPAPK--LEMRPIQPTIMGRETIFQRAWNRLMDDGVGTMGL 178

Query:   175 XXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
                    KTTLLTQI+N+   T N  D VIW VVS DLQ+ KIQE I +K+G   + W+ 
Sbjct:   179 YGMGGVGKTTLLTQIHNTLHDTKNGVDIVIWVVVSSDLQIHKIQEDIGEKLGFIGKEWNK 238

Query:   235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
             K   +KA +I   +  ++ VLLLDDIW+  DL ++G+P  +R +  KVVFTTR  +VC  
Sbjct:   239 KQESQKAVDILNCLSKKRFVLLLDDIWKKVDLTKIGIPSQTRENKCKVVFTTRSLDVCAR 298

Query:   295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
             M  H   +V+CL   DAW LF+EKVG+  L SHPDI ELA+ VA +C GLPLAL  +G  
Sbjct:   299 MGVHDPMEVQCLSTNDAWELFQEKVGQISLGSHPDILELAKKVAGKCRGLPLALNVIGET 358

Query:   355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
             MA K+A +EW HA++VL S A++FSGM+   L  LK+SYD L     R C  YC  +PED
Sbjct:   359 MAGKRAVQEWHHAVDVLTSYAAEFSGMDDHILLILKYSYDNLNDKHVRSCFQYCALYPED 418

Query:   415 YSISIEDLIDCWI 427
             YSI    LID WI
Sbjct:   419 YSIKKYRLIDYWI 431

GO:0000166 "nucleotide binding" evidence=IEA

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

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2034770 SUMM2 "AT1G12280" [Arabidopsis thaliana (taxid:3702)]

 Score = 862 (308.5 bits), Expect = 3.3e-86, P = 3.3e-86
 Identities = 182/434 (41%), Positives = 249/434 (57%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MG   + S SCD+ +++    +    GYIC L  N+ A++ + + L + R+DV  RV + 
Sbjct:     1 MGACLTLSFSCDEVVNQISQGLCINVGYICELSKNVVAMKKDMEVLKKKRDDVKRRVDIE 60

Query:    61 E-QRQMRRLQQVQGWLSXXXXXXX------XXXXXXXXXICLDGLRYRSSIKSYKYGKRV 113
             E  R+  RL QVQGWL+                      +CL G   ++   SY YGKRV
Sbjct:    61 EFTRRRERLSQVQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRV 120

Query:   114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXX 173
             V  LK ++ L  +GDF  V    P   ++E P+ PT+VG ++ L+RVW  LTE+      
Sbjct:   121 VLMLKEIESLSSQGDFDTVTLATPIARIEEMPIQPTIVGQETMLERVWTRLTEDGDEIVG 180

Query:   174 XXXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
                     KTTLLT+INN F    + F  VIW VVS+   + +IQ  I K++ L  E WD
Sbjct:   181 LYGMGGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEEWD 240

Query:   234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG 293
             N + +++A +I+  +  +K VLLLDDIWE  +L  +G+P PSR +  KVVFTTR  +VCG
Sbjct:   241 NVNENQRALDIYNVLGKQKFVLLLDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCG 300

Query:   294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
              M      +V CL   +AW LF+ KVG + L  HPDIPELA  VA +C GLPLAL  +G 
Sbjct:   301 RMRVDDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPELARKVAGKCCGLPLALNVIGE 360

Query:   354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
              MA K+  +EW +AI+VL S A++F GME+  L  LK+SYD L   + + C LYC  FPE
Sbjct:   361 TMACKRMVQEWRNAIDVLSSYAAEFPGMEQ-ILPILKYSYDNLNKEQVKPCFLYCSLFPE 419

Query:   414 DYSISIEDLIDCWI 427
             DY +  E LID WI
Sbjct:   420 DYRMEKERLIDYWI 433

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2036214 AT1G15890 [Arabidopsis thaliana (taxid:3702)]

 Score = 858 (307.1 bits), Expect = 8.9e-86, P = 8.9e-86
 Identities = 179/433 (41%), Positives = 250/433 (57%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MGN  +  +SCD T++    C+     YI  ++ NL+AL+   Q+L E R+D+L RV + 
Sbjct:     1 MGNCVALEISCDQTLNHACGCLFGDRNYILKMEANLEALQNTMQELEERRDDLLRRVVIE 60

Query:    61 EQRQMRRLQQVQGWLS------XXXXXXXXXXXXXXXXICLDGLRYRSSIKSYKYGKRVV 114
             E + ++RL QVQGWLS                      +CL G   ++ I    YG  V+
Sbjct:    61 EDKGLQRLAQVQGWLSRVKDVCSQVNDLLKAKSIQTERLCLCGYCSKNFISGRNYGINVL 120

Query:   115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXXX 174
             K LK+V+GL  +G F+ VA+ +P   V+++ +  T VG+ + + R W  L ++       
Sbjct:   121 KKLKHVEGLLAKGVFEVVAEKIPAPKVEKKHIQ-TTVGLDAMVGRAWNSLMKDERRTLGL 179

Query:   175 XXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
                    KTTLL  INN FL   N FD VIW VVS+DLQ   IQE I  ++GL+   W  
Sbjct:   180 YGMGGVGKTTLLASINNKFLEGMNGFDLVIWVVVSKDLQNEGIQEQILGRLGLHR-GWKQ 238

Query:   235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
              +  EKA  I   +  +K VLLLDD+W   DL ++G+P  +R + SK+VFTTR  +VC  
Sbjct:   239 VTEKEKASYICNILNVKKFVLLLDDLWSEVDLEKIGVPPLTRENGSKIVFTTRSKDVCRD 298

Query:   295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
             M+     KV+CL  ++AW LF++KVG   L SH DIP LA  VA +C GLPLAL  +G+A
Sbjct:   299 MEVDGEMKVDCLPPDEAWELFQKKVGPIPLQSHEDIPTLARKVAEKCCGLPLALSVIGKA 358

Query:   355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
             MAS++  +EW H I VL SS+ +F  ME+K L  LKFSYD L   + + C LYC  FPED
Sbjct:   359 MASRETVQEWQHVIHVLNSSSHEFPSMEEKILPVLKFSYDDLKDEKVKLCFLYCSLFPED 418

Query:   415 YSISIEDLIDCWI 427
             Y +  E+LI+ W+
Sbjct:   419 YEVRKEELIEYWM 431

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2201996 RPS5 "AT1G12220" [Arabidopsis thaliana (taxid:3702)]

 Score = 850 (304.3 bits), Expect = 6.2e-85, P = 6.2e-85
 Identities = 187/435 (42%), Positives = 246/435 (56%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARN-DVLIRVTV 59
             MG   S SL CD  +S+    +  +  YI +L  NL +L+ +  ++++AR  DV+ R+  
Sbjct:     1 MGGCFSVSLPCDQVVSQFSQLLCVRGSYIHNLSKNLASLQ-KAMRMLKARQYDVIRRLET 59

Query:    60 AE-QRQMRRLQQVQGWLSXXXXXXXXXXXXXXXX------ICLDGLRYRSSIKSYKYGKR 112
              E   + +RL QVQ WL+                      +CL G   +    SY+YGKR
Sbjct:    60 EEFTGRQQRLSQVQVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKR 119

Query:   113 VVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXX 172
             V+  LK V+ L  +G F  V++  P   VDE P  PT+VG +  L++ W  L E+     
Sbjct:   120 VIMMLKEVESLSSQGFFDVVSEATPFADVDEIPFQPTIVGQEIMLEKAWNRLMEDGSGIL 179

Query:   173 XXXXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW 232
                      KTTLLT+INN F    + FD VIW VVSR   + KIQ  IA+K+GL    W
Sbjct:   180 GLYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEW 239

Query:   233 DNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVC 292
               K+ ++ A +I   +R RK VLLLDDIWE  +L  VG+P PS+ +  KV FTTR  +VC
Sbjct:   240 SEKNDNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVC 299

Query:   293 GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG 352
             G M      +V CL  E++W LF+ KVG++ L SHPDIP LA  VAR+C GLPLAL  +G
Sbjct:   300 GRMGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIG 359

Query:   353 RAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFP 412
              AMA K+   EW HAI+VL SSA  FSGME + L  LK+SYD L     + C LYC  FP
Sbjct:   360 EAMACKRTVHEWCHAIDVLTSSAIDFSGMEDEILHVLKYSYDNLNGELMKSCFLYCSLFP 419

Query:   413 EDYSISIEDLIDCWI 427
             EDY I  E L+D WI
Sbjct:   420 EDYLIDKEGLVDYWI 434

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

GO:0006952 "defense response" evidence=IMP;TAS

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008219 "cell death" evidence=IMP

GO:0038023 "signaling receptor activity" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IMP

GO:0005622 "intracellular" evidence=ISS

TAIR|locus:2008510 AT1G61190 "AT1G61190" [Arabidopsis thaliana (taxid:3702)]

 Score = 840 (300.8 bits), Expect = 7.2e-84, P = 7.2e-84
 Identities = 180/433 (41%), Positives = 247/433 (57%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MGN     +S D  + R + C+  + GYI +L+ NL AL+ E + L   +++V  +V   
Sbjct:     1 MGNFVCIEISGDQMLDRIIRCLCGK-GYIRNLEKNLRALQREMEDLRATQHEVQNKVARE 59

Query:    61 EQRQMRRLQQVQGWLSXXXXXXXXXXXXXXXX------ICLDGLRYRSSIKSYKYGKRVV 114
             E R  +RL+ VQ WL                       +CL GL  +    SYKYGKRV 
Sbjct:    60 ESRHQQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVF 119

Query:   115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXXX 174
               L+ V  L+ EG+F +V+Q  P + V+ERP  PT+ G +  L + W  L E+       
Sbjct:   120 LLLEEVTKLKSEGNFDEVSQPPPRSEVEERPTQPTI-GQEEMLKKAWNRLMEDGVGIMGL 178

Query:   175 XXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
                    KTTL  +I+N F  T   FD VIW VVS+  +L K+QE IA+K+ L ++ W N
Sbjct:   179 HGMGGVGKTTLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKN 238

Query:   235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
             K+  +KA +I + ++ ++ VL+LDDIWE  DL  +G+P PS  +  KV FTTR+ +VCG 
Sbjct:   239 KNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRDQKVCGQ 298

Query:   295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
             M  HK  +V+CL  EDAW LF+ KVG + L S P I  LA  VA++C GLPLAL  +G  
Sbjct:   299 MGDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSCIGET 358

Query:   355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
             MASK   +EW HAI+VL  SA++FS M+ K L  LK+SYD L     + C LYC  FPED
Sbjct:   359 MASKTMVQEWEHAIDVLTRSAAEFSDMQNKILPILKYSYDSLEDEHIKSCFLYCALFPED 418

Query:   415 YSISIEDLIDCWI 427
               I  + LI+ WI
Sbjct:   419 DKIDTKTLINKWI 431

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2008440 AT1G61180 [Arabidopsis thaliana (taxid:3702)]

 Score = 839 (300.4 bits), Expect = 9.1e-84, P = 9.1e-84
 Identities = 180/433 (41%), Positives = 248/433 (57%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MG+  S  +S D T++R  +C++ ++ YI  L+ NL AL+ E + L   +++V  +V   
Sbjct:     1 MGSCFSLQVS-DQTLNRIFNCLIGKS-YIRTLEKNLRALQREMEDLRAIQHEVQNKVARD 58

Query:    61 EQRQMRRLQQVQGWLSXXXXXXXXXXXXXXXX------ICLDGLRYRSSIKSYKYGKRVV 114
             E R  RRL+ VQ WL                       +CL GL  +    SYKYGK+V 
Sbjct:    59 EARHQRRLEAVQVWLDRVNSVDIECKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVF 118

Query:   115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXXX 174
               L+ V+ L  EG+F +V+Q  P + V+ERP  PT+ G +  L++ W  L E+       
Sbjct:   119 LLLEEVKKLNSEGNFDEVSQPPPRSEVEERPTQPTI-GQEDMLEKAWNRLMEDGVGIMGL 177

Query:   175 XXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
                    KTTL  +I+N F      FD VIW VVS+ + + K+QE IA+K+ L ++ W N
Sbjct:   178 HGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDLWKN 237

Query:   235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
             K+  +KA +I + ++ ++ VL+LDDIWE  DL  +G+P PS  +  KV FTTR  EVCG 
Sbjct:   238 KNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCGE 297

Query:   295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
             M  HK  +V CL  EDAW LF+ KVG + L S P I ELA  VA++C GLPLAL  +G  
Sbjct:   298 MGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVELAREVAQKCRGLPLALNVIGET 357

Query:   355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
             M+SK   +EW HAI V  +SA++FS M+ K L  LK+SYD L     + C LYC  FPED
Sbjct:   358 MSSKTMVQEWEHAIHVFNTSAAEFSDMQNKILPILKYSYDSLGDEHIKSCFLYCALFPED 417

Query:   415 YSISIEDLIDCWI 427
               I  E LID WI
Sbjct:   418 GEIYNEKLIDYWI 430

GO:0005886 "plasma membrane" evidence=ISM;IDA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2201986 RFL1 "AT1G12210" [Arabidopsis thaliana (taxid:3702)]

 Score = 838 (300.0 bits), Expect = 1.2e-83, P = 1.2e-83
 Identities = 181/434 (41%), Positives = 245/434 (56%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MG   S SLSCD  +++    +     YI +L +NL +L+     L   R+DV  R+   
Sbjct:     1 MGGCVSVSLSCDREVNQFSQWLCVSGSYIQNLSENLASLQKAMGVLNAKRDDVQGRINRE 60

Query:    61 E-QRQMRRLQQVQGWLSXXXXXXXXXXXXXXX------XICLDGLRYRSSIKSYKYGKRV 113
             E     RRL QVQ WL+                      +CL G   ++   SY YGKRV
Sbjct:    61 EFTGHRRRLAQVQVWLTRIQTIENQFNDLLSTCNAEIQRLCLCGFCSKNVKMSYLYGKRV 120

Query:   114 VKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXX 173
             +  L+ V+GL  +G F  V +  P   V+E P+  T+VG  S LD+VW CL E+      
Sbjct:   121 IVLLREVEGLSSQGVFDIVTEAAPIAEVEELPIQSTIVGQDSMLDKVWNCLMEDKVWIVG 180

Query:   174 XXXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD 233
                     KTTLLTQINN F      FD VIW VVS++  + KIQ+SI +K+GL  ++WD
Sbjct:   181 LYGMGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVGKNWD 240

Query:   234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG 293
              K+ +++A +I   +R +K VLLLDDIWE  +L  +G+P PS  +  KV FTT   EVCG
Sbjct:   241 EKNKNQRALDIHNVLRRKKFVLLLDDIWEKVELKVIGVPYPSGENGCKVAFTTHSKEVCG 300

Query:   294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR 353
              M      ++ CL   +AW L ++KVG + L SHPDIP+LA  V+ +C GLPLAL  +G 
Sbjct:   301 RMGVDNPMEISCLDTGNAWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPLALNVIGE 360

Query:   354 AMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPE 413
              M+ K+  +EW HA EVL +SA+ FSGME + L  LK+SYD L   + + C LYC  FPE
Sbjct:   361 TMSFKRTIQEWRHATEVL-TSATDFSGMEDEILPILKYSYDSLNGEDAKSCFLYCSLFPE 419

Query:   414 DYSISIEDLIDCWI 427
             D+ I  E LI+ WI
Sbjct:   420 DFEIRKEMLIEYWI 433

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

GO:0009617 "response to bacterium" evidence=ISS

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

TAIR|locus:2034765 AT1G12290 [Arabidopsis thaliana (taxid:3702)]

 Score = 822 (294.4 bits), Expect = 5.8e-82, P = 5.8e-82
 Identities = 171/433 (39%), Positives = 243/433 (56%)

Query:     1 MGNVCSTSLSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVA 60
             MG   S  +SCD  ++    C   +  YI ++K+NL +L    + L   R+D+L +V  A
Sbjct:     1 MGGCVSVQVSCDQLLNHLGRCFCRKLYYIQNIKENLTSLEEAMEDLKALRDDLLRKVQTA 60

Query:    61 EQRQMRRLQQVQGWLSXXXXXXX------XXXXXXXXXICLDGLRYRSSIKSYKYGKRVV 114
             E+  ++RL Q++ WL                       +C  G+  R+   SY YG+RV 
Sbjct:    61 EEGGLQRLHQIKVWLKRVKTIESQFNDLDSSRTVELQRLCCCGVGSRNLRLSYDYGRRVF 120

Query:   115 KSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXXX 174
               L  V+ L+ +G F++VA        +ERPL PT+VG ++ L++ W  L ++       
Sbjct:   121 LMLNIVEDLKSKGIFEEVAHPATRAVGEERPLQPTIVGQETILEKAWDHLMDDGTKIMGL 180

Query:   175 XXXXXXXKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN 234
                    KTTLLTQINN F  T +  + VIW VVS DLQ+ KIQ+ I +KIG     W+ 
Sbjct:   181 YGMGGVGKTTLLTQINNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGEKIGFIGVEWNQ 240

Query:   235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL 294
             KS ++KA +I   +  ++ VLLLDDIW+  +L ++G+P P+  +  K+ FTTR   VC  
Sbjct:   241 KSENQKAVDILNFLSKKRFVLLLDDIWKRVELTEIGIPNPTSENGCKIAFTTRCQSVCAS 300

Query:   295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA 354
             M  H   +V CLG +DAW LF++KVG   L SHPDIPE+A  VA+ C GLPLAL  +G  
Sbjct:   301 MGVHDPMEVRCLGADDAWDLFKKKVGDITLSSHPDIPEIARKVAQACCGLPLALNVIGET 360

Query:   355 MASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPED 414
             MA KK  +EW  A++V  + A+ F  ++++ L  LK+SYD L S   + C LYC  FPED
Sbjct:   361 MACKKTTQEWDRAVDVSTTYAANFGAVKERILPILKYSYDNLESESVKTCFLYCSLFPED 420

Query:   415 YSISIEDLIDCWI 427
               I  E LID WI
Sbjct:   421 DLIEKERLIDYWI 433

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

TAIR|locus:2170892 AT5G43730 [Arabidopsis thaliana (taxid:3702)]

 Score = 790 (283.2 bits), Expect = 1.4e-78, P = 1.4e-78
 Identities = 169/413 (40%), Positives = 235/413 (56%)

Query:    21 CIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSXXXX 80
             C +S + YI  ++ NLDAL+   ++L   R+D+L RV++ E + ++RL  V GWLS    
Sbjct:    20 CFLSDSNYIHLMESNLDALQKTMEELKNGRDDLLARVSIEEDKGLQRLALVNGWLSRVQI 79

Query:    81 XXXX------XXXXXXXXICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQ 134
                               +CL G      I SY YG +V+K+L+ V+ L  + +F+ VAQ
Sbjct:    80 VESEFKDLLEAMSIETGRLCLFGYCSEDCISSYNYGGKVMKNLEEVKELLSKKNFEVVAQ 139

Query:   135 TVPENPVDERPLPPTVVGMQSTLDRVWRCLTEEPXXXXXXXXXXXXXKTTLLTQINNSFL 194
              +   P  E+    T VG+ + +   W  L ++              KTTLL  +NN F+
Sbjct:   140 KII--PKAEKKHIQTTVGLDTMVGIAWESLIDDEIRTLGLYGMGGIGKTTLLESLNNKFV 197

Query:   195 HTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIV 254
                ++FD VIW VVS+D QL  IQ+ I  ++    E W+ ++  +KA  I   ++ +K V
Sbjct:   198 ELESEFDVVIWVVVSKDFQLEGIQDQILGRLRPDKE-WERETESKKASLINNNLKRKKFV 256

Query:   255 LLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRL 314
             LLLDD+W   DL ++G+P PSR + SK+VFTTR  EVC  M A K  KV+CL  ++AW L
Sbjct:   257 LLLDDLWSEVDLIKIGVPPPSRENGSKIVFTTRSKEVCKHMKADKQIKVDCLSPDEAWEL 316

Query:   315 FEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSS 374
             F   VG  IL SH DIP LA  VA +C GLPLAL  +G+AM  K+  +EW HAI VL S 
Sbjct:   317 FRLTVGDIILRSHQDIPALARIVAAKCHGLPLALNVIGKAMVCKETVQEWRHAINVLNSP 376

Query:   375 ASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI 427
               KF GME++ L  LKFSYD L + E + C LYC  FPED+ I  + LI+ WI
Sbjct:   377 GHKFPGMEERILPILKFSYDSLKNGEIKLCFLYCSLFPEDFEIEKDKLIEYWI 429

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

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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

Your Input: fgenesh4_pm.C_LG_I001004 cc-nbs-lrr resistance protein (880 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	427
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-80
pfam13401	124	pfam13401, AAA_22, AAA domain	7e-04
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.004

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

 Score =  249 bits (638), Expect = 2e-80
 Identities = 104/277 (37%), Positives = 153/277 (55%), Gaps = 6/277 (2%)

Query: 154 QSTLDRVWRCLTEEP--VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD 211
           +  ++ +   L E    +G+VG+ GMGGVGKTTL  QI N        FD V W VVS+ 
Sbjct: 2   EDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDD-SVGGHFDSVAWVVVSKT 60

Query: 212 LQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGL 271
               ++Q+ I +++GL +  W  K+  E A +I + +  ++ +L+LDD+WE  D  ++G+
Sbjct: 61  YTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDKIGV 120

Query: 272 PVPSRASASKVVFTTREFEVCGLMDA-HKSFKVECLGYEDAWRLFEEKVGRDILDSHPDI 330
           P P   + S+V+ TTR   V G M    K  +VE L  E++W LF  KV    L   P++
Sbjct: 121 PFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPEL 180

Query: 331 PELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSRLK 390
            E+A+ +  +C GLPLAL  +G  +A K   +EW H +E L +  +   G+  + LS L 
Sbjct: 181 EEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLN-EVLSILS 239

Query: 391 FSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI 427
            SYD LP    + C LY   FPEDY+I  E LI  WI
Sbjct: 240 LSYDNLPM-HLKRCFLYLALFPEDYNIRKEQLIKLWI 275

Length = 285

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

 Score = 38.8 bits (91), Expect = 7e-04
 Identities = 23/113 (20%), Positives = 43/113 (38%), Gaps = 14/113 (12%)

Query: 170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN 229
           GI  L G  G GKTTLL ++     +       V++           +   I + +GL  
Sbjct: 5   GIGVLTGESGSGKTTLLRRLARQLPNRR-----VVYVEAPSLGTPKDLLRKILRALGLPL 59

Query: 230 ESWDNKSFDEKAQEIFKTMRNRKIVL---------LLDDIWELFDLAQVGLPV 273
                    E   +  K      +++          L+++ +L+DL++ G+ V
Sbjct: 60  SGGTTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQV 112

Length = 124

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

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 23/144 (15%), Positives = 44/144 (30%), Gaps = 14/144 (9%)

Query: 155 STLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFL-HTPNDFDFVIWEVVSRDLQ 213
             L    R         V L G  G GKT+LL ++    L               +    
Sbjct: 10  ERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQA 69

Query: 214 LGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM------------RNRKIVLLLDDI- 260
           L ++   + +++                 E+ + +            R R +VL+LDD+ 
Sbjct: 70  LRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARPLVLVLDDLQ 129

Query: 261 WELFDLAQVGLPVPSRASASKVVF 284
           W   +   +   +  R     ++ 
Sbjct: 130 WADEESLDLLAALLRRLERLPLLV 153

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	427
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.57
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.53
PRK04841	903	transcriptional regulator MalT; Provisional	99.53
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.48
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.48
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.31
PF05729	166	NACHT: NACHT domain	99.3
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.29
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.27
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.13
PRK06893	229	DNA replication initiation factor; Validated	99.12
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.09
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.08
COG3899	849	Predicted ATPase [General function prediction only	99.08
PRK13342	413	recombination factor protein RarA; Reviewed	99.07
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.05
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.03
PRK12402	337	replication factor C small subunit 2; Reviewed	98.99
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.97
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.92
PF13173	128	AAA_14: AAA domain	98.92
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.92
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.91
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.91
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.9
PRK08727	233	hypothetical protein; Validated	98.89
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.88
PRK04195	482	replication factor C large subunit; Provisional	98.87
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.87
PLN03025	319	replication factor C subunit; Provisional	98.86
PTZ00202	550	tuzin; Provisional	98.86
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.84
PRK08084	235	DNA replication initiation factor; Provisional	98.83
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.82
KOG2028	554	consensus ATPase related to the helicase subunit o	98.82
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.8
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.8
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.78
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.77
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.77
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.77
COG3903	414	Predicted ATPase [General function prediction only	98.77
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.75
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.75
PRK13341	725	recombination factor protein RarA/unknown domain f	98.74
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.74
PRK09087	226	hypothetical protein; Validated	98.74
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.74
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.73
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.73
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.72
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.7
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.7
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.69
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.68
PF14516	331	AAA_35: AAA-like domain	98.68
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.68
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.68
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.67
cd01128	249	rho_factor Transcription termination factor rho is	98.65
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.64
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.64
PRK05642	234	DNA replication initiation factor; Validated	98.64
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.64
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.63
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.62
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.6
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.6
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.59
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.57
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.53
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.53
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.52
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.49
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.47
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.47
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.47
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.46
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	98.46
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.46
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.45
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.45
PRK09376	416	rho transcription termination factor Rho; Provisio	98.44
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.42
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.42
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.42
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.42
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.4
CHL00181	287	cbbX CbbX; Provisional	98.38
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.38
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.38
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.35
TIGR00767	415	rho transcription termination factor Rho. Members	98.35
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.34
PRK06620	214	hypothetical protein; Validated	98.33
PHA02544	316	44 clamp loader, small subunit; Provisional	98.33
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.32
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.31
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.3
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.29
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.27
PRK07399	314	DNA polymerase III subunit delta'; Validated	98.27
PRK12422	445	chromosomal replication initiation protein; Provis	98.26
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.21
CHL00095	821	clpC Clp protease ATP binding subunit	98.2
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.19
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.16
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.14
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.14
PRK10865	857	protein disaggregation chaperone; Provisional	98.14
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.13
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.1
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.09
smart00382	148	AAA ATPases associated with a variety of cellular	98.08
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	98.05
PF00004	132	AAA: ATPase family associated with various cellula	98.03
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.02
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.01
CHL00176	638	ftsH cell division protein; Validated	97.98
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.98
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.95
PRK10536	262	hypothetical protein; Provisional	97.94
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.93
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.93
PRK08116	268	hypothetical protein; Validated	97.9
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.89
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.89
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.88
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.88
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.84
PRK12608	380	transcription termination factor Rho; Provisional	97.82
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.8
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.8
PRK08118	167	topology modulation protein; Reviewed	97.8
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.77
CHL00195	489	ycf46 Ycf46; Provisional	97.76
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.75
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.73
PRK07261	171	topology modulation protein; Provisional	97.72
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.7
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.7
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.7
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.69
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.66
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.64
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	97.64
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.63
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.63
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.63
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.62
PRK08181	269	transposase; Validated	97.6
PRK04296	190	thymidine kinase; Provisional	97.58
PRK04132	846	replication factor C small subunit; Provisional	97.57
PRK06526	254	transposase; Provisional	97.53
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.5
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.48
PRK10865	857	protein disaggregation chaperone; Provisional	97.44
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.44
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.43
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.42
PRK12377	248	putative replication protein; Provisional	97.41
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.4
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	97.4
PRK09183	259	transposase/IS protein; Provisional	97.39
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.39
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.39
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	97.39
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.39
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.38
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.38
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.38
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.38
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.37
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.36
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.35
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.35
PRK06921	266	hypothetical protein; Provisional	97.35
CHL00095	821	clpC Clp protease ATP binding subunit	97.35
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.34
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.34
PRK08699	325	DNA polymerase III subunit delta'; Validated	97.34
PRK08939	306	primosomal protein DnaI; Reviewed	97.33
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.32
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.31
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.3
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	97.3
PRK09354	349	recA recombinase A; Provisional	97.29
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	97.28
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.28
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	97.28
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.26
PRK06835	329	DNA replication protein DnaC; Validated	97.22
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	97.2
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	97.2
KOG1969	877	consensus DNA replication checkpoint protein CHL12	97.19
PRK07952	244	DNA replication protein DnaC; Validated	97.18
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.17
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.16
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.16
PRK06696	223	uridine kinase; Validated	97.15
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.15
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.15
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.12
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.12
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.11
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.1
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.09
PRK06067	234	flagellar accessory protein FlaH; Validated	97.08
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	97.07
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	97.06
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	97.06
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.06
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	97.05
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	97.05
PRK05541	176	adenylylsulfate kinase; Provisional	97.04
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	97.03
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.02
cd03115	173	SRP The signal recognition particle (SRP) mediates	97.02
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	97.0
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	96.99
PRK15455	644	PrkA family serine protein kinase; Provisional	96.99
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.97
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.95
PRK10867	433	signal recognition particle protein; Provisional	96.94
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.94
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.93
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.92
TIGR00959	428	ffh signal recognition particle protein. This mode	96.92
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.92
PHA00729	226	NTP-binding motif containing protein	96.91
PRK13531	498	regulatory ATPase RavA; Provisional	96.91
PTZ00494	664	tuzin-like protein; Provisional	96.9
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.89
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.89
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.88
KOG0736	953	consensus Peroxisome assembly factor 2 containing	96.88
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.88
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.88
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.88
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.87
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.87
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.86
PRK04328	249	hypothetical protein; Provisional	96.86
PRK06547	172	hypothetical protein; Provisional	96.85
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	96.84
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.84
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.82
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.81
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	96.79
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.79
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	96.79
PRK14527	191	adenylate kinase; Provisional	96.79
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.78
PTZ00035	337	Rad51 protein; Provisional	96.78
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.78
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.78
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.78
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.77
PRK07667	193	uridine kinase; Provisional	96.76
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.75
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.75
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.74
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	96.74
PRK11823	446	DNA repair protein RadA; Provisional	96.73
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	96.72
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.71
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.7
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	96.7
PRK08233	182	hypothetical protein; Provisional	96.7
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	96.68
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.68
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.68
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	96.67
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	96.67
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	96.67
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	96.66
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.65
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.65
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.64
COG0488	530	Uup ATPase components of ABC transporters with dup	96.62
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.62
PF07726	131	AAA_3: ATPase family associated with various cellu	96.61
PRK05973	237	replicative DNA helicase; Provisional	96.61
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.61
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.61
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.6
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.59
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.59
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.59
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.57
PRK14974	336	cell division protein FtsY; Provisional	96.57
PRK06762	166	hypothetical protein; Provisional	96.57
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.57
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	96.57
PTZ00301	210	uridine kinase; Provisional	96.56
PF00154	322	RecA: recA bacterial DNA recombination protein; In	96.55
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.54
PTZ00088	229	adenylate kinase 1; Provisional	96.52
PRK05439	311	pantothenate kinase; Provisional	96.52
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.52
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.51
PRK05480	209	uridine/cytidine kinase; Provisional	96.5
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.5
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.5
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	96.49
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	96.49
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.49
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.48
PRK13765	637	ATP-dependent protease Lon; Provisional	96.47
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.47
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	96.47
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	96.45
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.45
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.43
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.42
COG0714	329	MoxR-like ATPases [General function prediction onl	96.41
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.41
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.41
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	96.39
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.39
PRK03839	180	putative kinase; Provisional	96.39
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.38
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.37
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.35
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	96.35
cd03246	173	ABCC_Protease_Secretion This family represents the	96.35
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.34
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	96.33
PRK06217	183	hypothetical protein; Validated	96.32
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	96.32
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.31
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	96.31
PRK00279	215	adk adenylate kinase; Reviewed	96.31
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.3
PRK04040	188	adenylate kinase; Provisional	96.3
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.29
PRK00131	175	aroK shikimate kinase; Reviewed	96.28
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.28
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.28
PRK12678	672	transcription termination factor Rho; Provisional	96.27
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.25
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.24
PRK07132	299	DNA polymerase III subunit delta'; Validated	96.23
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	96.22
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.22
PRK00625	173	shikimate kinase; Provisional	96.2
PRK15453	290	phosphoribulokinase; Provisional	96.18
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	96.17
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	96.17
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.16
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	96.14
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.13
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	96.12
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.1
PF13245	76	AAA_19: Part of AAA domain	96.1
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	96.08
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.08
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	96.07
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	96.07
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	96.07
PRK14528	186	adenylate kinase; Provisional	96.07
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.06
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.06
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	96.05
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	96.05
) 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	96.05
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.03
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.03
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.02
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.01
PRK00409	782	recombination and DNA strand exchange inhibitor pr	96.01
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.0
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.0
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.0
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.99
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.98
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.98
PRK14530	215	adenylate kinase; Provisional	95.96
PRK05922	434	type III secretion system ATPase; Validated	95.96
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	95.95
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.95
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	95.95
PRK00889	175	adenylylsulfate kinase; Provisional	95.95
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	95.95
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.94
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	95.93
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	95.93
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.9
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	95.9
PRK10416	318	signal recognition particle-docking protein FtsY;	95.89
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.89
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	95.88
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	95.88
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.88
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	95.86
PRK14529	223	adenylate kinase; Provisional	95.85
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	95.85
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	95.84
PRK08149	428	ATP synthase SpaL; Validated	95.84
PRK13949	169	shikimate kinase; Provisional	95.83
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	95.83
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.82
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	95.82
CHL00206	2281	ycf2 Ycf2; Provisional	95.82
PLN02165	334	adenylate isopentenyltransferase	95.81
PRK09302	509	circadian clock protein KaiC; Reviewed	95.81
PRK13947	171	shikimate kinase; Provisional	95.8
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.8
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.79
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.79
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.79
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	95.78
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	95.78
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	95.77
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.77
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.76
PRK10875	615	recD exonuclease V subunit alpha; Provisional	95.75
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.75
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	95.75
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.73
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.73
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	95.73
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	95.72
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	95.71
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	95.7
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.69
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.69
PRK05917	290	DNA polymerase III subunit delta'; Validated	95.69
PRK00300	205	gmk guanylate kinase; Provisional	95.68
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.68
PRK09099	441	type III secretion system ATPase; Provisional	95.67
PTZ00185	574	ATPase alpha subunit; Provisional	95.67
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.67
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	95.66
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	95.64
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	95.64
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.64
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.62
PLN02200	234	adenylate kinase family protein	95.62
PRK13975	196	thymidylate kinase; Provisional	95.61
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	95.59
PRK06761	282	hypothetical protein; Provisional	95.58
COG4240	300	Predicted kinase [General function prediction only	95.58
PRK06936	439	type III secretion system ATPase; Provisional	95.57
PRK09302	509	circadian clock protein KaiC; Reviewed	95.56
PRK14737	186	gmk guanylate kinase; Provisional	95.56
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	95.54
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.53
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.53
PHA02244	383	ATPase-like protein	95.52
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.51
PRK14532	188	adenylate kinase; Provisional	95.51
PHA02774	613	E1; Provisional	95.51
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.5
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	95.49
PRK05057	172	aroK shikimate kinase I; Reviewed	95.47
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.47
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	95.46
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	95.46
PRK03846	198	adenylylsulfate kinase; Provisional	95.46
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.45
PRK14531	183	adenylate kinase; Provisional	95.45
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	95.45
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.45
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	95.43
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.42
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	95.4
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	95.39
COG1158	422	Rho Transcription termination factor [Transcriptio	95.38
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.37
PRK13948	182	shikimate kinase; Provisional	95.36
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	95.34
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.34
PRK14738	206	gmk guanylate kinase; Provisional	95.33
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	95.33
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	95.33
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	95.31
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.3
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	95.3
PRK13946	184	shikimate kinase; Provisional	95.29
PRK04182	180	cytidylate kinase; Provisional	95.27
COG0488	530	Uup ATPase components of ABC transporters with dup	95.27
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.26
PRK07276	290	DNA polymerase III subunit delta'; Validated	95.24
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	95.24
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	95.23
TIGR01287	275	nifH nitrogenase iron protein. This model describe	95.21
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	95.18
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	95.17
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	95.17
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	95.15
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.15
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	95.15
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	95.14
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	95.14
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	95.12
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.12

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=1.5e-63  Score=513.44  Aligned_cols=407  Identities=43%  Similarity=0.757  Sum_probs=349.0

Q ss_pred             HHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHHH-----
Q 042645           12 DDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVR-----   86 (427)
Q Consensus        12 ~~~~~~l~~~l~~e~~~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~~ae~~~~~~~~~v~~wl~~v~~~~~~~~-----   86 (427)
                      +..++++.+.+.+++..+.+.++.+..|++++..|++++.|+++.-.        ....+..|...++++.|+++     
T Consensus         6 s~~~~~~~~~l~~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~--------~~~~~~~~~e~~~~~~~~~e~~~~~   77 (889)
T KOG4658|consen    6 SFGVEKLDQLLNRESECLDGKDNYILELKENLKALQSALEDLDAKRD--------DLERRVNWEEDVGDLVYLAEDIIWL   77 (889)
T ss_pred             EEehhhHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhhcc--------hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55677888899999999999999999999999999999998653321        12445566666666666555     


Q ss_pred             -----------------HhhhhhhhccCccCCCchhhhhHHHHHHHHHHHHHHHHhcCCCccccc-cCCCCCCCCCCCCC
Q 042645           87 -----------------RREQEVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQ-TVPENPVDERPLPP  148 (427)
Q Consensus        87 -----------------~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  148 (427)
                                       ....+..|....|.......|.+++++.++.+.++.+..++.|..... ..|......+|..+
T Consensus        78 ~~v~~~~~~~~~~l~~~~~~~~~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e~~~~~~  157 (889)
T KOG4658|consen   78 FLVEEIERKANDLLSTRSVERQRLCLCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQS  157 (889)
T ss_pred             HHHHHHHHHHhHHhhhhHHHHHHHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcccCCCCc
Confidence                             112334455566667777888899999999999999888776766554 22222333333333


Q ss_pred             cc-ccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          149 TV-VGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       149 ~~-vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      .. ||.+..++++.+.|.+++..+++|+||||+||||||++++|+...+..+|+.++||+||+.++...++.+|+..++.
T Consensus       158 ~~~VG~e~~~~kl~~~L~~d~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~  237 (889)
T KOG4658|consen  158 ESDVGLETMLEKLWNRLMEDDVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGL  237 (889)
T ss_pred             cccccHHHHHHHHHHHhccCCCCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhcc
Confidence            33 99999999999999998889999999999999999999999994489999999999999999999999999999998


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhh-cCCCcceeccCC
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL-MDAHKSFKVECL  306 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~-~~~~~~~~l~~L  306 (427)
                      ..........+++...|.+.|++|||||||||||+..+|+.+..++|....||+|++|||+..||.. +++...+++..|
T Consensus       238 ~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L  317 (889)
T KOG4658|consen  238 LDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECL  317 (889)
T ss_pred             CCcccchhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCcccccccc
Confidence            6655555556889999999999999999999999999999999999999899999999999999998 888889999999


Q ss_pred             ChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHhhc-cccCCCChHHH
Q 042645          307 GYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSS-ASKFSGMEKKA  385 (427)
Q Consensus       307 ~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~~~-~~~~~~~~~~~  385 (427)
                      +++|||.||++.++.......+.++++|++++++|+|+|||++++|++|+.+.+..+|+++.+.+.+. ..+.+++.+.+
T Consensus       318 ~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i  397 (889)
T KOG4658|consen  318 TPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESI  397 (889)
T ss_pred             CccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhh
Confidence            99999999999998876566677999999999999999999999999999999999999999999888 66667778899


Q ss_pred             HHHHhhhcCCCCCChHhHHHhhhcCCCCCccccHHHHHhhcC
Q 042645          386 LSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI  427 (427)
Q Consensus       386 ~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~Wi  427 (427)
                      +.+|.+||++||+ ++|.||+|||+||+||.|+++.||.+||
T Consensus       398 ~~iLklSyd~L~~-~lK~CFLycalFPED~~I~~e~Li~yWi  438 (889)
T KOG4658|consen  398 LPILKLSYDNLPE-ELKSCFLYCALFPEDYEIKKEKLIEYWI  438 (889)
T ss_pred             HHhhhccHhhhhH-HHHHHHHhhccCCcccccchHHHHHHHH
Confidence            9999999999996 9999999999999999999999999997

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=100.00  E-value=1.4e-48  Score=364.03  Aligned_cols=273  Identities=35%  Similarity=0.629  Sum_probs=227.2

Q ss_pred             chhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC
Q 042645          153 MQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE  230 (427)
Q Consensus       153 R~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~  230 (427)
                      ||.++++|.+.|.+  ++.++|+|+|+||+||||||..++++. ....+|+.++|+.++...+..+++..|+.+++....
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~-~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~   79 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDL-RIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDS   79 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHH-HHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-S
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeeccccc-cccccccccccccccccccccccccccccccccccc
Confidence            78999999999988  789999999999999999999999985 357899999999999999999999999999988754


Q ss_pred             CC-CCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhhcCC-CcceeccCCCh
Q 042645          231 SW-DNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDA-HKSFKVECLGY  308 (427)
Q Consensus       231 ~~-~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~~-~~~~~l~~L~~  308 (427)
                      .. ...+..+....+.+.|+++++||||||||+...|+.+...++....|++||||||+..++..+.. ...|++++|+.
T Consensus        80 ~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~  159 (287)
T PF00931_consen   80 SISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSE  159 (287)
T ss_dssp             TSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--H
T ss_pred             ccccccccccccccchhhhccccceeeeeeeccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            33 56677889999999999999999999999999998888888777789999999999998876654 67899999999


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHhhccccCCCChHHHHHH
Q 042645          309 EDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSR  388 (427)
Q Consensus       309 ~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~  388 (427)
                      +|+++||.+.++......++...+.+++|+++|+|+||||.++|++|+.+.+..+|+.+++.+.....+..+....+..+
T Consensus       160 ~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~~~  239 (287)
T PF00931_consen  160 EEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVFSA  239 (287)
T ss_dssp             HHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            99999999998765422345556779999999999999999999999776678899999999888765554455799999


Q ss_pred             HhhhcCCCCCChHhHHHhhhcCCCCCccccHHHHHhhcC
Q 042645          389 LKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI  427 (427)
Q Consensus       389 l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~Wi  427 (427)
                      +.+||+.||+ ++|.||+|||+||+++.|+++.|+++|+
T Consensus       240 l~~s~~~L~~-~~~~~f~~L~~f~~~~~i~~~~li~lW~  277 (287)
T PF00931_consen  240 LELSYDSLPD-ELRRCFLYLSIFPEGVPIPRERLIRLWV  277 (287)
T ss_dssp             HHHHHHSSHT-CCHHHHHHGGGSGTTS-EEHHHHHHHHT
T ss_pred             ceechhcCCc-cHHHHHhhCcCCCCCceECHHHHHHHHH
Confidence            9999999999 8999999999999999999999999996

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PLN03210 Resistant to P

Probab=100.00  E-value=1.5e-34  Score=313.19  Aligned_cols=257  Identities=19%  Similarity=0.267  Sum_probs=204.5

Q ss_pred             CCccccchhhHHHHHHHhc--cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEe---CCC----------
Q 042645          147 PPTVVGMQSTLDRVWRCLT--EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVV---SRD----------  211 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~---~~~----------  211 (427)
                      .+.+|||+..++++..+|.  .++.++|+|+||||+||||||+.+|+..   ..+|+..+|+..   +..          
T Consensus       183 ~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l---~~~F~g~vfv~~~~v~~~~~~~~~~~~~  259 (1153)
T PLN03210        183 FEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRL---SRQFQSSVFIDRAFISKSMEIYSSANPD  259 (1153)
T ss_pred             cccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHH---hhcCCeEEEeeccccccchhhccccccc
Confidence            3578999999999999885  3578999999999999999999999987   567888777642   111          


Q ss_pred             -CC-HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCCh
Q 042645          212 -LQ-LGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREF  289 (427)
Q Consensus       212 -~~-~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~  289 (427)
                       +. ...+...++..+..... .....    ...+++.|+++|+||||||||+...|+.+.......++|++||||||+.
T Consensus       260 ~~~~~~~l~~~~l~~il~~~~-~~~~~----~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~  334 (1153)
T PLN03210        260 DYNMKLHLQRAFLSEILDKKD-IKIYH----LGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDK  334 (1153)
T ss_pred             ccchhHHHHHHHHHHHhCCCC-cccCC----HHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcH
Confidence             00 12234444444321110 01111    2456788999999999999999888888866555567899999999999


Q ss_pred             hHHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHH
Q 042645          290 EVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIE  369 (427)
Q Consensus       290 ~v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~  369 (427)
                      .++..++..+.|+++.|++++||+||+.+++... ..+..+.+++++|+++|+|+|||++++|+.|+. ++..+|+.+++
T Consensus       335 ~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~-~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~-k~~~~W~~~l~  412 (1153)
T PLN03210        335 HFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKN-SPPDGFMELASEVALRAGNLPLGLNVLGSYLRG-RDKEDWMDMLP  412 (1153)
T ss_pred             HHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCC-CCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcC-CCHHHHHHHHH
Confidence            9988777778999999999999999999998754 334567899999999999999999999999998 57899999999


Q ss_pred             HHhhccccCCCChHHHHHHHhhhcCCCCCChHhHHHhhhcCCCCCccccH
Q 042645          370 VLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISI  419 (427)
Q Consensus       370 ~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~  419 (427)
                      .|+..+      +..+..+|++||+.|+++..|.||+++|+|+.++.++.
T Consensus       413 ~L~~~~------~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~~  456 (1153)
T PLN03210        413 RLRNGL------DGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVND  456 (1153)
T ss_pred             HHHhCc------cHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHHH
Confidence            987643      24899999999999987458999999999998876643

syringae 6; Provisional

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.57  E-value=5.7e-13  Score=129.84  Aligned_cols=205  Identities=17%  Similarity=0.147  Sum_probs=131.5

Q ss_pred             CCCCccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHH
Q 042645          145 PLPPTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       145 ~~~~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  220 (427)
                      ..|+.++||++++++|...+..    ...+.+.|+|++|+|||++++.++++.. .....-.++++++....+...++..
T Consensus        27 ~~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~-~~~~~~~~v~in~~~~~~~~~~~~~  105 (394)
T PRK00411         27 YVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELE-EIAVKVVYVYINCQIDRTRYAIFSE  105 (394)
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHH-HhcCCcEEEEEECCcCCCHHHHHHH
Confidence            3567899999999999998743    3456789999999999999999999872 2222345677777777788899999


Q ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCcc---c---ccccccCCCCCCCC--cEEEEecCChh
Q 042645          221 IAKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELF---D---LAQVGLPVPSRASA--SKVVFTTREFE  290 (427)
Q Consensus       221 i~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~---~---~~~~~~~l~~~~~g--s~IivTtR~~~  290 (427)
                      ++.++..........+.++....+.+.+.  +++.+||||+++...   .   +..+...+.. ..+  ..+|.++....
T Consensus       106 i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~-~~~~~v~vI~i~~~~~  184 (394)
T PRK00411        106 IARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEE-YPGARIGVIGISSDLT  184 (394)
T ss_pred             HHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhc-cCCCeEEEEEEECCcc
Confidence            99998753222234456777777777775  456899999998653   1   1122111111 122  23566665544


Q ss_pred             HHhhcC-------CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHc----CCCchHHHHHH
Q 042645          291 VCGLMD-------AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVAREC----GGLPLALITVG  352 (427)
Q Consensus       291 v~~~~~-------~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~----~G~Plai~~~~  352 (427)
                      +.....       ....+.+++++.++..+++..++.... ....-..+..+.|++.+    |..+.|+.++-
T Consensus       185 ~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~-~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~  256 (394)
T PRK00411        185 FLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGF-YPGVVDDEVLDLIADLTAREHGDARVAIDLLR  256 (394)
T ss_pred             hhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhc-ccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            322211       124678999999999999998763211 00011123344444444    44666766654

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

Probab=99.53  E-value=4.8e-12  Score=116.69  Aligned_cols=181  Identities=15%  Similarity=0.171  Sum_probs=116.4

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK  246 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~  246 (427)
                      .+.+.+.|+|++|+|||||++.+++... . ... ...|+ +....+..+++..++..++....   ..+.......+..
T Consensus        41 ~~~~~~~l~G~~G~GKTtl~~~l~~~l~-~-~~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~---~~~~~~~~~~l~~  113 (269)
T TIGR03015        41 QREGFILITGEVGAGKTTLIRNLLKRLD-Q-ERV-VAAKL-VNTRVDAEDLLRMVAADFGLETE---GRDKAALLRELED  113 (269)
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHHhcC-C-CCe-EEeee-eCCCCCHHHHHHHHHHHcCCCCC---CCCHHHHHHHHHH
Confidence            4456899999999999999999998872 1 111 22233 33445778899999999887542   2233333344433


Q ss_pred             H-----hcCCcEEEEEeccCCcc--cccccccC---CCCCCCCcEEEEecCChhHHhhcC----------CCcceeccCC
Q 042645          247 T-----MRNRKIVLLLDDIWELF--DLAQVGLP---VPSRASASKVVFTTREFEVCGLMD----------AHKSFKVECL  306 (427)
Q Consensus       247 ~-----L~~k~~LlVlDdv~~~~--~~~~~~~~---l~~~~~gs~IivTtR~~~v~~~~~----------~~~~~~l~~L  306 (427)
                      .     ..+++.+||+||++...  .++.+...   .........|++|.... ....+.          ....+.+++|
T Consensus       114 ~l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l  192 (269)
T TIGR03015       114 FLIEQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPL  192 (269)
T ss_pred             HHHHHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCC
Confidence            2     25788999999998753  23333211   11122233556665542 221111          1245789999


Q ss_pred             ChHHHHHHHHHHhCCCCCC-CCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          307 GYEDAWRLFEEKVGRDILD-SHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       307 ~~~e~~~lf~~~~~~~~~~-~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      +.+|..+++...+...+.. ...-..+..+.|++.|+|.|..|..++..+
T Consensus       193 ~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       193 DREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            9999999998876433211 122345789999999999999999988776

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.53  E-value=7.3e-13  Score=142.91  Aligned_cols=244  Identities=16%  Similarity=0.210  Sum_probs=154.6

Q ss_pred             CCCCCCccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC-CCCCHHHHHHHH
Q 042645          143 ERPLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS-RDLQLGKIQESI  221 (427)
Q Consensus       143 ~~~~~~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~-~~~~~~~l~~~i  221 (427)
                      +|+.++.++-|...++.+-+.   ...+++.|+|++|.||||++..+.+..    +   .++|+++. .+.++..+...+
T Consensus         9 ~p~~~~~~~~R~rl~~~l~~~---~~~~~~~v~apaG~GKTtl~~~~~~~~----~---~~~w~~l~~~d~~~~~f~~~l   78 (903)
T PRK04841          9 RPVRLHNTVVRERLLAKLSGA---NNYRLVLVTSPAGYGKTTLISQWAAGK----N---NLGWYSLDESDNQPERFASYL   78 (903)
T ss_pred             CCCCccccCcchHHHHHHhcc---cCCCeEEEECCCCCCHHHHHHHHHHhC----C---CeEEEecCcccCCHHHHHHHH
Confidence            444456788888766666432   367899999999999999999988543    2   58999996 445667777777


Q ss_pred             HHHhCCCCCC-----------CCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc--cc-ccccCCCCCCCCcEEEEe
Q 042645          222 AKKIGLYNES-----------WDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD--LA-QVGLPVPSRASASKVVFT  285 (427)
Q Consensus       222 ~~~l~~~~~~-----------~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~--~~-~~~~~l~~~~~gs~IivT  285 (427)
                      +..++.....           ....+.......+...+.  +.+++|||||++...+  .. .+...+.....+.++|||
T Consensus        79 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~  158 (903)
T PRK04841         79 IAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVL  158 (903)
T ss_pred             HHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEE
Confidence            7777421111           011222333444444433  6899999999976532  12 222223333456788899


Q ss_pred             cCChhHH---hhcCCCcceecc----CCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCC
Q 042645          286 TREFEVC---GLMDAHKSFKVE----CLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASK  358 (427)
Q Consensus       286 tR~~~v~---~~~~~~~~~~l~----~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~  358 (427)
                      ||...-.   ..........+.    +|+.+|+.+||....+..-      ..+.+..|++.|+|+|+++..++..+...
T Consensus       159 sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~------~~~~~~~l~~~t~Gwp~~l~l~~~~~~~~  232 (903)
T PRK04841        159 SRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPI------EAAESSRLCDDVEGWATALQLIALSARQN  232 (903)
T ss_pred             eCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCC------CHHHHHHHHHHhCChHHHHHHHHHHHhhC
Confidence            9984321   111112234555    9999999999988765321      23457889999999999999998777553


Q ss_pred             CChHHHHHHHHHHhhccccCCCC-hHHHHHHHhh-hcCCCCCChHhHHHhhhcCCC
Q 042645          359 KAPREWAHAIEVLRSSASKFSGM-EKKALSRLKF-SYDFLPSNETRFCLLYCGFFP  412 (427)
Q Consensus       359 ~~~~~w~~~l~~l~~~~~~~~~~-~~~~~~~l~~-sy~~L~~~~~k~cf~~~s~fp  412 (427)
                      ....  ......+       .+. ...+...|.- .++.||+ ..+.++...|+++
T Consensus       233 ~~~~--~~~~~~~-------~~~~~~~~~~~l~~~v~~~l~~-~~~~~l~~~a~~~  278 (903)
T PRK04841        233 NSSL--HDSARRL-------AGINASHLSDYLVEEVLDNVDL-ETRHFLLRCSVLR  278 (903)
T ss_pred             CCch--hhhhHhh-------cCCCchhHHHHHHHHHHhcCCH-HHHHHHHHhcccc
Confidence            2210  1111111       111 1245555443 3789999 8999999999997

>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=99.48  E-value=1.9e-13  Score=123.17  Aligned_cols=196  Identities=18%  Similarity=0.236  Sum_probs=104.9

Q ss_pred             cccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH--------
Q 042645          150 VVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI--------  221 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i--------  221 (427)
                      |+||+.++++|.+++..+..+.+.|+|+.|+|||+|++.+.+... . ..+ .++|+....... ......+        
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~-~-~~~-~~~y~~~~~~~~-~~~~~~~~~~~~~~~   76 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELK-E-KGY-KVVYIDFLEESN-ESSLRSFIEETSLAD   76 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT----EE-CCCHHCCTTBSH-HHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhh-h-cCC-cEEEEecccchh-hhHHHHHHHHHHHHH
Confidence            799999999999999887788999999999999999999999872 1 111 233443333322 2222222        


Q ss_pred             --HHHhCCCCCC--------CCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCcc-ccc-------ccccCCCC--CCCC
Q 042645          222 --AKKIGLYNES--------WDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELF-DLA-------QVGLPVPS--RASA  279 (427)
Q Consensus       222 --~~~l~~~~~~--------~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~-~~~-------~~~~~l~~--~~~g  279 (427)
                        ...+....+.        ............+.+.+.  +++++||+||++... ...       .+...+..  ....
T Consensus        77 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  156 (234)
T PF01637_consen   77 ELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQN  156 (234)
T ss_dssp             HCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TT
T ss_pred             HHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCC
Confidence              1112111000        011122333344444443  355999999997665 111       11111111  1233


Q ss_pred             cEEEEecCChhHHhh--------cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          280 SKVVFTTREFEVCGL--------MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       280 s~IivTtR~~~v~~~--------~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ..+++++.+..+...        .+....+.+++|+.+++++++...+... ... +...+..++|+..+||+|..|..+
T Consensus       157 ~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~-~~~-~~~~~~~~~i~~~~gG~P~~l~~~  234 (234)
T PF01637_consen  157 VSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKEL-IKL-PFSDEDIEEIYSLTGGNPRYLQEL  234 (234)
T ss_dssp             EEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC--------HHHHHHHHHHHTT-HHHHHHH
T ss_pred             ceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHh-hcc-cCCHHHHHHHHHHhCCCHHHHhcC
Confidence            445555555544332        1223458999999999999999976443 122 223556799999999999988653

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

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.48  E-value=1.8e-11  Score=118.10  Aligned_cols=204  Identities=15%  Similarity=0.153  Sum_probs=129.3

Q ss_pred             CCCccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCC---CcEEEEEEeCCCCCHHHHH
Q 042645          146 LPPTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPND---FDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       146 ~~~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~---f~~~~wv~~~~~~~~~~l~  218 (427)
                      .|+.++||++++++|..++..    ...+.+.|+|++|+|||++++.++++.......   --..+|+++....+...++
T Consensus        13 ~p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~   92 (365)
T TIGR02928        13 VPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVL   92 (365)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHH
Confidence            356899999999999999863    345679999999999999999999876211111   1245778887777888999


Q ss_pred             HHHHHHhC---CCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCcc-cc----cccccCC-CCCC--CCcEEEEe
Q 042645          219 ESIAKKIG---LYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELF-DL----AQVGLPV-PSRA--SASKVVFT  285 (427)
Q Consensus       219 ~~i~~~l~---~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~-~~----~~~~~~l-~~~~--~gs~IivT  285 (427)
                      ..|+.++.   ...+ ....+..+....+.+.+.  +++++||||+++... ..    ..+.... ....  ....+|.+
T Consensus        93 ~~i~~~l~~~~~~~~-~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i  171 (365)
T TIGR02928        93 VELANQLRGSGEEVP-TTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGI  171 (365)
T ss_pred             HHHHHHHhhcCCCCC-CCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEE
Confidence            99999983   3221 123345566666666664  568899999998762 11    1111110 1111  22344555


Q ss_pred             cCChhHHhhcC-------CCcceeccCCChHHHHHHHHHHhCC--CCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          286 TREFEVCGLMD-------AHKSFKVECLGYEDAWRLFEEKVGR--DILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       286 tR~~~v~~~~~-------~~~~~~l~~L~~~e~~~lf~~~~~~--~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                      |........+.       ....+.+++++.+|..+++..++..  .....+++..+.+..++..+.|.|..+..
T Consensus       172 ~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~  245 (365)
T TIGR02928       172 SNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAID  245 (365)
T ss_pred             ECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHH
Confidence            54433211111       1246889999999999999988741  11112233334555677777898865543

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.31  E-value=7.5e-11  Score=118.08  Aligned_cols=245  Identities=18%  Similarity=0.194  Sum_probs=160.9

Q ss_pred             CCCCccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHH
Q 042645          145 PLPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAK  223 (427)
Q Consensus       145 ~~~~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~  223 (427)
                      ..+...+-|....+.|-+.   .+.+.+.|..|+|.|||||+.++....    ..-..+.|.++.. +.++..+...++.
T Consensus        16 ~~~~~~v~R~rL~~~L~~~---~~~RL~li~APAGfGKttl~aq~~~~~----~~~~~v~Wlslde~dndp~rF~~yLi~   88 (894)
T COG2909          16 VRPDNYVVRPRLLDRLRRA---NDYRLILISAPAGFGKTTLLAQWRELA----ADGAAVAWLSLDESDNDPARFLSYLIA   88 (894)
T ss_pred             CCcccccccHHHHHHHhcC---CCceEEEEeCCCCCcHHHHHHHHHHhc----CcccceeEeecCCccCCHHHHHHHHHH
Confidence            3355667776554444332   378999999999999999999998733    3445789999865 4578889999988


Q ss_pred             HhCCCCCCC-----------CCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc---ccccccCCCCCCCCcEEEEecC
Q 042645          224 KIGLYNESW-----------DNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD---LAQVGLPVPSRASASKVVFTTR  287 (427)
Q Consensus       224 ~l~~~~~~~-----------~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~---~~~~~~~l~~~~~gs~IivTtR  287 (427)
                      .++.-.+..           ...+...+...+..-+.  .+++.+||||.+-..+   -..+...+.+...+-..++|||
T Consensus        89 al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR  168 (894)
T COG2909          89 ALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSR  168 (894)
T ss_pred             HHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEec
Confidence            887332211           12333445555555444  4789999999875432   1222233344556788999999


Q ss_pred             ChhHHhhcC---CCcceec----cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCC
Q 042645          288 EFEVCGLMD---AHKSFKV----ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKA  360 (427)
Q Consensus       288 ~~~v~~~~~---~~~~~~l----~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~  360 (427)
                      +.+-.....   ....+++    =.|+.+|+.++|....+..      -...-++.|.+..+|-+-|+.+++=.++.+.+
T Consensus       169 ~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~------Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~  242 (894)
T COG2909         169 SRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLP------LDAADLKALYDRTEGWAAALQLIALALRNNTS  242 (894)
T ss_pred             cCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCC------CChHHHHHHHhhcccHHHHHHHHHHHccCCCc
Confidence            976432211   1122232    3588999999998876432      22344889999999999999999988884434


Q ss_pred             hHHHHHHHHHHhhccccCCCChHHHHHHHh-hhcCCCCCChHhHHHhhhcCCCC
Q 042645          361 PREWAHAIEVLRSSASKFSGMEKKALSRLK-FSYDFLPSNETRFCLLYCGFFPE  413 (427)
Q Consensus       361 ~~~w~~~l~~l~~~~~~~~~~~~~~~~~l~-~sy~~L~~~~~k~cf~~~s~fp~  413 (427)
                      .+.--          ..+++..+-+...|. --++.||+ ++|.+++.||+++.
T Consensus       243 ~~q~~----------~~LsG~~~~l~dYL~eeVld~Lp~-~l~~FLl~~svl~~  285 (894)
T COG2909         243 AEQSL----------RGLSGAASHLSDYLVEEVLDRLPP-ELRDFLLQTSVLSR  285 (894)
T ss_pred             HHHHh----------hhccchHHHHHHHHHHHHHhcCCH-HHHHHHHHHHhHHH
Confidence            32211          122233333444333 45789999 89999999999875

>PF05729 NACHT: NACHT domain

Probab=99.30  E-value=1.9e-11  Score=103.90  Aligned_cols=142  Identities=16%  Similarity=0.263  Sum_probs=90.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCC---CCcEEEEEEeCCCCCHH---HHHHHHHHHhCCCCCCCCCCCHHHHHHH
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPN---DFDFVIWEVVSRDLQLG---KIQESIAKKIGLYNESWDNKSFDEKAQE  243 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---~f~~~~wv~~~~~~~~~---~l~~~i~~~l~~~~~~~~~~~~~~~~~~  243 (427)
                      +++.|+|.+|+||||+++.++..+.....   .+...+|.+.+......   .+...+..+.....     .....   .
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~-----~~~~~---~   72 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESI-----APIEE---L   72 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccch-----hhhHH---H
Confidence            57999999999999999999988742221   14566777765543322   34444444433211     11111   2


Q ss_pred             HHHH-hcCCcEEEEEeccCCccc---------cccc-ccCCCC-CCCCcEEEEecCChhH---HhhcCCCcceeccCCCh
Q 042645          244 IFKT-MRNRKIVLLLDDIWELFD---------LAQV-GLPVPS-RASASKVVFTTREFEV---CGLMDAHKSFKVECLGY  308 (427)
Q Consensus       244 l~~~-L~~k~~LlVlDdv~~~~~---------~~~~-~~~l~~-~~~gs~IivTtR~~~v---~~~~~~~~~~~l~~L~~  308 (427)
                      +... .+.++++||||++++...         +..+ ...+.. ..++++++||||....   .........+.+.+|++
T Consensus        73 ~~~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~  152 (166)
T PF05729_consen   73 LQELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSE  152 (166)
T ss_pred             HHHHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCH
Confidence            2222 247899999999986533         1111 122222 3568999999999776   33334446789999999


Q ss_pred             HHHHHHHHHHh
Q 042645          309 EDAWRLFEEKV  319 (427)
Q Consensus       309 ~e~~~lf~~~~  319 (427)
                      ++..+++.+.+
T Consensus       153 ~~~~~~~~~~f  163 (166)
T PF05729_consen  153 EDIKQYLRKYF  163 (166)
T ss_pred             HHHHHHHHHHh
Confidence            99999998876

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.29  E-value=2.7e-11  Score=114.72  Aligned_cols=239  Identities=17%  Similarity=0.128  Sum_probs=128.6

Q ss_pred             CccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..|+|+++.++.+...+..     ...+.+.|+|++|+|||+||+.+++...   ..+   .++..+. ......+..++
T Consensus        25 ~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~---~~~---~~~~~~~-~~~~~~l~~~l   97 (328)
T PRK00080         25 DEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMG---VNI---RITSGPA-LEKPGDLAAIL   97 (328)
T ss_pred             HHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhC---CCe---EEEeccc-ccChHHHHHHH
Confidence            5699999999998877752     3456789999999999999999999872   211   1122111 11122223333


Q ss_pred             HHhCCCC----CCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhhcC--
Q 042645          223 KKIGLYN----ESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMD--  296 (427)
Q Consensus       223 ~~l~~~~----~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~--  296 (427)
                      ..+....    ++.+..+ ....+.+...+.+.+..+++|+..+.....   ..++   +.+-|..|++...+...+.  
T Consensus        98 ~~l~~~~vl~IDEi~~l~-~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~---~~l~---~~~li~at~~~~~l~~~L~sR  170 (328)
T PRK00080         98 TNLEEGDVLFIDEIHRLS-PVVEEILYPAMEDFRLDIMIGKGPAARSIR---LDLP---PFTLIGATTRAGLLTSPLRDR  170 (328)
T ss_pred             HhcccCCEEEEecHhhcc-hHHHHHHHHHHHhcceeeeeccCcccccee---ecCC---CceEEeecCCcccCCHHHHHh
Confidence            3332110    0000001 112223444455555555565543322111   1111   2345666666543322211  


Q ss_pred             CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHhhccc
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSAS  376 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~~~~~  376 (427)
                      ....+.+++++.++..+++.+.+...+...+   .+.+..|++.|+|.|..+..+...+.      .|...    .....
T Consensus       171 f~~~~~l~~~~~~e~~~il~~~~~~~~~~~~---~~~~~~ia~~~~G~pR~a~~~l~~~~------~~a~~----~~~~~  237 (328)
T PRK00080        171 FGIVQRLEFYTVEELEKIVKRSARILGVEID---EEGALEIARRSRGTPRIANRLLRRVR------DFAQV----KGDGV  237 (328)
T ss_pred             cCeeeecCCCCHHHHHHHHHHHHHHcCCCcC---HHHHHHHHHHcCCCchHHHHHHHHHH------HHHHH----cCCCC
Confidence            1346899999999999999998865443332   45689999999999976666554332      11110    00000


Q ss_pred             cCCCChHHHHHHHhhhcCCCCCChHhHHHh-hhcCCCCC
Q 042645          377 KFSGMEKKALSRLKFSYDFLPSNETRFCLL-YCGFFPED  414 (427)
Q Consensus       377 ~~~~~~~~~~~~l~~sy~~L~~~~~k~cf~-~~s~fp~~  414 (427)
                      -....-......+...+..|++ ..+..+. .+..|+.+
T Consensus       238 I~~~~v~~~l~~~~~~~~~l~~-~~~~~l~~~~~~~~~~  275 (328)
T PRK00080        238 ITKEIADKALDMLGVDELGLDE-MDRKYLRTIIEKFGGG  275 (328)
T ss_pred             CCHHHHHHHHHHhCCCcCCCCH-HHHHHHHHHHHHcCCC
Confidence            0000012344455566677776 4555553 55666654

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.27  E-value=2.1e-10  Score=107.78  Aligned_cols=190  Identities=17%  Similarity=0.154  Sum_probs=112.2

Q ss_pred             CccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..|+|+++.+++|..++..     ...+.+.++|++|+|||+||+.+++...   ..+   ..+..+....... +...+
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~---~~~---~~~~~~~~~~~~~-l~~~l   76 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMG---VNL---KITSGPALEKPGD-LAAIL   76 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhC---CCE---EEeccchhcCchh-HHHHH
Confidence            4689999999999888862     3456788999999999999999998872   222   1122111111222 22223


Q ss_pred             HHhCCCC----CCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhhcC--
Q 042645          223 KKIGLYN----ESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMD--  296 (427)
Q Consensus       223 ~~l~~~~----~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~--  296 (427)
                      ..++...    ++.+..+ ....+.+...+.+.+..+|+|+..+...+..   .+   .+.+-|..||+...+...+.  
T Consensus        77 ~~~~~~~vl~iDEi~~l~-~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~---~~---~~~~li~~t~~~~~l~~~l~sR  149 (305)
T TIGR00635        77 TNLEEGDVLFIDEIHRLS-PAVEELLYPAMEDFRLDIVIGKGPSARSVRL---DL---PPFTLVGATTRAGMLTSPLRDR  149 (305)
T ss_pred             HhcccCCEEEEehHhhhC-HHHHHHhhHHHhhhheeeeeccCccccceee---cC---CCeEEEEecCCccccCHHHHhh
Confidence            3332110    0001111 1223445556666666677766544333321   12   12455666777644322111  


Q ss_pred             CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHH
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA  354 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~  354 (427)
                      ....+.+++++.++..+++.+.+.......   ..+....|++.|+|.|..+..++..
T Consensus       150 ~~~~~~l~~l~~~e~~~il~~~~~~~~~~~---~~~al~~ia~~~~G~pR~~~~ll~~  204 (305)
T TIGR00635       150 FGIILRLEFYTVEELAEIVSRSAGLLNVEI---EPEAALEIARRSRGTPRIANRLLRR  204 (305)
T ss_pred             cceEEEeCCCCHHHHHHHHHHHHHHhCCCc---CHHHHHHHHHHhCCCcchHHHHHHH
Confidence            134578999999999999998886443222   2456889999999999877655543

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.

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

Probab=99.13  E-value=1.4e-09  Score=100.47  Aligned_cols=175  Identities=21%  Similarity=0.223  Sum_probs=105.8

Q ss_pred             ccccchhhH---HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          149 TVVGMQSTL---DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       149 ~~vGR~~~~---~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      .+||.+..+   .-|.+.+..+......+||++|+||||||+.+....   ...|.     .++...+-..-++      
T Consensus        25 e~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~---~~~f~-----~~sAv~~gvkdlr------   90 (436)
T COG2256          25 EVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTT---NAAFE-----ALSAVTSGVKDLR------   90 (436)
T ss_pred             HhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhh---CCceE-----EeccccccHHHHH------
Confidence            456655433   233444556788889999999999999999999876   33332     2222211111111      


Q ss_pred             CCCCCCCCCCCHHHHHHHH-HHHhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEE--ecCChhH---HhhcCC
Q 042645          226 GLYNESWDNKSFDEKAQEI-FKTMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVF--TTREFEV---CGLMDA  297 (427)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~l-~~~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~Iiv--TtR~~~v---~~~~~~  297 (427)
                                   ...+.- .....+++.+|++|+|+...  +-+.   .||.-..|.-|+|  ||-|...   .....-
T Consensus        91 -------------~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~---lLp~vE~G~iilIGATTENPsF~ln~ALlSR  154 (436)
T COG2256          91 -------------EIIEEARKNRLLGRRTILFLDEIHRFNKAQQDA---LLPHVENGTIILIGATTENPSFELNPALLSR  154 (436)
T ss_pred             -------------HHHHHHHHHHhcCCceEEEEehhhhcChhhhhh---hhhhhcCCeEEEEeccCCCCCeeecHHHhhh
Confidence                         222222 12234899999999997542  2222   2444566777776  5555443   233345


Q ss_pred             CcceeccCCChHHHHHHHHHHhCCCCC--C-CCC-CHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          298 HKSFKVECLGYEDAWRLFEEKVGRDIL--D-SHP-DIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       298 ~~~~~l~~L~~~e~~~lf~~~~~~~~~--~-~~~-~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      ..++.+++|+.++...++.+.+.....  . ... -..+....|++.++|--.++-....
T Consensus       155 ~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE  214 (436)
T COG2256         155 ARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLE  214 (436)
T ss_pred             hheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHH
Confidence            578999999999999999994422111  1 111 2245678899999997765544433

>PRK06893 DNA replication initiation factor; Validated

Probab=99.12  E-value=6.5e-10  Score=99.49  Aligned_cols=155  Identities=11%  Similarity=0.137  Sum_probs=96.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ..+.+.|+|++|+|||+|++.+++....   ....+.|+......   ....                       .+.+.
T Consensus        38 ~~~~l~l~G~~G~GKThL~~ai~~~~~~---~~~~~~y~~~~~~~---~~~~-----------------------~~~~~   88 (229)
T PRK06893         38 QQPFFYIWGGKSSGKSHLLKAVSNHYLL---NQRTAIYIPLSKSQ---YFSP-----------------------AVLEN   88 (229)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHH---cCCCeEEeeHHHhh---hhhH-----------------------HHHhh
Confidence            4467899999999999999999998721   22344666543110   0000                       11111


Q ss_pred             hcCCcEEEEEeccCCc---ccccc-cccCCCCC-CCCcEEEE-ecCC---------hhHHhhcCCCcceeccCCChHHHH
Q 042645          248 MRNRKIVLLLDDIWEL---FDLAQ-VGLPVPSR-ASASKVVF-TTRE---------FEVCGLMDAHKSFKVECLGYEDAW  312 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~---~~~~~-~~~~l~~~-~~gs~Iiv-TtR~---------~~v~~~~~~~~~~~l~~L~~~e~~  312 (427)
                      +. +.-+|+|||+|..   ..|+. +...+... ..|+.+|| |+..         ..+...+.....+++++++.++.+
T Consensus        89 ~~-~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~  167 (229)
T PRK06893         89 LE-QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKI  167 (229)
T ss_pred             cc-cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHH
Confidence            21 3349999999864   33442 22222211 23455554 4443         245555556678899999999999


Q ss_pred             HHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          313 RLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       313 ~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      +++++.+.......   .+++..-|++.+.|..-.+..+-..|
T Consensus       168 ~iL~~~a~~~~l~l---~~~v~~~L~~~~~~d~r~l~~~l~~l  207 (229)
T PRK06893        168 IVLQRNAYQRGIEL---SDEVANFLLKRLDRDMHTLFDALDLL  207 (229)
T ss_pred             HHHHHHHHHcCCCC---CHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            99999886443222   35668889999988777666555444

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.09  E-value=4.4e-09  Score=105.84  Aligned_cols=195  Identities=16%  Similarity=0.167  Sum_probs=115.0

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.|.+++..++ .+.+.++|..|+||||+|+.+.+.+... ..+..       ..+..-.....|...-.
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe-~~~~~-------~PCG~C~sCr~I~~G~h   87 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCE-TGVTS-------QPCGVCRACREIDEGRF   87 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCc-cCCCC-------CCCcccHHHHHHhcCCC
Confidence            468999999999999998765 4466899999999999999998876211 11100       00111111111111000


Q ss_pred             C---CCCCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChhH-H-hhc
Q 042645          227 L---YNESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFEV-C-GLM  295 (427)
Q Consensus       227 ~---~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~v-~-~~~  295 (427)
                      .   ..+.......++..+.+...    ..++.-++|||+++....  +..+...+.......++|+||++.+- . ...
T Consensus        88 ~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIr  167 (830)
T PRK07003         88 VDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVL  167 (830)
T ss_pred             ceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhh
Confidence            0   00000111222222222221    124556899999987643  55554444444456788887776442 1 222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch-HHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL-ALITVGR  353 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl-ai~~~~~  353 (427)
                      .-...+.+.+++.++..+.+.+.+..++...   ..+....|++.++|... ++.++-.
T Consensus       168 SRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~i---d~eAL~lIA~~A~GsmRdALsLLdQ  223 (830)
T PRK07003        168 SRCLQFNLKQMPAGHIVSHLERILGEERIAF---EPQALRLLARAAQGSMRDALSLTDQ  223 (830)
T ss_pred             hheEEEecCCcCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            2335789999999999999999876544322   24568889999998664 5555433

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

Probab=99.08  E-value=1.3e-08  Score=96.61  Aligned_cols=193  Identities=13%  Similarity=0.214  Sum_probs=130.2

Q ss_pred             CCCccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          146 LPPTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       146 ~~~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      .|..+.+|+.+++++...|..    +.+..+.|+|.+|+|||+.++.+.+.........+ +++|++....++.+++..|
T Consensus        15 iP~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~-~~yINc~~~~t~~~i~~~i   93 (366)
T COG1474          15 IPEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVE-VVYINCLELRTPYQVLSKI   93 (366)
T ss_pred             CcccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCc-eEEEeeeeCCCHHHHHHHH
Confidence            345689999999999988853    33445999999999999999999999843222232 7899999999999999999


Q ss_pred             HHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccccc--ccccCCCCCC-CCcE--EEEecCChhHHh-
Q 042645          222 AKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFDLA--QVGLPVPSRA-SASK--VVFTTREFEVCG-  293 (427)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~~~--~~~~~l~~~~-~gs~--IivTtR~~~v~~-  293 (427)
                      +.+++..  +..+.+..+....+.+.+.  ++.+++|||+++....-.  -+...+.... ..++  +|..+-+..+.. 
T Consensus        94 ~~~~~~~--p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~  171 (366)
T COG1474          94 LNKLGKV--PLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDY  171 (366)
T ss_pred             HHHcCCC--CCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHH
Confidence            9999722  2245666777778887775  588999999998654332  2211121111 1343  344444443322 


Q ss_pred             -------hcCCCcceeccCCChHHHHHHHHHHhC---CCCCCCCCCHHHHHHHHHHHcCC
Q 042645          294 -------LMDAHKSFKVECLGYEDAWRLFEEKVG---RDILDSHPDIPELAETVARECGG  343 (427)
Q Consensus       294 -------~~~~~~~~~l~~L~~~e~~~lf~~~~~---~~~~~~~~~~~~~~~~i~~~~~G  343 (427)
                             .++. ..+..+|.+.+|..+++..++.   ..+ ..++..-+++..++..-+|
T Consensus       172 ld~rv~s~l~~-~~I~F~pY~a~el~~Il~~R~~~~~~~~-~~~~~vl~lia~~~a~~~G  229 (366)
T COG1474         172 LDPRVKSSLGP-SEIVFPPYTAEELYDILRERVEEGFSAG-VIDDDVLKLIAALVAAESG  229 (366)
T ss_pred             hhhhhhhccCc-ceeeeCCCCHHHHHHHHHHHHHhhccCC-CcCccHHHHHHHHHHHcCc
Confidence                   2222 3488999999999999998873   222 2334444555555555555

>COG3899 Predicted ATPase [General function prediction only]

Probab=99.08  E-value=1.1e-09  Score=115.00  Aligned_cols=257  Identities=15%  Similarity=0.174  Sum_probs=153.0

Q ss_pred             cccchhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCC---HHHHHHHHHH
Q 042645          150 VVGMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ---LGKIQESIAK  223 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~---~~~l~~~i~~  223 (427)
                      ++||+.+++.|...+..   +...++.+.|..|+|||+|++.|.....+....|-...+-.......   ..+.++++..
T Consensus         2 l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~~~~i~~~f~q~~~~ipl~~lvq~~r~l~~   81 (849)
T COG3899           2 LYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRGYFIKGKFDQFERNIPLSPLVQAFRDLMG   81 (849)
T ss_pred             CCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhccceeeeHhhcccccCCCchHHHHHHHHHHHH
Confidence            68999999999998864   56779999999999999999999988743322222222222222222   2233444444


Q ss_pred             Hh-------------------CCCCCC------------------C--CCCCHHH-----HHHHHHHHh-cCCcEEEEEe
Q 042645          224 KI-------------------GLYNES------------------W--DNKSFDE-----KAQEIFKTM-RNRKIVLLLD  258 (427)
Q Consensus       224 ~l-------------------~~~~~~------------------~--~~~~~~~-----~~~~l~~~L-~~k~~LlVlD  258 (427)
                      ++                   +.....                  .  .+.....     ....+.... +.|+.++|+|
T Consensus        82 ~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi~le  161 (849)
T COG3899          82 QLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVIVLE  161 (849)
T ss_pred             HHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEEEEe
Confidence            33                   111000                  0  0000011     111222233 3569999999


Q ss_pred             ccC-Cccc-ccccccCCCCCC----CCcEEEEecCChhH----HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCC
Q 042645          259 DIW-ELFD-LAQVGLPVPSRA----SASKVVFTTREFEV----CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHP  328 (427)
Q Consensus       259 dv~-~~~~-~~~~~~~l~~~~----~gs~IivTtR~~~v----~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~  328 (427)
                      |++ -+.. ..-+........    ....|..+......    .........|.|.||+..+...+.....+...    .
T Consensus       162 DlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~~----~  237 (849)
T COG3899         162 DLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGCTK----L  237 (849)
T ss_pred             cccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCCcc----c
Confidence            994 2211 111111110000    01123322222211    12223446899999999999999999987633    2


Q ss_pred             CHHHHHHHHHHHcCCCchHHHHHHHHHcCC------CChHHHHHHHHHHhhccccCCCChHHHHHHHhhhcCCCCCChHh
Q 042645          329 DIPELAETVARECGGLPLALITVGRAMASK------KAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETR  402 (427)
Q Consensus       329 ~~~~~~~~i~~~~~G~Plai~~~~~~L~~~------~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k  402 (427)
                      ...+..+.|+++..|+|+.+..+...+..+      .+...|..-...+.    ..+.. +.+...+..-.+.||+ ..|
T Consensus       238 ~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~----~~~~~-~~vv~~l~~rl~kL~~-~t~  311 (849)
T COG3899         238 LPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLG----ILATT-DAVVEFLAARLQKLPG-TTR  311 (849)
T ss_pred             ccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcC----Cchhh-HHHHHHHHHHHhcCCH-HHH
Confidence            334568999999999999999998888773      44555554222221    22222 2466678888999999 899


Q ss_pred             HHHhhhcCCCCCcc
Q 042645          403 FCLLYCGFFPEDYS  416 (427)
Q Consensus       403 ~cf~~~s~fp~~~~  416 (427)
                      +.+...|++...|.
T Consensus       312 ~Vl~~AA~iG~~F~  325 (849)
T COG3899         312 EVLKAAACIGNRFD  325 (849)
T ss_pred             HHHHHHHHhCccCC
Confidence            99999999987665

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.07  E-value=2.7e-09  Score=104.11  Aligned_cols=178  Identities=20%  Similarity=0.197  Sum_probs=108.1

Q ss_pred             CccccchhhHHH---HHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDR---VWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       148 ~~~vGR~~~~~~---l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..++|++..+..   |.+++..+..+.+.|+|++|+||||||+.+++..   ...|     +.++.......-++.+.  
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~---~~~~-----~~l~a~~~~~~~ir~ii--   81 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT---DAPF-----EALSAVTSGVKDLREVI--   81 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHh---CCCE-----EEEecccccHHHHHHHH--
Confidence            468999888666   7888877777789999999999999999999876   2222     22222111111111121  


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHH-hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEE--ecCChhH---HhhcC
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKT-MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVF--TTREFEV---CGLMD  296 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~-L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~Iiv--TtR~~~v---~~~~~  296 (427)
                                       ...... ..+++.+|++|+++...  ..+.+...+.   .+..++|  ||.+...   .....
T Consensus        82 -----------------~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le---~~~iilI~att~n~~~~l~~aL~S  141 (413)
T PRK13342         82 -----------------EEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVE---DGTITLIGATTENPSFEVNPALLS  141 (413)
T ss_pred             -----------------HHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhh---cCcEEEEEeCCCChhhhccHHHhc
Confidence                             111111 14578899999998653  2333333332   2444444  3333221   12222


Q ss_pred             CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      -...+.+.+++.++...++.+.+........+-..+..+.|++.|+|.|..+..+...+
T Consensus       142 R~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~~  200 (413)
T PRK13342        142 RAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLELA  200 (413)
T ss_pred             cceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            33678999999999999999876432100112335668889999999998776555443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.05  E-value=1.6e-08  Score=102.52  Aligned_cols=173  Identities=13%  Similarity=0.106  Sum_probs=108.9

Q ss_pred             CCccccchhhHHHHHHHhcc----C-CCeEEEEEecCCCcHHHHHHHHHhhccCC--CCCC--cEEEEEEeCCCCCHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE----E-PVGIVGLYGMGGVGKTTLLTQINNSFLHT--PNDF--DFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~----~-~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~~f--~~~~wv~~~~~~~~~~l  217 (427)
                      |..+.|||+++++|...|..    . ...++.|+|++|.|||++++.|.+.+...  ....  -.+++|++....++..+
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sI  833 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAA  833 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHH
Confidence            56789999999999988853    2 23467899999999999999998876311  1111  23577887777788899


Q ss_pred             HHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc---CCcEEEEEeccCCcccc--cccccCCC-CCCCCcEEEE--ecCCh
Q 042645          218 QESIAKKIGLYNESWDNKSFDEKAQEIFKTMR---NRKIVLLLDDIWELFDL--AQVGLPVP-SRASASKVVF--TTREF  289 (427)
Q Consensus       218 ~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~---~k~~LlVlDdv~~~~~~--~~~~~~l~-~~~~gs~Iiv--TtR~~  289 (427)
                      +..|..++....+. ...+..+....+...+.   +...+||||+++....-  +.+...+. ....+++|+|  +|.+.
T Consensus       834 YqvI~qqL~g~~P~-~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdl  912 (1164)
T PTZ00112        834 YQVLYKQLFNKKPP-NALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTM  912 (1164)
T ss_pred             HHHHHHHHcCCCCC-ccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCch
Confidence            99999988543322 23334455555655542   23469999999854310  11111111 1123444443  34322


Q ss_pred             hH--------HhhcCCCcceeccCCChHHHHHHHHHHhCC
Q 042645          290 EV--------CGLMDAHKSFKVECLGYEDAWRLFEEKVGR  321 (427)
Q Consensus       290 ~v--------~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~  321 (427)
                      .+        ...+. ...+..+|++.++..+++..++..
T Consensus       913 DLperLdPRLRSRLg-~eeIvF~PYTaEQL~dILk~RAe~  951 (1164)
T PTZ00112        913 DLPERLIPRCRSRLA-FGRLVFSPYKGDEIEKIIKERLEN  951 (1164)
T ss_pred             hcchhhhhhhhhccc-cccccCCCCCHHHHHHHHHHHHHh
Confidence            22        11111 234677999999999999998853

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.03  E-value=1.6e-09  Score=97.12  Aligned_cols=169  Identities=15%  Similarity=0.123  Sum_probs=103.1

Q ss_pred             chhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC
Q 042645          153 MQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW  232 (427)
Q Consensus       153 R~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~  232 (427)
                      .+..++.+.+++.....+.+.|+|++|+|||+||+.+++...   ......++++++.-.      ...           
T Consensus        22 ~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~---~~~~~~~~i~~~~~~------~~~-----------   81 (226)
T TIGR03420        22 NAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAE---ERGKSAIYLPLAELA------QAD-----------   81 (226)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHH---hcCCcEEEEeHHHHH------HhH-----------
Confidence            445677777776556677899999999999999999998862   223344555543221      000           


Q ss_pred             CCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc---ccc-ccccCCCC-CCCCcEEEEecCChh---------HHhhcCCC
Q 042645          233 DNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF---DLA-QVGLPVPS-RASASKVVFTTREFE---------VCGLMDAH  298 (427)
Q Consensus       233 ~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~---~~~-~~~~~l~~-~~~gs~IivTtR~~~---------v~~~~~~~  298 (427)
                               ..+...+.+ .-+|||||++...   .|. .+...+.. ...+..+|+||+...         +...+...
T Consensus        82 ---------~~~~~~~~~-~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~  151 (226)
T TIGR03420        82 ---------PEVLEGLEQ-ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWG  151 (226)
T ss_pred             ---------HHHHhhccc-CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcC
Confidence                     011111222 2489999998653   222 23222221 122347888887532         22222234


Q ss_pred             cceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHH
Q 042645          299 KSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA  354 (427)
Q Consensus       299 ~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~  354 (427)
                      ..+.+++++.++...++...+.....   +-..+..+.|.+.+.|+|..+..+...
T Consensus       152 ~~i~l~~l~~~e~~~~l~~~~~~~~~---~~~~~~l~~L~~~~~gn~r~L~~~l~~  204 (226)
T TIGR03420       152 LVFQLPPLSDEEKIAALQSRAARRGL---QLPDEVADYLLRHGSRDMGSLMALLDA  204 (226)
T ss_pred             eeEecCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHhccCCHHHHHHHHHH
Confidence            57899999999999999876532221   222455788888899999877766543

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.99  E-value=7e-09  Score=98.92  Aligned_cols=198  Identities=12%  Similarity=0.105  Sum_probs=113.0

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCc-EEEEEEeCCCCCHHHHHHHHH----
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFD-FVIWEVVSRDLQLGKIQESIA----  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~----  222 (427)
                      ..++|++..++.+.+++..+..+.+.++|++|+||||+|+.+++...  ...+. ..+.++++...+  .....+.    
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~--~~~~~~~~~~i~~~~~~~--~~~~~~~~~~~   90 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELY--GDPWENNFTEFNVADFFD--QGKKYLVEDPR   90 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhc--CcccccceEEechhhhhh--cchhhhhcCcc
Confidence            46899999999999999887767789999999999999999998772  11111 233444332110  0000000    


Q ss_pred             --HHhCCCCCCCCCCCHHHHHHHHH-HH---h--cCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-H
Q 042645          223 --KKIGLYNESWDNKSFDEKAQEIF-KT---M--RNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-V  291 (427)
Q Consensus       223 --~~l~~~~~~~~~~~~~~~~~~l~-~~---L--~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v  291 (427)
                        ..++.. .. ...........+. ..   .  .+.+-+||+||++....  ...+...+......+++|+||.+.. +
T Consensus        91 ~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~  168 (337)
T PRK12402         91 FAHFLGTD-KR-IRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKL  168 (337)
T ss_pred             hhhhhhhh-hh-hccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhC
Confidence              000000 00 0011111222221 11   1  13455899999976532  2223333322334567777775432 2


Q ss_pred             Hh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHH
Q 042645          292 CG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA  354 (427)
Q Consensus       292 ~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~  354 (427)
                      .. .......+.+.+++.++...++.+.+...+...   ..+..+.|++.++|.+-.+......
T Consensus       169 ~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~~---~~~al~~l~~~~~gdlr~l~~~l~~  229 (337)
T PRK12402        169 IPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDY---DDDGLELIAYYAGGDLRKAILTLQT  229 (337)
T ss_pred             chhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            11 222335678999999999999998765443222   2456888999999987776554443

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.97  E-value=2.4e-08  Score=99.49  Aligned_cols=193  Identities=11%  Similarity=0.122  Sum_probs=113.2

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+...+.|.+++..+. .+.+.++|+.|+||||+|+.+++.+... .      ++.. ..+..-...+.+...-.
T Consensus        15 ddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~-~------~~~~-~pCg~C~sC~~I~~g~h   86 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCE-T------GVTS-TPCEVCATCKAVNEGRF   86 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCC-c------CCCC-CCCccCHHHHHHhcCCC
Confidence            468999999999999998765 4577999999999999999998876211 0      0000 00011111111111000


Q ss_pred             CCC---CCCCCCCHHHHHHHHHH----HhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-HH-hhc
Q 042645          227 LYN---ESWDNKSFDEKAQEIFK----TMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-VC-GLM  295 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~----~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v~-~~~  295 (427)
                      ...   ........++..+.+..    -..++.-++|+|+++...  ....+...+.....+..+|++|.+.. +. ...
T Consensus        87 pDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIl  166 (702)
T PRK14960         87 IDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVI  166 (702)
T ss_pred             CceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHH
Confidence            000   00011122222222211    123566799999998653  34444444444345567777776533 21 222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .....+++.+++.++..+.+.+.+...+...   ..+....|++.++|.+..+..+
T Consensus       167 SRCq~feFkpLs~eEI~k~L~~Il~kEgI~i---d~eAL~~IA~~S~GdLRdALnL  219 (702)
T PRK14960        167 SRCLQFTLRPLAVDEITKHLGAILEKEQIAA---DQDAIWQIAESAQGSLRDALSL  219 (702)
T ss_pred             HhhheeeccCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHH
Confidence            3346789999999999999998875544222   2455788999999988655443

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.92  E-value=6.7e-08  Score=91.44  Aligned_cols=182  Identities=12%  Similarity=0.111  Sum_probs=109.1

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEe--CCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVV--SRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~--~~~~~~~~l~~~i~~~l  225 (427)
                      .+++|++..++.+..++..+..+.+.|+|++|+||||+++.+++....  ..+. ..++.+  +...... .....+..+
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~--~~~~-~~~i~~~~~~~~~~~-~~~~~i~~~   92 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYG--EDWR-ENFLELNASDERGID-VIRNKIKEF   92 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcC--Cccc-cceEEeccccccchH-HHHHHHHHH
Confidence            458999999999999998877777899999999999999999988621  1111 112222  2221111 111111111


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCCh-hH-HhhcCCCcce
Q 042645          226 GLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREF-EV-CGLMDAHKSF  301 (427)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~-~v-~~~~~~~~~~  301 (427)
                      ....+                .....+-++++|+++....  ...+...+......+.+|+++... .+ .........+
T Consensus        93 ~~~~~----------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~  156 (319)
T PRK00440         93 ARTAP----------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVF  156 (319)
T ss_pred             HhcCC----------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhhee
Confidence            10000                0012356899999875522  233333333333456677766432 11 1111223468


Q ss_pred             eccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          302 KVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       302 ~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      ++.+++.++...++...+...+...   ..+.+..+++.++|.+.-+....
T Consensus       157 ~~~~l~~~ei~~~l~~~~~~~~~~i---~~~al~~l~~~~~gd~r~~~~~l  204 (319)
T PRK00440        157 RFSPLKKEAVAERLRYIAENEGIEI---TDDALEAIYYVSEGDMRKAINAL  204 (319)
T ss_pred             eeCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999999999999998875443222   24568899999999888754433

>PF13173 AAA_14: AAA domain

Probab=98.92  E-value=1.6e-09  Score=87.72  Aligned_cols=120  Identities=18%  Similarity=0.186  Sum_probs=80.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      .+++.|.|+.|+|||||+++++++..    ....++++++.........                  ..+ ..+.+.+..
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~----~~~~~~yi~~~~~~~~~~~------------------~~~-~~~~~~~~~   58 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL----PPENILYINFDDPRDRRLA------------------DPD-LLEYFLELI   58 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc----ccccceeeccCCHHHHHHh------------------hhh-hHHHHHHhh
Confidence            46899999999999999999998872    3445667665543221100                  000 223333333


Q ss_pred             cCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhh------cCCCcceeccCCChHHH
Q 042645          249 RNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL------MDAHKSFKVECLGYEDA  311 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~------~~~~~~~~l~~L~~~e~  311 (427)
                      ..++.+|+||++....+|......+.+..+..+|++|+.+......      .+....+++.||+..|.
T Consensus        59 ~~~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   59 KPGKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             ccCCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            3478899999999988888776666665567899999998665422      11224678999998763

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.92  E-value=1.7e-08  Score=103.58  Aligned_cols=194  Identities=15%  Similarity=0.155  Sum_probs=111.5

Q ss_pred             CccccchhhHHHHHHHhccCCCeE-EEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGI-VGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~v-i~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..+..|.+++..++.+- +.++|+.|+||||+|+.+++.+... ......       .+..-.....+.....
T Consensus        16 ddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce-~~~~~~-------pCg~C~sC~~i~~g~~   87 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCE-QGVTAT-------PCGVCSSCVEIAQGRF   87 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCc-cCCCCC-------CCCCchHHHHHhcCCC
Confidence            468999999999999998876554 5899999999999999999887311 110000       0000000011111000


Q ss_pred             ---CCCCCCCCCCHHHH---HHHHHH-HhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCCh-hHH-hhc
Q 042645          227 ---LYNESWDNKSFDEK---AQEIFK-TMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREF-EVC-GLM  295 (427)
Q Consensus       227 ---~~~~~~~~~~~~~~---~~~l~~-~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~~  295 (427)
                         ...........+..   ...+.. -..+++-++|||+++..  .....+...+-......++|++|.+. .+. ...
T Consensus        88 ~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIl  167 (944)
T PRK14949         88 VDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVL  167 (944)
T ss_pred             ceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHH
Confidence               00000001111221   111111 12367779999999865  33444444443334456666655543 332 222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .-...|++.+|+.++...++.+.+...+..   ...+.+..|++.++|.|.-+..+.
T Consensus       168 SRCq~f~fkpLs~eEI~~~L~~il~~EgI~---~edeAL~lIA~~S~Gd~R~ALnLL  221 (944)
T PRK14949        168 SRCLQFNLKSLTQDEIGTQLNHILTQEQLP---FEAEALTLLAKAANGSMRDALSLT  221 (944)
T ss_pred             HhheEEeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            234678999999999999999877543322   224568889999999887554443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.91  E-value=4.3e-08  Score=94.03  Aligned_cols=193  Identities=18%  Similarity=0.225  Sum_probs=110.7

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.+.+.+..++. +.+.++|++|+||||+|+.+++..... ....       ..++..-....++.....
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~-~~~~-------~~pc~~c~~c~~~~~~~~   87 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQ-NGIT-------SNPCRKCIICKEIEKGLC   87 (363)
T ss_pred             hhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCC-CCCC-------CCCCCCCHHHHHHhcCCC
Confidence            4689999999999999987654 467899999999999999999876210 0000       000000011111111100


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-HHh-h
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-VCG-L  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v~~-~  294 (427)
                      ...   +.......++ ...+.+.+     .+++-++|+|+++...  .+..+...+.......++|++|.+.+ +.. .
T Consensus        88 ~d~~~~~~~~~~~v~~-ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI  166 (363)
T PRK14961         88 LDLIEIDAASRTKVEE-MREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTI  166 (363)
T ss_pred             CceEEecccccCCHHH-HHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHH
Confidence            000   0000011222 22222222     2455699999998764  34445444444445666777665432 322 1


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .+-...+++.+++.++..+.+...+...+..   -..+.+..|++.++|.|..+....
T Consensus       167 ~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~---i~~~al~~ia~~s~G~~R~al~~l  221 (363)
T PRK14961        167 LSRCLQFKLKIISEEKIFNFLKYILIKESID---TDEYALKLIAYHAHGSMRDALNLL  221 (363)
T ss_pred             HhhceEEeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            2223578999999999999998876443311   224557889999999887554443

>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=98.91  E-value=1.1e-08  Score=88.49  Aligned_cols=176  Identities=17%  Similarity=0.187  Sum_probs=95.0

Q ss_pred             CccccchhhHHHHHHHhc-----cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLT-----EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      .+|||.++.+..+.-.+.     .+....+.+||++|+||||||..+++..   ...|.   +.+.. ...         
T Consensus        24 ~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~---~~~~~---~~sg~-~i~---------   87 (233)
T PF05496_consen   24 DEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANEL---GVNFK---ITSGP-AIE---------   87 (233)
T ss_dssp             CCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHC---T--EE---EEECC-C-----------
T ss_pred             HHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhcc---CCCeE---eccch-hhh---------
Confidence            579999998887654443     2356789999999999999999999998   33332   22211 100         


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------cccccc--CCCC----------CCCCcE
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------LAQVGL--PVPS----------RASASK  281 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~~~~~~--~l~~----------~~~gs~  281 (427)
                                   ...++...+.. + +++.+|.+|+++....         .++...  ....          ..+-+-
T Consensus        88 -------------k~~dl~~il~~-l-~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTl  152 (233)
T PF05496_consen   88 -------------KAGDLAAILTN-L-KEGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTL  152 (233)
T ss_dssp             -------------SCHHHHHHHHT----TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EE
T ss_pred             -------------hHHHHHHHHHh-c-CCCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceE
Confidence                         01122222211 2 2455777788875311         111110  0000          012244


Q ss_pred             EEEecCChhHHhhcCCC--cceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcC
Q 042645          282 VVFTTREFEVCGLMDAH--KSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMAS  357 (427)
Q Consensus       282 IivTtR~~~v~~~~~~~--~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~  357 (427)
                      |=.|||...+...+...  ...+++..+.+|..+++.+.+..-+.   +-..+.+.+|+++|.|-|--..-+...++.
T Consensus       153 igATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i---~i~~~~~~~Ia~rsrGtPRiAnrll~rvrD  227 (233)
T PF05496_consen  153 IGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNI---EIDEDAAEEIARRSRGTPRIANRLLRRVRD  227 (233)
T ss_dssp             EEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT----EE-HHHHHHHHHCTTTSHHHHHHHHHHHCC
T ss_pred             eeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCC---CcCHHHHHHHHHhcCCChHHHHHHHHHHHH
Confidence            55688875554333332  23479999999999999987754432   223567999999999999877766665543

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.90  E-value=5.1e-08  Score=96.61  Aligned_cols=190  Identities=17%  Similarity=0.150  Sum_probs=111.7

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      .+++|.+..+..|.+++..+..+ .+.++|++|+||||+|+.+++.+.. .+.+...+|.|.+.        ..+.....
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c-~~~~~~~cg~C~sc--------~~i~~~~h   84 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNC-SGEDPKPCGECESC--------LAVRRGAH   84 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhc-cCCCCCCCCcChhh--------HHHhcCCC
Confidence            45799999999999998877544 5699999999999999999988731 11122222322111        00000000


Q ss_pred             CC---CCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCC-hhHHhh-
Q 042645          227 LY---NESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTRE-FEVCGL-  294 (427)
Q Consensus       227 ~~---~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~-~~v~~~-  294 (427)
                      ..   .........+. +..+.+.+     .+++-++|+|+++..  ..+..+...+......+.+|++|.. ..+... 
T Consensus        85 ~dv~el~~~~~~~vd~-iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I  163 (504)
T PRK14963         85 PDVLEIDAASNNSVED-VRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTI  163 (504)
T ss_pred             CceEEecccccCCHHH-HHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHH
Confidence            00   00001111222 12222222     246679999999855  2345554445443445555555543 333222 


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                      ......+++.+++.++..+++.+.+...+...   ..+.+..|++.++|.+.-+..
T Consensus       164 ~SRc~~~~f~~ls~~el~~~L~~i~~~egi~i---~~~Al~~ia~~s~GdlR~aln  216 (504)
T PRK14963        164 LSRTQHFRFRRLTEEEIAGKLRRLLEAEGREA---EPEALQLVARLADGAMRDAES  216 (504)
T ss_pred             hcceEEEEecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHH
Confidence            22345789999999999999999875443222   245688899999999875543

>PRK08727 hypothetical protein; Validated

Probab=98.89  E-value=3.3e-08  Score=88.69  Aligned_cols=171  Identities=11%  Similarity=0.070  Sum_probs=100.2

Q ss_pred             ccccc-hhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          149 TVVGM-QSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       149 ~~vGR-~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      +|++. ...+..+.....+.....+.|+|++|+|||+|++.+++...   .....+.|++..+      ....+.     
T Consensus        20 ~f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~---~~~~~~~y~~~~~------~~~~~~-----   85 (233)
T PRK08727         20 SYIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAE---QAGRSSAYLPLQA------AAGRLR-----   85 (233)
T ss_pred             hccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEEeHHH------hhhhHH-----
Confidence            34443 34444444443344445699999999999999999998862   2223455655322      111111     


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---ccc-cccCCCC-CCCCcEEEEecCChh---------HHh
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---LAQ-VGLPVPS-RASASKVVFTTREFE---------VCG  293 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---~~~-~~~~l~~-~~~gs~IivTtR~~~---------v~~  293 (427)
                                 .    ..+.+ .+.-+||+||++....   |.. +...+.. ...|..||+||+...         +..
T Consensus        86 -----------~----~~~~l-~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~S  149 (233)
T PRK08727         86 -----------D----ALEAL-EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRS  149 (233)
T ss_pred             -----------H----HHHHH-hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHH
Confidence                       0    11111 2335899999975432   221 2222211 123566999998532         223


Q ss_pred             hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       294 ~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .+.....+++++++.++...++.+++.......   ..+....|++.++|..-.+..+.
T Consensus       150 Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l~l---~~e~~~~La~~~~rd~r~~l~~L  205 (233)
T PRK08727        150 RLAQCIRIGLPVLDDVARAAVLRERAQRRGLAL---DEAAIDWLLTHGERELAGLVALL  205 (233)
T ss_pred             HHhcCceEEecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHhCCCCHHHHHHHH
Confidence            333456789999999999999998764433222   24568888999987766554333

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

Probab=98.88  E-value=3e-09  Score=86.58  Aligned_cols=117  Identities=21%  Similarity=0.259  Sum_probs=79.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC--CCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT--PNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~  245 (427)
                      +.+.+.|+|++|+|||+++..+.+.....  ......++|+.+....+...+...++..++.....  ..+..++.+.+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~l~~~~~   80 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKS--RQTSDELRSLLI   80 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSS--TS-HHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccc--cCCHHHHHHHHH
Confidence            34679999999999999999999876210  00134567999988889999999999999976542  456777888888


Q ss_pred             HHhcCCc-EEEEEeccCCc-c--cccccccCCCCCCCCcEEEEecCC
Q 042645          246 KTMRNRK-IVLLLDDIWEL-F--DLAQVGLPVPSRASASKVVFTTRE  288 (427)
Q Consensus       246 ~~L~~k~-~LlVlDdv~~~-~--~~~~~~~~l~~~~~gs~IivTtR~  288 (427)
                      +.+...+ .+||+||++.. .  .++.+.... + ..+.++|+..+.
T Consensus        81 ~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~-~-~~~~~vvl~G~~  125 (131)
T PF13401_consen   81 DALDRRRVVLLVIDEADHLFSDEFLEFLRSLL-N-ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHCTEEEEEEETTHHHHTHHHHHHHHHHT-C-SCBEEEEEEESS
T ss_pred             HHHHhcCCeEEEEeChHhcCCHHHHHHHHHHH-h-CCCCeEEEEECh
Confidence            8887655 59999999765 2  122222222 2 556778877765

>PRK04195 replication factor C large subunit; Provisional

Probab=98.87  E-value=7.6e-08  Score=95.88  Aligned_cols=182  Identities=19%  Similarity=0.239  Sum_probs=113.2

Q ss_pred             CccccchhhHHHHHHHhccC----CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEE----PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~----~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      ..++|.++.+++|.+|+...    ..+.+.|+|++|+||||+|+.+++...     ++ ++-++.+...+. ..+..++.
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~-----~~-~ielnasd~r~~-~~i~~~i~   86 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG-----WE-VIELNASDQRTA-DVIERVAG   86 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC-----CC-EEEEcccccccH-HHHHHHHH
Confidence            46899999999999998641    267899999999999999999999871     22 233344432222 22333332


Q ss_pred             HhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc------ccccccCCCCCCCCcEEEEecCChh-HH--hh
Q 042645          224 KIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD------LAQVGLPVPSRASASKVVFTTREFE-VC--GL  294 (427)
Q Consensus       224 ~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~------~~~~~~~l~~~~~gs~IivTtR~~~-v~--~~  294 (427)
                      ......                .....++-+||||+++....      ...+...+.  ..+..||+|+.+.. ..  ..
T Consensus        87 ~~~~~~----------------sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~~k~L  148 (482)
T PRK04195         87 EAATSG----------------SLFGARRKLILLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPYDPSLREL  148 (482)
T ss_pred             HhhccC----------------cccCCCCeEEEEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCccccchhhH
Confidence            221110                00113678999999986532      233332332  22344666664422 11  12


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcC
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMAS  357 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~  357 (427)
                      ......+.+.+++.++....+.+.+...+...+   .+....|++.++|....+......+..
T Consensus       149 rsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i~---~eaL~~Ia~~s~GDlR~ain~Lq~~a~  208 (482)
T PRK04195        149 RNACLMIEFKRLSTRSIVPVLKRICRKEGIECD---DEALKEIAERSGGDLRSAINDLQAIAE  208 (482)
T ss_pred             hccceEEEecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence            223467899999999999999888754443332   456899999999988777655544443

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.87  E-value=3.4e-08  Score=98.29  Aligned_cols=195  Identities=17%  Similarity=0.189  Sum_probs=112.8

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCC-CcEEEEEEeCCCCCHHHHHHHHHHH-
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPND-FDFVIWEVVSRDLQLGKIQESIAKK-  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~-f~~~~wv~~~~~~~~~~l~~~i~~~-  224 (427)
                      .++||.+..++.|.+++..++.. .+.++|+.|+||||+|+.+.+.+...... -....    +..+..-.....|... 
T Consensus        16 ddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~----~~PCG~C~sC~~I~aG~   91 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGIT----AQPCGQCRACTEIDAGR   91 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCC----CCCCcccHHHHHHHcCC
Confidence            46899999999999999887654 56899999999999999998877321000 00000    0001111111111110 


Q ss_pred             ----hCCCCCCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCC-hhHH-
Q 042645          225 ----IGLYNESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTRE-FEVC-  292 (427)
Q Consensus       225 ----l~~~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~-~~v~-  292 (427)
                          +.+...  .....+++.+.+...    ..++.-++|||+++..  ..++.+...+.....++.+|++|.+ ..+. 
T Consensus        92 hpDviEIdAa--s~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlp  169 (700)
T PRK12323         92 FVDYIEMDAA--SNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPV  169 (700)
T ss_pred             CCcceEeccc--ccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhh
Confidence                000000  112233333322221    2356679999999865  3344554444433445666655554 3332 


Q ss_pred             hhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          293 GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       293 ~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ...+-...+.+..++.++..+.+.+.+...+...   ..+..+.|++.++|.|.-...+
T Consensus       170 TIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~---d~eAL~~IA~~A~Gs~RdALsL  225 (700)
T PRK12323        170 TVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAH---EVNALRLLAQAAQGSMRDALSL  225 (700)
T ss_pred             HHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHH
Confidence            2222235789999999999999998775433222   2345688999999999755444

>PLN03025 replication factor C subunit; Provisional

Probab=98.86  E-value=3.5e-08  Score=93.08  Aligned_cols=184  Identities=13%  Similarity=0.123  Sum_probs=109.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCc-EEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFD-FVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.++.+..|..++..++.+.+.++|++|+||||+|..+++...  ...|. .++-++.+...... ..+++...+.
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~--~~~~~~~~~eln~sd~~~~~-~vr~~i~~~~   89 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELL--GPNYKEAVLELNASDDRGID-VVRNKIKMFA   89 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHh--cccCccceeeecccccccHH-HHHHHHHHHH
Confidence            45789999999998888877777788999999999999999998862  11222 12222222222211 2222222211


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-H-HhhcCCCccee
Q 042645          227 LYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-V-CGLMDAHKSFK  302 (427)
Q Consensus       227 ~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~~~~~~~  302 (427)
                      .....               .-.++.-+++||+++....  ...+...+......+++++++.... + .........++
T Consensus        90 ~~~~~---------------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~  154 (319)
T PLN03025         90 QKKVT---------------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVR  154 (319)
T ss_pred             hcccc---------------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhccc
Confidence            00000               0013567999999987532  2222222222234566777665422 2 11112235689


Q ss_pred             ccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          303 VECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       303 l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      +.+++.++....+...+...+...+   .+....|++.++|....+....
T Consensus       155 f~~l~~~~l~~~L~~i~~~egi~i~---~~~l~~i~~~~~gDlR~aln~L  201 (319)
T PLN03025        155 FSRLSDQEILGRLMKVVEAEKVPYV---PEGLEAIIFTADGDMRQALNNL  201 (319)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHH
Confidence            9999999999999988755442222   4558889999999776554443

>PTZ00202 tuzin; Provisional

Probab=98.86  E-value=2.3e-07  Score=87.65  Aligned_cols=163  Identities=15%  Similarity=0.086  Sum_probs=102.1

Q ss_pred             CCCCCCccccchhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHH
Q 042645          143 ERPLPPTVVGMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQE  219 (427)
Q Consensus       143 ~~~~~~~~vGR~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~  219 (427)
                      .|+.++.|+||+.++.+|...|.+   ...+++.|.|++|+|||||++.+.... .     ...++++..   +..+++.
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l-~-----~~qL~vNpr---g~eElLr  327 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKE-G-----MPAVFVDVR---GTEDTLR  327 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcC-C-----ceEEEECCC---CHHHHHH
Confidence            345567899999999999999864   234689999999999999999998765 1     113333333   6799999


Q ss_pred             HHHHHhCCCCCCCCCCCHHHHHHHHHHHh-----c-CCcEEEEEeccCCccccccc---ccCCCCCCCCcEEEEecCChh
Q 042645          220 SIAKKIGLYNESWDNKSFDEKAQEIFKTM-----R-NRKIVLLLDDIWELFDLAQV---GLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       220 ~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-----~-~k~~LlVlDdv~~~~~~~~~---~~~l~~~~~gs~IivTtR~~~  290 (427)
                      .++.+||.+.    .....++...|.+.+     . +++.+||+-==+ -.++..+   ...+.....-|.|++----+.
T Consensus       328 ~LL~ALGV~p----~~~k~dLLrqIqeaLl~~~~e~GrtPVLII~lre-g~~l~rvyne~v~la~drr~ch~v~evples  402 (550)
T PTZ00202        328 SVVKALGVPN----VEACGDLLDFISEACRRAKKMNGETPLLVLKLRE-GSSLQRVYNEVVALACDRRLCHVVIEVPLES  402 (550)
T ss_pred             HHHHHcCCCC----cccHHHHHHHHHHHHHHHHHhCCCCEEEEEEecC-CCcHHHHHHHHHHHHccchhheeeeeehHhh
Confidence            9999999743    222244445544433     2 566666664221 1111111   011223344566776443333


Q ss_pred             HHhhc---CCCcceeccCCChHHHHHHHHHHh
Q 042645          291 VCGLM---DAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       291 v~~~~---~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      +....   .--..|.+++++.++|..+..+..
T Consensus       403 lt~~~~~lprldf~~vp~fsr~qaf~y~~h~~  434 (550)
T PTZ00202        403 LTIANTLLPRLDFYLVPNFSRSQAFAYTQHAI  434 (550)
T ss_pred             cchhcccCccceeEecCCCCHHHHHHHHhhcc
Confidence            21111   111357899999999999887765

>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=98.84  E-value=2.8e-08  Score=82.26  Aligned_cols=123  Identities=22%  Similarity=0.166  Sum_probs=73.2

Q ss_pred             ccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC
Q 042645          151 VGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE  230 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~  230 (427)
                      +|++..+..+...+..+..+.+.|+|++|+|||++++.+++...   ..-..++++..+...........+...      
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~---~~~~~v~~~~~~~~~~~~~~~~~~~~~------   71 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELF---RPGAPFLYLNASDLLEGLVVAELFGHF------   71 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhh---cCCCCeEEEehhhhhhhhHHHHHhhhh------
Confidence            47888999999998876778899999999999999999999872   222345566554432221111111000      


Q ss_pred             CCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc-----ccccccccCCCC---CCCCcEEEEecCChh
Q 042645          231 SWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL-----FDLAQVGLPVPS---RASASKVVFTTREFE  290 (427)
Q Consensus       231 ~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~-----~~~~~~~~~l~~---~~~gs~IivTtR~~~  290 (427)
                              ............++.+|++||++..     ..+......+..   ...+..||+||....
T Consensus        72 --------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          72 --------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             --------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                    0001111223356789999999854     112222122211   135678888887643

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.83  E-value=5e-08  Score=87.67  Aligned_cols=173  Identities=13%  Similarity=0.091  Sum_probs=103.1

Q ss_pred             cccch-hhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 042645          150 VVGMQ-STLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLY  228 (427)
Q Consensus       150 ~vGR~-~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~  228 (427)
                      ++|.. ..+..+.++....+.+.+.|+|++|+|||+|++.+++...   .....+.++++.....               
T Consensus        25 ~~~~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~---~~~~~v~y~~~~~~~~---------------   86 (235)
T PRK08084         25 YPGDNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELS---QRGRAVGYVPLDKRAW---------------   86 (235)
T ss_pred             ccCccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHH---hCCCeEEEEEHHHHhh---------------
Confidence            34632 3344444444445557899999999999999999998762   1223456665532100               


Q ss_pred             CCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc---ccccc-cccCCCC-CCCC-cEEEEecCChh---------HHh
Q 042645          229 NESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL---FDLAQ-VGLPVPS-RASA-SKVVFTTREFE---------VCG  293 (427)
Q Consensus       229 ~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~---~~~~~-~~~~l~~-~~~g-s~IivTtR~~~---------v~~  293 (427)
                             ...+..    +.+.. --+|++||++..   ..|+. +...+.. ...| .++|+||+...         +..
T Consensus        87 -------~~~~~~----~~~~~-~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~S  154 (235)
T PRK08084         87 -------FVPEVL----EGMEQ-LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLAS  154 (235)
T ss_pred             -------hhHHHH----HHhhh-CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHH
Confidence                   001111    11111 237899999754   23432 1122221 1123 47999998643         344


Q ss_pred             hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       294 ~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      .+.....+++.+++.++-.+++.+++...+..   -.+++..-|++.+.|..-.+..+...+
T Consensus       155 Rl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~---l~~~v~~~L~~~~~~d~r~l~~~l~~l  213 (235)
T PRK08084        155 RLDWGQIYKLQPLSDEEKLQALQLRARLRGFE---LPEDVGRFLLKRLDREMRTLFMTLDQL  213 (235)
T ss_pred             HHhCCceeeecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence            45566789999999999999998866433322   235668889999988776665554443

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.82  E-value=1.9e-07  Score=87.92  Aligned_cols=176  Identities=13%  Similarity=0.187  Sum_probs=113.6

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEe-CCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVV-SRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~-~~~~~~~~l~~~i~  222 (427)
                      ..++|.+..++.+.+++..+. .+...++|+.|+||||+|..+++.+..   ...|++...|... +......+ .+++.
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~-ir~~~   82 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD-IRNII   82 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH-HHHHH
Confidence            357899999999999998764 456789999999999999999986521   2346666555432 22222222 22222


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCChhHH--hhcCCC
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREFEVC--GLMDAH  298 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~~v~--~~~~~~  298 (427)
                      ..+...                  -..+++-++|+|+++..  ..+..+...+.....++.+|++|.+.+..  ....-.
T Consensus        83 ~~~~~~------------------p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc  144 (313)
T PRK05564         83 EEVNKK------------------PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRC  144 (313)
T ss_pred             HHHhcC------------------cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhc
Confidence            322211                  01245567777877643  44666766666666788888888654321  112234


Q ss_pred             cceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          299 KSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       299 ~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      ..+.+.++++++...++.+.....       ..+.++.++..++|.|.-+.
T Consensus       145 ~~~~~~~~~~~~~~~~l~~~~~~~-------~~~~~~~l~~~~~g~~~~a~  188 (313)
T PRK05564        145 QIYKLNRLSKEEIEKFISYKYNDI-------KEEEKKSAIAFSDGIPGKVE  188 (313)
T ss_pred             eeeeCCCcCHHHHHHHHHHHhcCC-------CHHHHHHHHHHcCCCHHHHH
Confidence            678999999999998887765311       12336788899999987554

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

Probab=98.82  E-value=1.1e-07  Score=86.85  Aligned_cols=174  Identities=18%  Similarity=0.199  Sum_probs=108.0

Q ss_pred             ccccchhhH---HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          149 TVVGMQSTL---DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       149 ~~vGR~~~~---~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      ++||.+..+   .-|...+.++..+.+.+||++|+||||||+.+.+.-   +.+-  ..||..|....-..-.+.|.++-
T Consensus       139 dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~ts---k~~S--yrfvelSAt~a~t~dvR~ife~a  213 (554)
T KOG2028|consen  139 DYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTS---KKHS--YRFVELSATNAKTNDVRDIFEQA  213 (554)
T ss_pred             HhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhc---CCCc--eEEEEEeccccchHHHHHHHHHH
Confidence            355555433   223444556788999999999999999999998876   2221  45666655433333344444332


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEE--ecCChhH---HhhcCCC
Q 042645          226 GLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVF--TTREFEV---CGLMDAH  298 (427)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~Iiv--TtR~~~v---~~~~~~~  298 (427)
                      ..                 ...+.++|.+|.+|+++.-  .+-+   ..+|.-..|.-++|  ||-+.+.   ..++.-.
T Consensus       214 q~-----------------~~~l~krkTilFiDEiHRFNksQQD---~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC  273 (554)
T KOG2028|consen  214 QN-----------------EKSLTKRKTILFIDEIHRFNKSQQD---TFLPHVENGDITLIGATTENPSFQLNAALLSRC  273 (554)
T ss_pred             HH-----------------HHhhhcceeEEEeHHhhhhhhhhhh---cccceeccCceEEEecccCCCccchhHHHHhcc
Confidence            10                 1234578999999999743  2222   33555566776666  6666554   3344556


Q ss_pred             cceeccCCChHHHHHHHHHHh---CCCCC--CCCC-----CHHHHHHHHHHHcCCCchH
Q 042645          299 KSFKVECLGYEDAWRLFEEKV---GRDIL--DSHP-----DIPELAETVARECGGLPLA  347 (427)
Q Consensus       299 ~~~~l~~L~~~e~~~lf~~~~---~~~~~--~~~~-----~~~~~~~~i~~~~~G~Pla  347 (427)
                      .++.|++|+.++...++.+..   +....  ..-+     -...+.+-++..|+|-..+
T Consensus       274 ~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR~  332 (554)
T KOG2028|consen  274 RVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDARA  332 (554)
T ss_pred             ceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHHH
Confidence            788999999999999998843   22211  1111     2235677788889986653

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.80  E-value=2.3e-07  Score=92.23  Aligned_cols=194  Identities=12%  Similarity=0.111  Sum_probs=109.5

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..+||.+..++.|.+++..+..+ .+.++|+.|+||||+|+.+++.+... ..+..       .+++.-.....|...-.
T Consensus        16 ~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~-~~~~~-------~pCg~C~~C~~i~~g~~   87 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCE-KGVSA-------NPCNDCENCREIDEGRF   87 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCC-CCCCc-------ccCCCCHHHHHHhcCCC
Confidence            46899999999999999877554 57899999999999999998876211 11100       00000011111110000


Q ss_pred             CC---CCCCCCCCHHHHHHHHHH----HhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCCh-hHH-hhc
Q 042645          227 LY---NESWDNKSFDEKAQEIFK----TMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREF-EVC-GLM  295 (427)
Q Consensus       227 ~~---~~~~~~~~~~~~~~~l~~----~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~~  295 (427)
                      .+   .+.......++..+.+..    -..++.-++|+|+++..  .....+...+......+++|++|.+. .+. ...
T Consensus        88 ~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~  167 (509)
T PRK14958         88 PDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVL  167 (509)
T ss_pred             ceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHH
Confidence            00   000011122222211111    11356679999999865  33444444444334456676665443 222 222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .....+++.+++.++....+.+.+...+...   ..+....|++.++|.+.-+..+.
T Consensus       168 SRc~~~~f~~l~~~~i~~~l~~il~~egi~~---~~~al~~ia~~s~GslR~al~lL  221 (509)
T PRK14958        168 SRCLQFHLAQLPPLQIAAHCQHLLKEENVEF---ENAALDLLARAANGSVRDALSLL  221 (509)
T ss_pred             HHhhhhhcCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCcHHHHHHHH
Confidence            2335688999999999888887765443222   23457789999999887655443

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.80  E-value=3.4e-06  Score=86.15  Aligned_cols=202  Identities=15%  Similarity=0.075  Sum_probs=118.5

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCC---cEEEEEEeCC---CCCHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDF---DFVIWEVVSR---DLQLGKIQESI  221 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f---~~~~wv~~~~---~~~~~~l~~~i  221 (427)
                      +.++|++..+..+.+.+..+....+.|+|++|+||||||+.+++.. .....+   ...-|+.+..   ..+...+...+
T Consensus       154 ~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~-~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~l  232 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEA-KKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPL  232 (615)
T ss_pred             HhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhh-hhccCCcccCCCCeEEEechhccCCHHHHhHHh
Confidence            4689999999999888876666789999999999999999998765 222222   1123443321   11222221111


Q ss_pred             ---------------HHHhCCCC----------------CCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc--ccccc
Q 042645          222 ---------------AKKIGLYN----------------ESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL--FDLAQ  268 (427)
Q Consensus       222 ---------------~~~l~~~~----------------~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~--~~~~~  268 (427)
                                     +...+...                +.....+ ......+...++++++.++-|+.|..  ..|..
T Consensus       233 lg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld-~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~  311 (615)
T TIGR02903       233 LGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELD-PLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKY  311 (615)
T ss_pred             cCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCC-HHHHHHHHHHHhhCeEEeecceeccCCcccchh
Confidence                           11112110                0011112 33566777888888888887766643  34666


Q ss_pred             cccCCCCCCCCcEEEE--ecCChhH-H-hhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC
Q 042645          269 VGLPVPSRASASKVVF--TTREFEV-C-GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL  344 (427)
Q Consensus       269 ~~~~l~~~~~gs~Iiv--TtR~~~v-~-~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~  344 (427)
                      +...+....+...+++  ||++... . ........+.+.+++.++.+.++.+.+.......   ..++.+.|.+.+..-
T Consensus       312 ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~l---s~eal~~L~~ys~~g  388 (615)
T TIGR02903       312 IKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHL---AAGVEELIARYTIEG  388 (615)
T ss_pred             hhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHCCCcH
Confidence            6555554444444555  5554321 1 1111224678999999999999999875432111   245566676666655


Q ss_pred             chHHHHHHHH
Q 042645          345 PLALITVGRA  354 (427)
Q Consensus       345 Plai~~~~~~  354 (427)
                      +.++..++..
T Consensus       389 Rraln~L~~~  398 (615)
T TIGR02903       389 RKAVNILADV  398 (615)
T ss_pred             HHHHHHHHHH
Confidence            6777666544

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.78  E-value=3.7e-07  Score=86.97  Aligned_cols=196  Identities=14%  Similarity=0.079  Sum_probs=111.0

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCC-CCcE-EE-EEEeCCCCCHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPN-DFDF-VI-WEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~f~~-~~-wv~~~~~~~~~~l~~~i~~  223 (427)
                      ..++|.+.....|.+.+..+..+ .+.++|+.|+||+|+|..+.+.+..... .... .. -.++.. .......+.+..
T Consensus        19 ~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~-~~~c~~c~~i~~   97 (365)
T PRK07471         19 TALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAI-DPDHPVARRIAA   97 (365)
T ss_pred             hhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccC-CCCChHHHHHHc
Confidence            56899999999999999887644 5889999999999999998887632110 0000 00 000000 000011122211


Q ss_pred             HhCCC-----C---CC----CCCCCHHHHHHHHHHHhc-----CCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEE
Q 042645          224 KIGLY-----N---ES----WDNKSFDEKAQEIFKTMR-----NRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVF  284 (427)
Q Consensus       224 ~l~~~-----~---~~----~~~~~~~~~~~~l~~~L~-----~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~Iiv  284 (427)
                      .-..+     .   ..    ......++ ++.+.+.+.     +.+-++|+||++...  ....+...+.....++.+|+
T Consensus        98 ~~HPDl~~i~~~~~~~~~~~~~~I~Vdq-iR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~IL  176 (365)
T PRK07471         98 GAHGGLLTLERSWNEKGKRLRTVITVDE-VRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEPPARSLFLL  176 (365)
T ss_pred             cCCCCeEEEecccccccccccccccHHH-HHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEEEE
Confidence            10000     0   00    01122333 334444442     567799999998652  23334333333334566777


Q ss_pred             ecCChh-HHh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          285 TTREFE-VCG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       285 TtR~~~-v~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      +|.+.+ +.. .......+.+.+++.++..+++.+.....     +  ......++..++|.|+....+.
T Consensus       177 ~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~~-----~--~~~~~~l~~~s~Gsp~~Al~ll  239 (365)
T PRK07471        177 VSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPDL-----P--DDPRAALAALAEGSVGRALRLA  239 (365)
T ss_pred             EECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcccC-----C--HHHHHHHHHHcCCCHHHHHHHh
Confidence            666543 322 22334678999999999999998865321     1  1223678999999998665443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.77  E-value=1.4e-07  Score=93.71  Aligned_cols=181  Identities=17%  Similarity=0.172  Sum_probs=108.4

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCC------------------CCcEEEEEEe
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPN------------------DFDFVIWEVV  208 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~------------------~f~~~~wv~~  208 (427)
                      ..++|.+..++.|.+.+..+.. +.+.++|+.|+||||+|+.+++.+.....                  .|...+++..
T Consensus        16 ~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieida   95 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDA   95 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeec
Confidence            4679999999999999987654 45789999999999999999986621100                  0111111111


Q ss_pred             CCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH-HhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEe
Q 042645          209 SRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK-TMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFT  285 (427)
Q Consensus       209 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivT  285 (427)
                      .......                    +..++...+.. -..+++-++|+||++...  ..+.+...+......+.+|++
T Consensus        96 as~~gvd--------------------~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~  155 (546)
T PRK14957         96 ASRTGVE--------------------ETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILA  155 (546)
T ss_pred             ccccCHH--------------------HHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEE
Confidence            1111111                    11122222221 123567799999998653  344454444444445656655


Q ss_pred             cCC-hhHH-hhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch-HHHHH
Q 042645          286 TRE-FEVC-GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL-ALITV  351 (427)
Q Consensus       286 tR~-~~v~-~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl-ai~~~  351 (427)
                      |.+ ..+. ....-...+++.+++.++....+.+.+...+..   ...+....|++.++|.+. ++..+
T Consensus       156 Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~---~e~~Al~~Ia~~s~GdlR~alnlL  221 (546)
T PRK14957        156 TTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENIN---SDEQSLEYIAYHAKGSLRDALSLL  221 (546)
T ss_pred             ECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            543 3332 222334678999999999998888866443322   224557889999999775 44444

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.77  E-value=9.3e-08  Score=92.72  Aligned_cols=194  Identities=13%  Similarity=0.110  Sum_probs=112.4

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..+..|..++..+..+ .+.++|+.|+||||+|+.+++.+...  ....  ...+.....    ...+.....
T Consensus        18 ~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce--~~~~--~~pCg~C~s----C~~i~~g~~   89 (484)
T PRK14956         18 RDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCE--NPIG--NEPCNECTS----CLEITKGIS   89 (484)
T ss_pred             HHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcc--cccC--ccccCCCcH----HHHHHccCC
Confidence            46899999999999999887654 58999999999999999999887311  1100  001111111    111211111


Q ss_pred             CCC---CCCCCCCHHH---HHHHHHH-HhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCC-hhHH-hhc
Q 042645          227 LYN---ESWDNKSFDE---KAQEIFK-TMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTRE-FEVC-GLM  295 (427)
Q Consensus       227 ~~~---~~~~~~~~~~---~~~~l~~-~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~-~~v~-~~~  295 (427)
                      ...   ........+.   +.+.+.. ...++.-++|+|+++..  ..+..+...+........+|++|.+ ..+. ...
T Consensus        90 ~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~  169 (484)
T PRK14956         90 SDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETIL  169 (484)
T ss_pred             ccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHH
Confidence            000   0000111222   2222221 12356679999999865  3355554444333344555545544 3332 222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .-...|.+.+++.++..+.+.+.+...+...   ..+....|++.++|.+.-+..+.
T Consensus       170 SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~~---e~eAL~~Ia~~S~Gd~RdAL~lL  223 (484)
T PRK14956        170 SRCQDFIFKKVPLSVLQDYSEKLCKIENVQY---DQEGLFWIAKKGDGSVRDMLSFM  223 (484)
T ss_pred             hhhheeeecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCChHHHHHHHH
Confidence            2335689999999999999988875443222   24568899999999986554443

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.77  E-value=2.5e-07  Score=91.40  Aligned_cols=195  Identities=14%  Similarity=0.158  Sum_probs=112.2

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcE-EEEEEeCCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDF-VIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~-~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      .+++|.+..+..|.+.+..+. .+.+.++|++|+||||+|+.+++.+.... .... --+..+..+    .-...+....
T Consensus        21 ~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~-~~~~~~~~~~C~~C----~~C~~i~~~~   95 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSA-LITENTTIKTCEQC----TNCISFNNHN   95 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCcc-ccccCcCcCCCCCC----hHHHHHhcCC
Confidence            357999999999999887765 45789999999999999999998773111 0000 000000000    0111111100


Q ss_pred             CCCC---CCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEE-ecCChhHHhh-
Q 042645          226 GLYN---ESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVF-TTREFEVCGL-  294 (427)
Q Consensus       226 ~~~~---~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~Iiv-TtR~~~v~~~-  294 (427)
                      ....   +.......+++...+...    +.+++-++|+|+++..  ..+..+...+......+.+|+ ||....+... 
T Consensus        96 h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI  175 (507)
T PRK06645         96 HPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATI  175 (507)
T ss_pred             CCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHH
Confidence            0000   000112223332222221    2356779999999865  335555555544445566655 4444444332 


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                      ......+.+.+++.++....+.+.+...+...   ..+....|++.++|.+.-+..
T Consensus       176 ~SRc~~~ef~~ls~~el~~~L~~i~~~egi~i---e~eAL~~Ia~~s~GslR~al~  228 (507)
T PRK06645        176 ISRCQRYDLRRLSFEEIFKLLEYITKQENLKT---DIEALRIIAYKSEGSARDAVS  228 (507)
T ss_pred             HhcceEEEccCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHH
Confidence            22345789999999999999998886544222   245578899999998865543

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.77  E-value=5.9e-09  Score=97.05  Aligned_cols=238  Identities=21%  Similarity=0.246  Sum_probs=157.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ..+.+.++|.||+||||++-.+.+ ..  ..+-+.+.++.+.+-.+...+.-.+...++.+..     +-+.....+...
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~~--~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~-----~g~~~~~~~~~~   84 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-AA--SEYADGVAFVDLAPITDPALVFPTLAGALGLHVQ-----PGDSAVDTLVRR   84 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-Hh--hhcccceeeeeccccCchhHhHHHHHhhcccccc-----cchHHHHHHHHH
Confidence            347899999999999999999988 31  2344466677777777777777777777876542     223344456667


Q ss_pred             hcCCcEEEEEeccCCccc-ccccccCCCCCCCCcEEEEecCChhHHhhcCCCcceeccCCChH-HHHHHHHHHhCCCC--
Q 042645          248 MRNRKIVLLLDDIWELFD-LAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYE-DAWRLFEEKVGRDI--  323 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~~~-~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~~~~~~~l~~L~~~-e~~~lf~~~~~~~~--  323 (427)
                      ..+++.++|+||..+..+ -......+..+.+.-.|+.|+|....   ........+++|+.. ++.++|...+....  
T Consensus        85 ~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l---~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~  161 (414)
T COG3903          85 IGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAIL---VAGEVHRRVPSLSLFDEAIELFVCRAVLVALS  161 (414)
T ss_pred             HhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhc---ccccccccCCccccCCchhHHHHHHHHHhccc
Confidence            778999999999876532 12222223334455678889887433   234456678888764 78888887653221  


Q ss_pred             CCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHH----HHHHhhccccCCCChHHHHHHHhhhcCCCCCC
Q 042645          324 LDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHA----IEVLRSSASKFSGMEKKALSRLKFSYDFLPSN  399 (427)
Q Consensus       324 ~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~----l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~  399 (427)
                      ............+|.++.+|.|++|...++..+.- ...+.-..    ++.+........--+......+.+||.-|.. 
T Consensus       162 f~l~~~~~a~v~~icr~ldg~~laielaaarv~sl-~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtg-  239 (414)
T COG3903         162 FWLTDDNAAAVAEICRRLDGIPLAIELAAARVRSL-SPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTG-  239 (414)
T ss_pred             eeecCCchHHHHHHHHHhhcchHHHHHHHHHHHhc-CHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhh-
Confidence            11223345668899999999999999999888773 33222221    1222222111111123677889999999998 


Q ss_pred             hHhHHHhhhcCCCCCcccc
Q 042645          400 ETRFCLLYCGFFPEDYSIS  418 (427)
Q Consensus       400 ~~k~cf~~~s~fp~~~~i~  418 (427)
                      ..+..|.-++.|...|...
T Consensus       240 we~~~~~rLa~~~g~f~~~  258 (414)
T COG3903         240 WERALFGRLAVFVGGFDLG  258 (414)
T ss_pred             HHHHHhcchhhhhhhhccc
Confidence            7888999999998877654

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.75  E-value=2e-07  Score=91.39  Aligned_cols=193  Identities=15%  Similarity=0.133  Sum_probs=111.1

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      .+++|.+..++.|.+.+..+..+ .+.++|+.|+||||+|+.+++.+....+ ..       ..++..-.....|.....
T Consensus        13 ~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~-~~-------~~pCg~C~~C~~i~~~~~   84 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNG-PT-------SDPCGTCHNCISIKNSNH   84 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCC-CC-------CCCccccHHHHHHhccCC
Confidence            46799999999999998877655 7999999999999999999875411000 00       000111111111111111


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCC-hhHHh-hc
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTRE-FEVCG-LM  295 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~-~~v~~-~~  295 (427)
                      .+.   +.....+.++....+...    ..++.-++|+|+++...  ..+.+...+......+.+|++|.+ ..+.. ..
T Consensus        85 ~Dv~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~  164 (491)
T PRK14964         85 PDVIEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTII  164 (491)
T ss_pred             CCEEEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHH
Confidence            000   000011222222111111    12456699999997653  344454444444456666666643 33322 22


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .....+.+.+++.++....+.+.+...+...   ..+....|++.++|.+..+...
T Consensus       165 SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i---~~eAL~lIa~~s~GslR~alsl  217 (491)
T PRK14964        165 SRCQRFDLQKIPTDKLVEHLVDIAKKENIEH---DEESLKLIAENSSGSMRNALFL  217 (491)
T ss_pred             HhheeeecccccHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHH
Confidence            3346789999999999999998876544222   2455788999999988655433

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

Probab=98.75  E-value=2.4e-08  Score=86.48  Aligned_cols=46  Identities=26%  Similarity=0.372  Sum_probs=32.9

Q ss_pred             ccccchhhHHHHHHHhc---cCCCeEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          149 TVVGMQSTLDRVWRCLT---EEPVGIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      .|+||+++++++.+.+.   ....+.+.|+|++|+|||+|++.++....
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~   49 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLA   49 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            37999999999999993   34678999999999999999999998883

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

Probab=98.74  E-value=9.9e-08  Score=98.23  Aligned_cols=174  Identities=20%  Similarity=0.254  Sum_probs=101.2

Q ss_pred             CccccchhhHH---HHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          148 PTVVGMQSTLD---RVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       148 ~~~vGR~~~~~---~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..|+|.+..+.   .+.+.+..+..+.+.|+|++|+||||||+.+++..   ...|..   ++... ....         
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~---~~~f~~---lna~~-~~i~---------   91 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHT---RAHFSS---LNAVL-AGVK---------   91 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHh---cCccee---ehhhh-hhhH---------
Confidence            45899988774   56666777777788999999999999999999876   233311   11110 0000         


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHh--cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEe--cCChh--HH-hhc
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTM--RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFT--TREFE--VC-GLM  295 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L--~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivT--tR~~~--v~-~~~  295 (427)
                                 +..+........+  .+++.+|+|||++...  ..+.+...+   ..++.++|+  |.+..  +. ...
T Consensus        92 -----------dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~l---E~g~IiLI~aTTenp~~~l~~aL~  157 (725)
T PRK13341         92 -----------DLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWV---ENGTITLIGATTENPYFEVNKALV  157 (725)
T ss_pred             -----------HHHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHh---cCceEEEEEecCCChHhhhhhHhh
Confidence                       0111122222222  2467899999997542  233333322   234555553  33321  11 112


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCC----CCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDI----LDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~----~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .-...+.+++|+.++...++.+.+....    .....-..+....|++.+.|..-.+..+
T Consensus       158 SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~  217 (725)
T PRK13341        158 SRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNA  217 (725)
T ss_pred             ccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHH
Confidence            2245789999999999999988764100    0111223456788889998876544433

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.74  E-value=4.1e-07  Score=87.40  Aligned_cols=182  Identities=13%  Similarity=0.158  Sum_probs=109.2

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCC-C------------------CCcEEEEEE
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTP-N------------------DFDFVIWEV  207 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~------------------~f~~~~wv~  207 (427)
                      ..++|.+..++.|.+++..+.. +.+.++|++|+||||+|+.+.+...... .                  +++. +++.
T Consensus        14 ~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~-~~~~   92 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDV-IEID   92 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EEee
Confidence            4679999999999999987654 4678999999999999999987762110 0                  1221 1111


Q ss_pred             eCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEe
Q 042645          208 VSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFT  285 (427)
Q Consensus       208 ~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivT  285 (427)
                      ........ -.+.+...+...                  -..+++-++|+|+++..  .....+...+......+.+|++
T Consensus        93 ~~~~~~~~-~~~~l~~~~~~~------------------p~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~  153 (355)
T TIGR02397        93 AASNNGVD-DIREILDNVKYA------------------PSSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILA  153 (355)
T ss_pred             ccccCCHH-HHHHHHHHHhcC------------------cccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEE
Confidence            11111111 111122111100                  01245568999998755  2244444444333445666666


Q ss_pred             cCChh-HH-hhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          286 TREFE-VC-GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       286 tR~~~-v~-~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      |.+.. +. ........+++.++++++..+++...+...+...   ..+.+..|++.++|.|..+....
T Consensus       154 ~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i---~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       154 TTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKI---EDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             eCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCChHHHHHHH
Confidence            65543 22 2222345788999999999999988774433222   24568889999999997665544

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.

>PRK09087 hypothetical protein; Validated

Probab=98.74  E-value=1.1e-07  Score=84.57  Aligned_cols=146  Identities=16%  Similarity=0.059  Sum_probs=90.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ..+.+.|+|+.|+|||+|++.+++.. .       ..+++..      .+...+...                       
T Consensus        43 ~~~~l~l~G~~GsGKThLl~~~~~~~-~-------~~~i~~~------~~~~~~~~~-----------------------   85 (226)
T PRK09087         43 PSPVVVLAGPVGSGKTHLASIWREKS-D-------ALLIHPN------EIGSDAANA-----------------------   85 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHhc-C-------CEEecHH------HcchHHHHh-----------------------
Confidence            44679999999999999999988764 1       1133211      111111111                       


Q ss_pred             hcCCcEEEEEeccCCccc-ccccccCCCC-CCCCcEEEEecCC---------hhHHhhcCCCcceeccCCChHHHHHHHH
Q 042645          248 MRNRKIVLLLDDIWELFD-LAQVGLPVPS-RASASKVVFTTRE---------FEVCGLMDAHKSFKVECLGYEDAWRLFE  316 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~~~-~~~~~~~l~~-~~~gs~IivTtR~---------~~v~~~~~~~~~~~l~~L~~~e~~~lf~  316 (427)
                      +.+  -+|++||++.... -..+...+.. ...|..+|+|++.         ..+...+.....+++++++.++-.++++
T Consensus        86 ~~~--~~l~iDDi~~~~~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~  163 (226)
T PRK09087         86 AAE--GPVLIEDIDAGGFDETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIF  163 (226)
T ss_pred             hhc--CeEEEECCCCCCCCHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHH
Confidence            111  2788899965321 1122222211 1236779998874         2344455666789999999999999999


Q ss_pred             HHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          317 EKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      +.+.......   .+++..-|++.+.|..-.+..+...|
T Consensus       164 ~~~~~~~~~l---~~ev~~~La~~~~r~~~~l~~~l~~L  199 (226)
T PRK09087        164 KLFADRQLYV---DPHVVYYLVSRMERSLFAAQTIVDRL  199 (226)
T ss_pred             HHHHHcCCCC---CHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            9885443222   25668889999988887776544333

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.74  E-value=2.9e-07  Score=90.60  Aligned_cols=196  Identities=17%  Similarity=0.155  Sum_probs=107.7

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+.....|.+.+..+.. +.+.++|++|+||||+|+.+++.........    +    .++..-.....+.....
T Consensus        14 ~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~----~----~pc~~c~~c~~i~~g~~   85 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKG----V----EPCNECRACRSIDEGTF   85 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCC----C----CCCcccHHHHHHhcCCC
Confidence            4689999998888888887765 4578999999999999999988762110000    0    00000000011100000


Q ss_pred             CC---CCCCCCCCHHHHHHHHHHH-----hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCC-hhHHh-h
Q 042645          227 LY---NESWDNKSFDEKAQEIFKT-----MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTRE-FEVCG-L  294 (427)
Q Consensus       227 ~~---~~~~~~~~~~~~~~~l~~~-----L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~-~~v~~-~  294 (427)
                      ..   .........++. ..+.+.     ..+++-++|+|+++...  ....+...+........+|++|.+ ..+.. .
T Consensus        86 ~dv~el~aa~~~gid~i-R~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L  164 (472)
T PRK14962         86 MDVIELDAASNRGIDEI-RKIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTI  164 (472)
T ss_pred             CccEEEeCcccCCHHHH-HHHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHH
Confidence            00   000001111221 122222     22466799999997542  233343444333334444444443 33322 2


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCC-CchHHHHHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGG-LPLALITVGRAM  355 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G-~Plai~~~~~~L  355 (427)
                      ......+.+.+++.++....+.+.+...+..   -..+....|++.++| ++.++..+-.+.
T Consensus       165 ~SR~~vv~f~~l~~~el~~~L~~i~~~egi~---i~~eal~~Ia~~s~GdlR~aln~Le~l~  223 (472)
T PRK14962        165 ISRCQVIEFRNISDELIIKRLQEVAEAEGIE---IDREALSFIAKRASGGLRDALTMLEQVW  223 (472)
T ss_pred             hcCcEEEEECCccHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            2334678999999999999998887543322   224567888988865 466666665543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.73  E-value=2e-07  Score=93.85  Aligned_cols=197  Identities=16%  Similarity=0.168  Sum_probs=112.6

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCC-CCcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPN-DFDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      .+++|.+..+..|.+++..+.. ..+.++|+.|+||||+|+.+++.+..... .....-.    ..++.-...+.|...-
T Consensus        16 ~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~----~pCg~C~~C~~i~~g~   91 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITA----TPCGVCQACRDIDSGR   91 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCC----CCCCccHHHHHHHcCC
Confidence            4689999999999999988765 45689999999999999999877621100 0000000    0111112222221100


Q ss_pred             CCC---CCCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCC-hhHH-hh
Q 042645          226 GLY---NESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTRE-FEVC-GL  294 (427)
Q Consensus       226 ~~~---~~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~-~~v~-~~  294 (427)
                      ...   .+.......++..+.+...    ..++.-++|||+++..  ..+..+...+......+++|++|.+ ..+. ..
T Consensus        92 h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TI  171 (618)
T PRK14951         92 FVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTV  171 (618)
T ss_pred             CCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHH
Confidence            000   0000112222322222211    1245569999999865  3344454444443445566655543 3332 22


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ..-...+++.+++.++..+.+.+.+...+...   ..+....|++.++|.+.-+..+
T Consensus       172 lSRc~~~~f~~Ls~eei~~~L~~i~~~egi~i---e~~AL~~La~~s~GslR~al~l  225 (618)
T PRK14951        172 LSRCLQFNLRPMAPETVLEHLTQVLAAENVPA---EPQALRLLARAARGSMRDALSL  225 (618)
T ss_pred             HHhceeeecCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHH
Confidence            33446789999999999999998875544222   2455788999999988655544

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.73  E-value=1.7e-07  Score=94.32  Aligned_cols=192  Identities=15%  Similarity=0.158  Sum_probs=110.1

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH--
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK--  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~--  224 (427)
                      ..++|.+..++.|.+++..++. +.+.++|+.|+||||+|+.+.+.+... ....   +..+..    ......+...  
T Consensus        16 ddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~-~~~~---~~pCg~----C~sCr~i~~g~~   87 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCE-NAQH---GEPCGV----CQSCTQIDAGRY   87 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhccc-CCCC---CCCCcc----cHHHHHHhccCc
Confidence            4689999999999999987754 468999999999999999998876211 1000   000000    0001111000  


Q ss_pred             ---hCCCCCCCCCCCHHHHHHHHHH----HhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-HH-h
Q 042645          225 ---IGLYNESWDNKSFDEKAQEIFK----TMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-VC-G  293 (427)
Q Consensus       225 ---l~~~~~~~~~~~~~~~~~~l~~----~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v~-~  293 (427)
                         +.+..  ......+.+.+.+..    -..+++-++|+|+++....  ...+...+......+++|++|.+.. +. .
T Consensus        88 ~DvlEida--As~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~T  165 (709)
T PRK08691         88 VDLLEIDA--ASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVT  165 (709)
T ss_pred             cceEEEec--cccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchH
Confidence               00000  011122222222211    1235667999999976532  3334333433334566776665432 21 1


Q ss_pred             hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       294 ~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      ..+-...+.+.+++.++....+.+.+...+...   ..+.+..|++.++|.+.-+..+.
T Consensus       166 IrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~i---d~eAL~~Ia~~A~GslRdAlnLL  221 (709)
T PRK08691        166 VLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAY---EPPALQLLGRAAAGSMRDALSLL  221 (709)
T ss_pred             HHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCc---CHHHHHHHHHHhCCCHHHHHHHH
Confidence            112234678899999999999998876544222   24568899999999986655443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.72  E-value=1.5e-07  Score=94.94  Aligned_cols=194  Identities=15%  Similarity=0.164  Sum_probs=111.7

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..+||.+..+..|.+.+..+..+ .+.++|+.|+||||+|+.+++.+..... .       ....+..-...+.|...-.
T Consensus        16 ~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~-~-------~~~pCg~C~~C~~i~~g~~   87 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETG-I-------TATPCGECDNCREIEQGRF   87 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccC-C-------CCCCCCCCHHHHHHHcCCC
Confidence            46899999999999999887654 4689999999999999999887631100 0       0011111122222221100


Q ss_pred             CCC---CCCCCCCHHHHHHHHHH----HhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCC-hhHH-hhc
Q 042645          227 LYN---ESWDNKSFDEKAQEIFK----TMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTRE-FEVC-GLM  295 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~----~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~-~~v~-~~~  295 (427)
                      .+.   ........++..+.+..    -..+++-++|+|+++...  ..+.+...+-......++|++|.+ ..+. ...
T Consensus        88 ~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~  167 (647)
T PRK07994         88 VDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTIL  167 (647)
T ss_pred             CCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHH
Confidence            000   00001122222222111    124567799999998652  344443334333345556655554 3332 222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .-...|.+.+++.++....+.+.+...+..   ........|++.++|.+.-+..+.
T Consensus       168 SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~---~e~~aL~~Ia~~s~Gs~R~Al~ll  221 (647)
T PRK07994        168 SRCLQFHLKALDVEQIRQQLEHILQAEQIP---FEPRALQLLARAADGSMRDALSLT  221 (647)
T ss_pred             hhheEeeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            234678999999999999998876433211   224557889999999887554443

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.70  E-value=2.8e-07  Score=87.34  Aligned_cols=197  Identities=11%  Similarity=0.091  Sum_probs=112.9

Q ss_pred             CCccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCC-CCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPN-DFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      -..++|.+.....+...+..+.. ..+.|+|+.|+||||+|..+++.+..... .+...   ....++......+.+...
T Consensus        22 ~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~---~~~~~~~~c~~c~~i~~~   98 (351)
T PRK09112         22 NTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPE---TLADPDPASPVWRQIAQG   98 (351)
T ss_pred             hhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcc---ccCCCCCCCHHHHHHHcC
Confidence            35689999999999999987754 46899999999999999999988732110 01111   011111111233333222


Q ss_pred             hC-----C--CC-CC----CCCCCHHHHHHHHHHHhc-----CCcEEEEEeccCCccc--ccccccCCCCCCCCcEEE-E
Q 042645          225 IG-----L--YN-ES----WDNKSFDEKAQEIFKTMR-----NRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVV-F  284 (427)
Q Consensus       225 l~-----~--~~-~~----~~~~~~~~~~~~l~~~L~-----~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~Ii-v  284 (427)
                      -.     +  +. ..    ......++. ..+.+++.     +++-++|+|+++....  .+.+...+.....++.+| +
T Consensus        99 ~hPdl~~l~~~~~~~~~~~~~~I~vd~i-R~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiLi  177 (351)
T PRK09112         99 AHPNLLHITRPFDEKTGKFKTAITVDEI-RRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILI  177 (351)
T ss_pred             CCCCEEEeecccccccccccccCCHHHH-HHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEEE
Confidence            10     0  00 00    011223333 34444442     5677999999986532  333333332223344444 4


Q ss_pred             ecCChhHHh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          285 TTREFEVCG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       285 TtR~~~v~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      |++...+.. ..+-...+.+.+++.++..+++.+.....    . ...+....|++.++|.|.....+.
T Consensus       178 t~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~----~-~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        178 SHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQ----G-SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             ECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhccc----C-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            444433322 22233578999999999999998843211    1 224457889999999998665443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.70  E-value=1.7e-07  Score=84.06  Aligned_cols=168  Identities=13%  Similarity=0.077  Sum_probs=96.2

Q ss_pred             cchhhH-HHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 042645          152 GMQSTL-DRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       152 GR~~~~-~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  229 (427)
                      |..... ..+.++... ...+.+.|+|++|+|||+||+.+++....  .. ..+.+++.....      ..    +    
T Consensus        23 ~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~--~~-~~~~~i~~~~~~------~~----~----   85 (227)
T PRK08903         23 GENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASY--GG-RNARYLDAASPL------LA----F----   85 (227)
T ss_pred             CCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHh--CC-CcEEEEehHHhH------HH----H----
Confidence            544433 444444332 34567899999999999999999987621  11 233444433210      00    0    


Q ss_pred             CCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccccc--ccccCCCC-CCCCc-EEEEecCChhHHh--------hcCC
Q 042645          230 ESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLA--QVGLPVPS-RASAS-KVVFTTREFEVCG--------LMDA  297 (427)
Q Consensus       230 ~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~--~~~~~l~~-~~~gs-~IivTtR~~~v~~--------~~~~  297 (427)
                                      ... ...-+||+||++....+.  .+...+.. ...+. .+|+|++......        .+..
T Consensus        86 ----------------~~~-~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~  148 (227)
T PRK08903         86 ----------------DFD-PEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGW  148 (227)
T ss_pred             ----------------hhc-ccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhc
Confidence                            011 233478999997643221  22222221 11233 4666666533211        2223


Q ss_pred             CcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHc
Q 042645          298 HKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMA  356 (427)
Q Consensus       298 ~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~  356 (427)
                      ...+.++++++++-..++.+.+......   -.++..+.|++.+.|++..+..+...+.
T Consensus       149 ~~~i~l~pl~~~~~~~~l~~~~~~~~v~---l~~~al~~L~~~~~gn~~~l~~~l~~l~  204 (227)
T PRK08903        149 GLVYELKPLSDADKIAALKAAAAERGLQ---LADEVPDYLLTHFRRDMPSLMALLDALD  204 (227)
T ss_pred             CeEEEecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            4678999999988777777654322222   2345688888899999998877776553

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.69  E-value=6.1e-07  Score=86.21  Aligned_cols=184  Identities=13%  Similarity=0.075  Sum_probs=103.9

Q ss_pred             CccccchhhHHHHHHHhccCC----------CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP----------VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~----------~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l  217 (427)
                      ..++|.+..++.|.+++..+.          .+.+.++|++|+|||++|..+++........     ..+++..    ..
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~-----~~~Cg~C----~~   75 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPD-----EPGCGEC----RA   75 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCC-----CCCCCCC----HH
Confidence            457899999999999997653          4678899999999999999998765211100     0000000    11


Q ss_pred             HHHHHHHhCCC----CCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEec
Q 042645          218 QESIAKKIGLY----NESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTT  286 (427)
Q Consensus       218 ~~~i~~~l~~~----~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTt  286 (427)
                      .+.+...-..+    .+.......+++. .+.+.+     .+++-++|+|+++...  ....+...+.....++.+|++|
T Consensus        76 C~~~~~~~hpD~~~i~~~~~~i~i~~iR-~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a  154 (394)
T PRK07940         76 CRTVLAGTHPDVRVVAPEGLSIGVDEVR-ELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCA  154 (394)
T ss_pred             HHHHhcCCCCCEEEeccccccCCHHHHH-HHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEE
Confidence            11111000000    0000112222222 222222     2455689999998652  2233333333334456666666


Q ss_pred             CCh-hHHh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          287 REF-EVCG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       287 R~~-~v~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      .+. .+.. ...-...+.+.+++.++..+++.+..+.     +   .+.+..++..++|.|....
T Consensus       155 ~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~~-----~---~~~a~~la~~s~G~~~~A~  211 (394)
T PRK07940        155 PSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDGV-----D---PETARRAARASQGHIGRAR  211 (394)
T ss_pred             CChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcCC-----C---HHHHHHHHHHcCCCHHHHH
Confidence            553 3322 2223467899999999999988754321     1   3447789999999997553

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.68  E-value=3.6e-07  Score=91.09  Aligned_cols=190  Identities=12%  Similarity=0.118  Sum_probs=107.2

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|++..++.+.+++..+. .+.+.++|+.|+||||+|+.+++.+... .      |.... .+......+.+.....
T Consensus        16 ~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~-~------~~~~~-~Cg~C~sCr~i~~~~h   87 (605)
T PRK05896         16 KQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCL-N------PKDGD-CCNSCSVCESINTNQS   87 (605)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCC-C------CCCCC-CCcccHHHHHHHcCCC
Confidence            467999999999999997754 4578899999999999999998876211 1      11100 1111112222211110


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHH-----hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecC-ChhHH-hh
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKT-----MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTR-EFEVC-GL  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~-----L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR-~~~v~-~~  294 (427)
                      ...   ........++... +.+.     ..+++-++|+|+++..  ..+..+...+......+.+|++|. ...+. ..
T Consensus        88 ~DiieIdaas~igVd~IRe-Ii~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI  166 (605)
T PRK05896         88 VDIVELDAASNNGVDEIRN-IIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTI  166 (605)
T ss_pred             CceEEeccccccCHHHHHH-HHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHH
Confidence            000   0001112222221 2121     1234447999999764  234444444433334455555553 33332 22


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      ......+++.+++.++....+...+...+...+   .+.+..|++.++|.+.-+.
T Consensus       167 ~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~Is---~eal~~La~lS~GdlR~Al  218 (605)
T PRK05896        167 ISRCQRYNFKKLNNSELQELLKSIAKKEKIKIE---DNAIDKIADLADGSLRDGL  218 (605)
T ss_pred             HhhhhhcccCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCcHHHHH
Confidence            233467899999999999999987754332222   3457889999999775443

>PF14516 AAA_35: AAA-like domain

Probab=98.68  E-value=3.1e-06  Score=80.09  Aligned_cols=201  Identities=11%  Similarity=0.107  Sum_probs=120.9

Q ss_pred             CCccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-----CCHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-----LQLGKIQESI  221 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-----~~~~~l~~~i  221 (427)
                      .+.+|.|...-+++.+.+.+++ ..+.|.|+-.+|||+|...+.+... . .. ..++++++..-     .+...+++.+
T Consensus        10 ~~~Yi~R~~~e~~~~~~i~~~G-~~~~I~apRq~GKTSll~~l~~~l~-~-~~-~~~v~id~~~~~~~~~~~~~~f~~~~   85 (331)
T PF14516_consen   10 SPFYIERPPAEQECYQEIVQPG-SYIRIKAPRQMGKTSLLLRLLERLQ-Q-QG-YRCVYIDLQQLGSAIFSDLEQFLRWF   85 (331)
T ss_pred             CCcccCchHHHHHHHHHHhcCC-CEEEEECcccCCHHHHHHHHHHHHH-H-CC-CEEEEEEeecCCCcccCCHHHHHHHH
Confidence            4567899977788888887643 5799999999999999999998873 2 22 34456766532     2455555555


Q ss_pred             H----HHhCCCCCCC-----CCCCHHHHHHHHHHHh-c--CCcEEEEEeccCCcccc----cccccCC----CC---CC-
Q 042645          222 A----KKIGLYNESW-----DNKSFDEKAQEIFKTM-R--NRKIVLLLDDIWELFDL----AQVGLPV----PS---RA-  277 (427)
Q Consensus       222 ~----~~l~~~~~~~-----~~~~~~~~~~~l~~~L-~--~k~~LlVlDdv~~~~~~----~~~~~~l----~~---~~-  277 (427)
                      +    +++++...-.     ...+.......+.+.+ .  +++.+|+||+++.....    .++...+    ..   .. 
T Consensus        86 ~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~  165 (331)
T PF14516_consen   86 CEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPI  165 (331)
T ss_pred             HHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcc
Confidence            4    4555432100     0112223333344432 2  68999999999865321    1111111    10   00 


Q ss_pred             CCcEEEEecCChh--HH-h----hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          278 SASKVVFTTREFE--VC-G----LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       278 ~gs~IivTtR~~~--v~-~----~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                      ..+-.++...+..  .. .    .......+.|++++.+|...|+.+.-..-    .   ....+.|...+||+|..+..
T Consensus       166 ~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~----~---~~~~~~l~~~tgGhP~Lv~~  238 (331)
T PF14516_consen  166 WQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLEF----S---QEQLEQLMDWTGGHPYLVQK  238 (331)
T ss_pred             cceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhccC----C---HHHHHHHHHHHCCCHHHHHH
Confidence            1111122221111  11 0    11233578999999999999998764221    1   22389999999999999999


Q ss_pred             HHHHHcCC
Q 042645          351 VGRAMASK  358 (427)
Q Consensus       351 ~~~~L~~~  358 (427)
                      ++..+..+
T Consensus       239 ~~~~l~~~  246 (331)
T PF14516_consen  239 ACYLLVEE  246 (331)
T ss_pred             HHHHHHHc
Confidence            99999774

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.68  E-value=6.2e-07  Score=86.48  Aligned_cols=182  Identities=12%  Similarity=0.191  Sum_probs=105.8

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCC-----CCCCcEEE-EEEeCCCCCHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHT-----PNDFDFVI-WEVVSRDLQLGKIQES  220 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~-----~~~f~~~~-wv~~~~~~~~~~l~~~  220 (427)
                      ..++|.+...+.+.+.+..+.. +.+.++|++|+||||+|..+.+.....     ...|...+ -+......+.. -...
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~i~~   95 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVD-DIRN   95 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHH-HHHH
Confidence            4579999999999999987654 588899999999999999998876221     01121111 11101111111 1112


Q ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecC-ChhHH-hhcC
Q 042645          221 IAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTR-EFEVC-GLMD  296 (427)
Q Consensus       221 i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR-~~~v~-~~~~  296 (427)
                      +...+...                  -..+++-++++|+++....  +..+...+......+.+|++|. ...+. ....
T Consensus        96 l~~~~~~~------------------p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~s  157 (367)
T PRK14970         96 LIDQVRIP------------------PQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILS  157 (367)
T ss_pred             HHHHHhhc------------------cccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHh
Confidence            22211100                  0124556899999975432  4444333333233455555553 32222 2223


Q ss_pred             CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ....+++.++++++....+.+.+...+...+   .+.++.|++.++|.+-.+...
T Consensus       158 r~~~v~~~~~~~~~l~~~l~~~~~~~g~~i~---~~al~~l~~~~~gdlr~~~~~  209 (367)
T PRK14970        158 RCQIFDFKRITIKDIKEHLAGIAVKEGIKFE---DDALHIIAQKADGALRDALSI  209 (367)
T ss_pred             cceeEecCCccHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhCCCCHHHHHHH
Confidence            3457899999999999999887754332222   456888999999977654433

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.68  E-value=1.7e-07  Score=90.92  Aligned_cols=198  Identities=13%  Similarity=0.123  Sum_probs=111.9

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEE-eCCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEV-VSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~-~~~~~~~~~l~~~i~~~l  225 (427)
                      ..++|.+..++.|.+++..+..+ .+.++|++|+||||+|..+++..... .......|.. ...++..-...+.+....
T Consensus        16 ~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~-~~~~~~~~~~~~~~~c~~c~~c~~~~~~~   94 (397)
T PRK14955         16 ADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQ-RMIDDADYLQEVTEPCGECESCRDFDAGT   94 (397)
T ss_pred             hhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCC-CCcCcccccccCCCCCCCCHHHHHHhcCC
Confidence            46899999999999999887654 48899999999999999998877321 1111000110 001111111111111110


Q ss_pred             CCCC---CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEec-CChhHHhh
Q 042645          226 GLYN---ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTT-REFEVCGL  294 (427)
Q Consensus       226 ~~~~---~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTt-R~~~v~~~  294 (427)
                      ....   ........+++.+ +.+.+     .+++-++|+|+++...  .+..+...+....+.+.+|++| +...+...
T Consensus        95 ~~n~~~~~~~~~~~id~Ir~-l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~t  173 (397)
T PRK14955         95 SLNISEFDAASNNSVDDIRL-LRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPAT  173 (397)
T ss_pred             CCCeEeecccccCCHHHHHH-HHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHH
Confidence            0000   0001111233322 23333     2455689999998653  4555555554444566666555 33333221


Q ss_pred             -cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          295 -MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       295 -~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                       ......+++.++++++....+...+...+..   -..+.+..|++.++|.+.-+..
T Consensus       174 l~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~---i~~~al~~l~~~s~g~lr~a~~  227 (397)
T PRK14955        174 IASRCQRFNFKRIPLEEIQQQLQGICEAEGIS---VDADALQLIGRKAQGSMRDAQS  227 (397)
T ss_pred             HHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHH
Confidence             1223568899999999999998877433211   2245688999999998865544

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.67  E-value=4.6e-07  Score=94.56  Aligned_cols=190  Identities=14%  Similarity=0.146  Sum_probs=109.6

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH--
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK--  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~--  224 (427)
                      ..+||.+..++.|.+.+..+... .+.++|+.|+||||+|+.+.+.+..... ....   .+    ..-...+.|...  
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~-~~~~---pC----g~C~sC~~~~~g~~   86 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEG-PTST---PC----GECDSCVALAPGGP   86 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccC-CCCC---CC----cccHHHHHHHcCCC
Confidence            45799999999999999886554 5789999999999999999888731110 0000   00    000111111111  


Q ss_pred             --hCCC-CCCCCCCCHHHHHHHHHH-----HhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCC-hhHHh
Q 042645          225 --IGLY-NESWDNKSFDEKAQEIFK-----TMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTRE-FEVCG  293 (427)
Q Consensus       225 --l~~~-~~~~~~~~~~~~~~~l~~-----~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~-~~v~~  293 (427)
                        ..+. .+.......+++.+ +.+     -..++.-++|||+++..  ...+.|...+......+.+|++|.+ ..+..
T Consensus        87 ~~~dv~eidaas~~~Vd~iR~-l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~  165 (824)
T PRK07764         87 GSLDVTEIDAASHGGVDDARE-LRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIG  165 (824)
T ss_pred             CCCcEEEecccccCCHHHHHH-HHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhH
Confidence              0000 00001112222222 222     12356668999999865  3344454555444455666655543 33432


Q ss_pred             -hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          294 -LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       294 -~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                       .......|++.+++.++..+++.+.+...+...   ..+....|++.++|.+..+.
T Consensus       166 TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~i---d~eal~lLa~~sgGdlR~Al  219 (824)
T PRK07764        166 TIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPV---EPGVLPLVIRAGGGSVRDSL  219 (824)
T ss_pred             HHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHH
Confidence             223356789999999999999988764433222   23456789999999885443

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

Probab=98.65  E-value=4.3e-08  Score=88.10  Aligned_cols=92  Identities=20%  Similarity=0.179  Sum_probs=62.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC--CCHHHHHHHHHHHhCCCCCCCCCCCHH------H
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD--LQLGKIQESIAKKIGLYNESWDNKSFD------E  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~--~~~~~l~~~i~~~l~~~~~~~~~~~~~------~  239 (427)
                      ....++|.|++|+|||||++.+++.. .. .+|+.++|+++...  .++.++++.+...+-....  +.....      .
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l-~~-~~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~--~~~~~~~~~~~~~   90 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAI-TK-NHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTF--DEPPERHVQVAEM   90 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc-cc-ccCCeEEEEEEccCCCccHHHHHHHhccEEEEecC--CCCHHHHHHHHHH
Confidence            45679999999999999999999988 32 38999999997665  7899999998333222111  111111      1


Q ss_pred             HHHHHHHH-hcCCcEEEEEeccCCc
Q 042645          240 KAQEIFKT-MRNRKIVLLLDDIWEL  263 (427)
Q Consensus       240 ~~~~l~~~-L~~k~~LlVlDdv~~~  263 (427)
                      ........ -.+++++|++|++...
T Consensus        91 ~~~~a~~~~~~G~~vll~iDei~r~  115 (249)
T cd01128          91 VLEKAKRLVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHHHHHHHHCCCCEEEEEECHHHh
Confidence            11222222 2479999999999643

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.64  E-value=4.4e-07  Score=90.79  Aligned_cols=190  Identities=14%  Similarity=0.146  Sum_probs=106.8

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.|.+++..+..+ .+.++|+.|+||||+|+.+++.+..... ..       ..++..-.....+...-.
T Consensus        16 ~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~-~~-------~~pcg~C~~C~~i~~~~~   87 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETG-VT-------ATPCGVCSACLEIDSGRF   87 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCC-CC-------CCCCCCCHHHHHHhcCCC
Confidence            46799999999999999886554 5689999999999999999887621100 00       000000001111100000


Q ss_pred             CC---CCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCCh-hHH-hh
Q 042645          227 LY---NESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREF-EVC-GL  294 (427)
Q Consensus       227 ~~---~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~  294 (427)
                      ..   .+.......+++. .+.+..     .+++-++|+|+++....  ...+...+......+.+|++|.+. .+. ..
T Consensus        88 ~d~~ei~~~~~~~vd~ir-~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI  166 (527)
T PRK14969         88 VDLIEVDAASNTQVDAMR-ELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTV  166 (527)
T ss_pred             CceeEeeccccCCHHHHH-HHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhH
Confidence            00   0000011222222 122211     35667999999986532  444444444334456666655443 222 11


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      ..-...+++.+++.++..+.+.+.+...+..   ...+....|++.++|.+.-+.
T Consensus       167 ~SRc~~~~f~~l~~~~i~~~L~~il~~egi~---~~~~al~~la~~s~Gslr~al  218 (527)
T PRK14969        167 LSRCLQFNLKQMPPPLIVSHLQHILEQENIP---FDATALQLLARAAAGSMRDAL  218 (527)
T ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHH
Confidence            1223568999999999999988877543322   223457889999999886443

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.64  E-value=1.4e-06  Score=87.31  Aligned_cols=196  Identities=16%  Similarity=0.190  Sum_probs=112.4

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..+..|.+.+..+. .+.+.++|+.|+||||+|+.+++.+... .....       ..++.-...+.|.....
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~-~~~~~-------~pCg~C~sC~~i~~g~h   87 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCE-TAPTG-------EPCNTCEQCRKVTQGMH   87 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhcccc-CCCCC-------CCCcccHHHHHHhcCCC
Confidence            457999999999999888765 5778899999999999999999887311 10000       00111111122211100


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHH-----hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCC-hhHHh-h
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKT-----MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTRE-FEVCG-L  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~-----L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~-~~v~~-~  294 (427)
                      ...   ........++. +.+.+.     ..+++-++|+|+++..  .....+...+........+|++|.+ ..+.. .
T Consensus        88 pDv~eId~a~~~~Id~i-R~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI  166 (624)
T PRK14959         88 VDVVEIDGASNRGIDDA-KRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTI  166 (624)
T ss_pred             CceEEEecccccCHHHH-HHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHH
Confidence            000   00001112221 122222     2356679999999765  2234444444332334556665554 33332 2


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc-hHHHHHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP-LALITVGRAM  355 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P-lai~~~~~~L  355 (427)
                      ......+++.+++.++....+...+...+...   ..+.++.|++.++|.+ .|+..+..++
T Consensus       167 ~SRcq~i~F~pLs~~eL~~~L~~il~~egi~i---d~eal~lIA~~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        167 VSRCQHFTFTRLSEAGLEAHLTKVLGREGVDY---DPAAVRLIARRAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             HhhhhccccCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            22335789999999999999988765433222   2456888999999965 5666665544

>PRK05642 DNA replication initiation factor; Validated

Probab=98.64  E-value=3.7e-07  Score=81.96  Aligned_cols=154  Identities=16%  Similarity=0.202  Sum_probs=93.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.|+|..|+|||.|++.+++... .  .-..++|++..      ++...                .    ..+.+.+
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~-~--~~~~v~y~~~~------~~~~~----------------~----~~~~~~~   95 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFE-Q--RGEPAVYLPLA------ELLDR----------------G----PELLDNL   95 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH-h--CCCcEEEeeHH------HHHhh----------------h----HHHHHhh
Confidence            35789999999999999999988762 1  12345666543      22111                0    1122223


Q ss_pred             cCCcEEEEEeccCCc---ccccc-cccCCCC-CCCCcEEEEecCChhH---------HhhcCCCcceeccCCChHHHHHH
Q 042645          249 RNRKIVLLLDDIWEL---FDLAQ-VGLPVPS-RASASKVVFTTREFEV---------CGLMDAHKSFKVECLGYEDAWRL  314 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~---~~~~~-~~~~l~~-~~~gs~IivTtR~~~v---------~~~~~~~~~~~l~~L~~~e~~~l  314 (427)
                      .+-. +||+||+...   ..|.. +...+.. ...|..+|+|++..+-         ...+.....+++++++.++-.++
T Consensus        96 ~~~d-~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~i  174 (234)
T PRK05642         96 EQYE-LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRA  174 (234)
T ss_pred             hhCC-EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHH
Confidence            2222 6889999743   23433 3333321 1245678898875432         23333456789999999999999


Q ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          315 FEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       315 f~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      ++.++......   -.+++..-|++.+.|..-.+..+...|
T Consensus       175 l~~ka~~~~~~---l~~ev~~~L~~~~~~d~r~l~~~l~~l  212 (234)
T PRK05642        175 LQLRASRRGLH---LTDEVGHFILTRGTRSMSALFDLLERL  212 (234)
T ss_pred             HHHHHHHcCCC---CCHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            99665433222   225678888888888776665554444

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.64  E-value=1.4e-06  Score=75.61  Aligned_cols=157  Identities=16%  Similarity=0.141  Sum_probs=92.5

Q ss_pred             HHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCC-------------------CCCcEEEEEEeCCCCCHHHHH
Q 042645          159 RVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTP-------------------NDFDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       159 ~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~~f~~~~wv~~~~~~~~~~l~  218 (427)
                      .|.+.+..+.. +.+.++|+.|+||||+|..+.+......                   .+.+. .++.....       
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~-~~~~~~~~-------   74 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDL-HRLEPEGQ-------   74 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcE-EEeccccC-------
Confidence            45566666554 6799999999999999999988763210                   11111 11111100       


Q ss_pred             HHHHHHhCCCCCCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCCh-hH
Q 042645          219 ESIAKKIGLYNESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREF-EV  291 (427)
Q Consensus       219 ~~i~~~l~~~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~-~v  291 (427)
                                     ....++....+...    ..+.+-++|+||++...  ..+.+...+......+.+|++|++. .+
T Consensus        75 ---------------~~~~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l  139 (188)
T TIGR00678        75 ---------------SIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKL  139 (188)
T ss_pred             ---------------cCCHHHHHHHHHHHccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhC
Confidence                           11112221111111    12456789999997653  2444444444434456677666643 22


Q ss_pred             Hh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          292 CG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       292 ~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      .. .......+.+.+++.++..+++.+. +     .+   .+.+..|++.++|.|..
T Consensus       140 ~~~i~sr~~~~~~~~~~~~~~~~~l~~~-g-----i~---~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       140 LPTIRSRCQVLPFPPLSEEALLQWLIRQ-G-----IS---EEAAELLLALAGGSPGA  187 (188)
T ss_pred             hHHHHhhcEEeeCCCCCHHHHHHHHHHc-C-----CC---HHHHHHHHHHcCCCccc
Confidence            11 1123357899999999999999887 2     11   35588999999999863

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.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.63  E-value=2.2e-06  Score=77.79  Aligned_cols=195  Identities=16%  Similarity=0.143  Sum_probs=115.9

Q ss_pred             hHHHHHHHhccC---CCeEEEEEecCCCcHHHHHHHHHhhccCCCC---CCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 042645          156 TLDRVWRCLTEE---PVGIVGLYGMGGVGKTTLLTQINNSFLHTPN---DFDFVIWEVVSRDLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       156 ~~~~l~~~l~~~---~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  229 (427)
                      .++.|.+.+..+   ..+-+.|+|.+|.|||++++++...+....+   .--.++.+.....++...++..|+.+++.+.
T Consensus        45 ~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~  124 (302)
T PF05621_consen   45 ALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPY  124 (302)
T ss_pred             HHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCccc
Confidence            344455555433   4567999999999999999999987732211   1124677888889999999999999999886


Q ss_pred             CCCCCCCHHHHHHHHHHHhcC-CcEEEEEeccCCccc-----cccc---ccCCCCCCCCcEEEEecCChhHHhh-----c
Q 042645          230 ESWDNKSFDEKAQEIFKTMRN-RKIVLLLDDIWELFD-----LAQV---GLPVPSRASASKVVFTTREFEVCGL-----M  295 (427)
Q Consensus       230 ~~~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~~~~~-----~~~~---~~~l~~~~~gs~IivTtR~~~v~~~-----~  295 (427)
                      ..  ..+...+.......++. +.=+||+|++++.-.     -.++   ...+.+.-.=+-|.+-|++.--+-.     .
T Consensus       125 ~~--~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa  202 (302)
T PF05621_consen  125 RP--RDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLA  202 (302)
T ss_pred             CC--CCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHH
Confidence            43  33445555555566654 455999999987411     1111   1122222222345555543221111     0


Q ss_pred             CCCcceeccCCChHH-HHHHHHHHhC--CCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          296 DAHKSFKVECLGYED-AWRLFEEKVG--RDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e-~~~lf~~~~~--~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      +-...+.++....++ ...|+...-.  .-...++-...+++..|...++|+.--+..+-
T Consensus       203 ~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~~ll  262 (302)
T PF05621_consen  203 SRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELSRLL  262 (302)
T ss_pred             hccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHHHHH
Confidence            112456666666544 4444433221  11112333456789999999999876665443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.62  E-value=5.1e-07  Score=86.82  Aligned_cols=171  Identities=19%  Similarity=0.238  Sum_probs=99.8

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|++..+++|.+.+..             ...+-+.|+|++|+|||++|+.+++..   ...|     +.+.    .
T Consensus       122 ~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l---~~~~-----~~v~----~  189 (364)
T TIGR01242       122 EDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET---NATF-----IRVV----G  189 (364)
T ss_pred             HHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhC---CCCE-----Eecc----h
Confidence            4689999999999887642             124569999999999999999999987   2232     2221    1


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCccc----------------ccccccCCC--C
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFD----------------LAQVGLPVP--S  275 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~  275 (427)
                      ..+....   .+         ........+.+.. ...+.+|+|||++....                +..+...+.  .
T Consensus       190 ~~l~~~~---~g---------~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~  257 (364)
T TIGR01242       190 SELVRKY---IG---------EGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFD  257 (364)
T ss_pred             HHHHHHh---hh---------HHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCC
Confidence            1111110   00         0112222232222 34678999999975411                111111111  1


Q ss_pred             CCCCcEEEEecCChhH-----HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          276 RASASKVVFTTREFEV-----CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       276 ~~~gs~IivTtR~~~v-----~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ...+..||.||.....     .........+.++..+.++..++|..+..........+    ...+++.+.|..-
T Consensus       258 ~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~----~~~la~~t~g~sg  329 (364)
T TIGR01242       258 PRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVD----LEAIAKMTEGASG  329 (364)
T ss_pred             CCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCC----HHHHHHHcCCCCH
Confidence            1235678888875432     11111235688999999999999998875433222122    5677788887643

Many proteins may score above the trusted cutoff because an internal

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.60  E-value=8.8e-07  Score=89.47  Aligned_cols=197  Identities=14%  Similarity=0.166  Sum_probs=113.3

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCc-EEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFD-FVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      ..++|.+..++.|.+++..++. ..+.++|+.|+||||+|+.+++.+......-. ...+-.+    ....-.+.|....
T Consensus        24 ~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~c----g~c~~C~~i~~g~   99 (598)
T PRK09111         24 DDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLC----GVGEHCQAIMEGR   99 (598)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccC----cccHHHHHHhcCC
Confidence            4689999999999999987754 46899999999999999999987631110000 0000000    1111112222111


Q ss_pred             CCCC---CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecC-ChhHH-h
Q 042645          226 GLYN---ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTR-EFEVC-G  293 (427)
Q Consensus       226 ~~~~---~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR-~~~v~-~  293 (427)
                      ..+.   ........+++.+ +.+.+     .+++-++|+|+++...  ..+.+...+......+.+|++|. ...+. .
T Consensus       100 h~Dv~e~~a~s~~gvd~IRe-Iie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~t  178 (598)
T PRK09111        100 HVDVLEMDAASHTGVDDIRE-IIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVT  178 (598)
T ss_pred             CCceEEecccccCCHHHHHH-HHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHH
Confidence            1000   0001122233222 22222     2455689999997653  24444444444445566666553 33332 2


Q ss_pred             hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          294 LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       294 ~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .......+.+.+++.++....+.+.+...+...   ..+....|++.++|.+.-+....
T Consensus       179 I~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i---~~eAl~lIa~~a~Gdlr~al~~L  234 (598)
T PRK09111        179 VLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEV---EDEALALIARAAEGSVRDGLSLL  234 (598)
T ss_pred             HHhheeEEEecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHH
Confidence            222345789999999999999998875443222   23568889999999987665544

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

Probab=98.60  E-value=4.4e-07  Score=81.26  Aligned_cols=187  Identities=13%  Similarity=0.143  Sum_probs=116.8

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEE-EEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVI-WEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~-wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..+.-|.+.+.....+....||++|.|||+.|..++..+. ....|.+.+ -.|.|..-... +.+.      
T Consensus        36 de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~-~~~~~~~rvl~lnaSderGis-vvr~------  107 (346)
T KOG0989|consen   36 DELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALN-CEQLFPCRVLELNASDERGIS-VVRE------  107 (346)
T ss_pred             HhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhc-Cccccccchhhhccccccccc-chhh------
Confidence            46799999999999999888889999999999999999999998873 334555443 23333332211 0000      


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhc--CCc-EEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCChh-HHhh-cCCCc
Q 042645          227 LYNESWDNKSFDEKAQEIFKTMR--NRK-IVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREFE-VCGL-MDAHK  299 (427)
Q Consensus       227 ~~~~~~~~~~~~~~~~~l~~~L~--~k~-~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~~-v~~~-~~~~~  299 (427)
                            ...+.+.+.........  .++ -++|||+++..  +.|..+...+.+....++.++.|..-. +... ..-..
T Consensus       108 ------Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~  181 (346)
T KOG0989|consen  108 ------KIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQ  181 (346)
T ss_pred             ------hhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHH
Confidence                  01111111111100000  133 48999999876  457777666655555666665555432 2111 11224


Q ss_pred             ceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          300 SFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       300 ~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .|..++|..++...-++..+..++...+   .+..+.|++.++|.=.-..++
T Consensus       182 KfrFk~L~d~~iv~rL~~Ia~~E~v~~d---~~al~~I~~~S~GdLR~Ait~  230 (346)
T KOG0989|consen  182 KFRFKKLKDEDIVDRLEKIASKEGVDID---DDALKLIAKISDGDLRRAITT  230 (346)
T ss_pred             HhcCCCcchHHHHHHHHHHHHHhCCCCC---HHHHHHHHHHcCCcHHHHHHH
Confidence            5889999999999999998876654444   345888999999854433333

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.59  E-value=1.5e-06  Score=87.38  Aligned_cols=194  Identities=14%  Similarity=0.111  Sum_probs=109.6

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.|.+++..+..+ .+.++|+.|+||||+|+.+++.+.... ....   ..+    +.-...+.+...-+
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~-~~~~---~pC----g~C~~C~~i~~~~~   84 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQ-GPTA---TPC----GVCESCVALAPNGP   84 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcccc-CCCC---Ccc----cccHHHHHhhcccC
Confidence            46899999999999999887655 468999999999999999998763111 0000   000    00011111111000


Q ss_pred             CC-----CCCCCCCCHHHHHHHHHHH-----hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEec-CChhHHh
Q 042645          227 LY-----NESWDNKSFDEKAQEIFKT-----MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTT-REFEVCG  293 (427)
Q Consensus       227 ~~-----~~~~~~~~~~~~~~~l~~~-----L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTt-R~~~v~~  293 (427)
                      ..     .+.......++.. .+.+.     ..+++-++|+|+++..  ...+.+...+......+.+|++| ....+..
T Consensus        85 ~~~dvieidaas~~gvd~iR-el~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~  163 (584)
T PRK14952         85 GSIDVVELDAASHGGVDDTR-ELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLP  163 (584)
T ss_pred             CCceEEEeccccccCHHHHH-HHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHH
Confidence            00     0000111222221 12221     1345669999999854  23444444444434455555555 4443332


Q ss_pred             -hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch-HHHHHHH
Q 042645          294 -LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL-ALITVGR  353 (427)
Q Consensus       294 -~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl-ai~~~~~  353 (427)
                       ..+-...+.+.+++.++..+++.+.+...+...   ..+....|++.++|.+. ++..+-.
T Consensus       164 TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i---~~~al~~Ia~~s~GdlR~aln~Ldq  222 (584)
T PRK14952        164 TIRSRTHHYPFRLLPPRTMRALIARICEQEGVVV---DDAVYPLVIRAGGGSPRDTLSVLDQ  222 (584)
T ss_pred             HHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHHHH
Confidence             223356789999999999999988775433222   23457888999999875 3344433

>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=98.57  E-value=1e-06  Score=78.19  Aligned_cols=162  Identities=19%  Similarity=0.141  Sum_probs=95.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.|+|+.|+|||.|++.+++....... -..++++      +..++...+...+...       .    ...+.+.+
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~-~~~v~y~------~~~~f~~~~~~~~~~~-------~----~~~~~~~~   95 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQHP-GKRVVYL------SAEEFIREFADALRDG-------E----IEEFKDRL   95 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHHCT-TS-EEEE------EHHHHHHHHHHHHHTT-------S----HHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhccc-cccceee------cHHHHHHHHHHHHHcc-------c----chhhhhhh
Confidence            346899999999999999999998732112 2234554      3456666666655321       1    12344444


Q ss_pred             cCCcEEEEEeccCCccc---ccc-cccCCCC-CCCCcEEEEecCChh---------HHhhcCCCcceeccCCChHHHHHH
Q 042645          249 RNRKIVLLLDDIWELFD---LAQ-VGLPVPS-RASASKVVFTTREFE---------VCGLMDAHKSFKVECLGYEDAWRL  314 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~---~~~-~~~~l~~-~~~gs~IivTtR~~~---------v~~~~~~~~~~~l~~L~~~e~~~l  314 (427)
                      + .-=+|++||++....   |.+ +...+.. ...|.+||+|+...+         +...+...-.+++.+++.++-.++
T Consensus        96 ~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~i  174 (219)
T PF00308_consen   96 R-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRI  174 (219)
T ss_dssp             C-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHH
T ss_pred             h-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHH
Confidence            4 334889999976532   222 2111211 134668999996532         334445667899999999999999


Q ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          315 FEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       315 f~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      +.+.+...+..   -.+++++-|++.+.+..-.+.-+.
T Consensus       175 l~~~a~~~~~~---l~~~v~~~l~~~~~~~~r~L~~~l  209 (219)
T PF00308_consen  175 LQKKAKERGIE---LPEEVIEYLARRFRRDVRELEGAL  209 (219)
T ss_dssp             HHHHHHHTT-----S-HHHHHHHHHHTTSSHHHHHHHH
T ss_pred             HHHHHHHhCCC---CcHHHHHHHHHhhcCCHHHHHHHH
Confidence            99988544322   335667778887776655554433

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.53  E-value=3.6e-06  Score=82.75  Aligned_cols=167  Identities=12%  Similarity=0.080  Sum_probs=104.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.|+|..|+|||+|++.+++.... ...-..+++++      ..++...+...++..         ......+.+.+
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~l~~-~~~~~~v~yv~------~~~f~~~~~~~l~~~---------~~~~~~~~~~~  204 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNYIES-NFSDLKVSYMS------GDEFARKAVDILQKT---------HKEIEQFKNEI  204 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHHHHH-hCCCCeEEEEE------HHHHHHHHHHHHHHh---------hhHHHHHHHHh
Confidence            346899999999999999999987621 12222344543      346677776665421         01223344444


Q ss_pred             cCCcEEEEEeccCCcc---cc-cccccCCCC-CCCCcEEEEecCChh---------HHhhcCCCcceeccCCChHHHHHH
Q 042645          249 RNRKIVLLLDDIWELF---DL-AQVGLPVPS-RASASKVVFTTREFE---------VCGLMDAHKSFKVECLGYEDAWRL  314 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~---~~-~~~~~~l~~-~~~gs~IivTtR~~~---------v~~~~~~~~~~~l~~L~~~e~~~l  314 (427)
                      + ..-+|||||+....   .+ +.+...+.. ...|..||+|+...+         +...+...-.+.+++++.++-.++
T Consensus       205 ~-~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~i  283 (450)
T PRK14087        205 C-QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAI  283 (450)
T ss_pred             c-cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHH
Confidence            4 34488899997542   12 223222221 123456888876532         233334556788999999999999


Q ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          315 FEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       315 f~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      +.+.+...+.. ..-.+++..-|++.++|.|..+.-+..
T Consensus       284 L~~~~~~~gl~-~~l~~evl~~Ia~~~~gd~R~L~gaL~  321 (450)
T PRK14087        284 IKKEIKNQNIK-QEVTEEAINFISNYYSDDVRKIKGSVS  321 (450)
T ss_pred             HHHHHHhcCCC-CCCCHHHHHHHHHccCCCHHHHHHHHH
Confidence            99988543211 123467799999999999998865553

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.53  E-value=3e-06  Score=85.82  Aligned_cols=197  Identities=13%  Similarity=0.116  Sum_probs=109.8

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEE-eCCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEV-VSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~-~~~~~~~~~l~~~i~~~l  225 (427)
                      ..++|.+..+..|.+++..+.. ..+.++|+.|+||||+|..+++.+... ...+.-.|.. ....+..-...+.+...-
T Consensus        16 ~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~-~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~   94 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQ-RMIDDPVYLQEVTEPCGECESCRDFDAGT   94 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCC-CcCCccccccccCCCCccCHHHHHHhccC
Confidence            4689999999999999987655 458899999999999999998877321 1110000110 001111111122221110


Q ss_pred             CCCC---CCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEec-CChhHH-hh
Q 042645          226 GLYN---ESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTT-REFEVC-GL  294 (427)
Q Consensus       226 ~~~~---~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTt-R~~~v~-~~  294 (427)
                      ....   +.......+++...+...    ..+.+-++|+||++...  ..+.+...+......+.+|++| +...+. ..
T Consensus        95 ~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI  174 (620)
T PRK14954         95 SLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATI  174 (620)
T ss_pred             CCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHH
Confidence            0000   000111233333322221    23455689999997653  2444544444433445555544 333333 22


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLAL  348 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai  348 (427)
                      ......+++.+++.++....+.+.+...+...   ..+.++.|++.++|..--+
T Consensus       175 ~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I---~~eal~~La~~s~Gdlr~a  225 (620)
T PRK14954        175 ASRCQRFNFKRIPLDEIQSQLQMICRAEGIQI---DADALQLIARKAQGSMRDA  225 (620)
T ss_pred             HhhceEEecCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHhCCCHHHH
Confidence            33456789999999999988888764332122   2455888999999966544

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.52  E-value=3e-06  Score=86.31  Aligned_cols=195  Identities=17%  Similarity=0.204  Sum_probs=113.6

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.|.+++..+.. +.+.++|+.|+||||+|+.+++.+........       ...++.....+.+.....
T Consensus        16 ~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~-------~~~c~~c~~c~~i~~~~~   88 (585)
T PRK14950         16 AELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPK-------GRPCGTCEMCRAIAEGSA   88 (585)
T ss_pred             HHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC-------CCCCccCHHHHHHhcCCC
Confidence            4689999999999999887654 45789999999999999999987621000000       011122233333332221


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCC-hhHHh-h
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTRE-FEVCG-L  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~-~~v~~-~  294 (427)
                      ...   ........++.. .+.+.+     .+++-++|+|+++...  ..+.+...+......+.+|++|.+ ..+.. .
T Consensus        89 ~d~~~i~~~~~~~vd~ir-~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI  167 (585)
T PRK14950         89 VDVIEMDAASHTSVDDAR-EIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATI  167 (585)
T ss_pred             CeEEEEeccccCCHHHHH-HHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHH
Confidence            110   000112222222 222222     2456799999997552  344444444433445666666544 23322 2


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      ......+.+.+++.++....+...+...+...   ..+.+..|++.++|.+..+.....
T Consensus       168 ~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i---~~eal~~La~~s~Gdlr~al~~Le  223 (585)
T PRK14950        168 LSRCQRFDFHRHSVADMAAHLRKIAAAEGINL---EPGALEAIARAATGSMRDAENLLQ  223 (585)
T ss_pred             HhccceeeCCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHHH
Confidence            22345688999999999999888775443222   245688999999999976654433

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.49  E-value=1.2e-05  Score=76.23  Aligned_cols=205  Identities=13%  Similarity=0.126  Sum_probs=126.5

Q ss_pred             CCccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      +..++||+.+++.+.+++..    ...+.+-|.|.+|.|||.+...++.+... ...-..++++++..-.....++..|.
T Consensus       149 p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~-~~~~~~~v~inc~sl~~~~aiF~kI~  227 (529)
T KOG2227|consen  149 PGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSK-SSKSPVTVYINCTSLTEASAIFKKIF  227 (529)
T ss_pred             CCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhh-hcccceeEEEeeccccchHHHHHHHH
Confidence            46789999999999999864    35678889999999999999999998732 22223557777766566778888888


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcC--CcEEEEEeccCCccc--ccccccCCC-CCCCCcEEEEecCCh--h----H
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRN--RKIVLLLDDIWELFD--LAQVGLPVP-SRASASKVVFTTREF--E----V  291 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~--k~~LlVlDdv~~~~~--~~~~~~~l~-~~~~gs~IivTtR~~--~----v  291 (427)
                      ..+.....  ......+....+..+..+  ..+|+|||+.+....  -..+...|. ..-+++++|+.---.  +    .
T Consensus       228 ~~~~q~~~--s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~  305 (529)
T KOG2227|consen  228 SSLLQDLV--SPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRF  305 (529)
T ss_pred             HHHHHHhc--CCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHH
Confidence            77621111  111224556666666654  368999999875421  111111111 112345554432211  1    1


Q ss_pred             HhhcC-----CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHc
Q 042645          292 CGLMD-----AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMA  356 (427)
Q Consensus       292 ~~~~~-----~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~  356 (427)
                      ...+.     ....+...|.+.++..++|..+.....  ........++.++++|.|.---+..+....+
T Consensus       306 LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~--t~~~~~~Aie~~ArKvaa~SGDlRkaLdv~R  373 (529)
T KOG2227|consen  306 LPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEES--TSIFLNAAIELCARKVAAPSGDLRKALDVCR  373 (529)
T ss_pred             hhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhccc--ccccchHHHHHHHHHhccCchhHHHHHHHHH
Confidence            11111     235678899999999999999885443  2233334566677777766655555555544

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

Probab=98.47  E-value=9.4e-06  Score=72.15  Aligned_cols=222  Identities=18%  Similarity=0.155  Sum_probs=129.4

Q ss_pred             CccccchhhHHHHHHHhc-----cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLT-----EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..|+|.++.+++|.=.+.     +.....+.++|++|.||||||..+++...   ..+..    +.++...         
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emg---vn~k~----tsGp~le---------   89 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELG---VNLKI----TSGPALE---------   89 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhc---CCeEe----ccccccc---------
Confidence            468999998888866554     24567899999999999999999999882   22211    1111111         


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------ccccccCC-CC-----------CCCCcE
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------LAQVGLPV-PS-----------RASASK  281 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~~~~~~~l-~~-----------~~~gs~  281 (427)
                                   .+.+++..+.. |+ ..=+|.+|+++...-         .+++.... -.           -.+-+-
T Consensus        90 -------------K~gDlaaiLt~-Le-~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTL  154 (332)
T COG2255          90 -------------KPGDLAAILTN-LE-EGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTL  154 (332)
T ss_pred             -------------ChhhHHHHHhc-CC-cCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeE
Confidence                         11111111111 11 223555676654211         11110000 00           112234


Q ss_pred             EEEecCChhHHhhcC--CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCC-
Q 042645          282 VVFTTREFEVCGLMD--AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASK-  358 (427)
Q Consensus       282 IivTtR~~~v~~~~~--~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~-  358 (427)
                      |=.|||.-.+..-+.  -....+++..+.+|..++..+.+..-+...+   .+-+.+|+++..|-|.-..-+.+..+.- 
T Consensus       155 IGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~---~~~a~eIA~rSRGTPRIAnRLLrRVRDfa  231 (332)
T COG2255         155 IGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGIEID---EEAALEIARRSRGTPRIANRLLRRVRDFA  231 (332)
T ss_pred             eeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCCCCC---hHHHHHHHHhccCCcHHHHHHHHHHHHHH
Confidence            556888754432221  2245689999999999999998854433333   3458999999999998777666655531 


Q ss_pred             -------CChHHHHHHHHHHhhccccCCCChHHHHHHHhhhcCCCCCChHhHH
Q 042645          359 -------KAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFC  404 (427)
Q Consensus       359 -------~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~c  404 (427)
                             -+..--..++..|.-....++..+..++.++.-.|+.=|- .++..
T Consensus       232 ~V~~~~~I~~~ia~~aL~~L~Vd~~GLd~~D~k~L~~li~~f~GgPV-Gl~ti  283 (332)
T COG2255         232 QVKGDGDIDRDIADKALKMLDVDELGLDEIDRKYLRALIEQFGGGPV-GLDTI  283 (332)
T ss_pred             HHhcCCcccHHHHHHHHHHhCcccccccHHHHHHHHHHHHHhCCCCc-cHHHH
Confidence                   1223334455566555555566666777888777876665 55543

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.47  E-value=4.4e-06  Score=82.11  Aligned_cols=190  Identities=13%  Similarity=0.155  Sum_probs=105.8

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH--
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK--  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~--  224 (427)
                      .+++|.+..+..|.+++..+.. +.+.++|+.|+||||+|+.+++.+.......+....       ........+...  
T Consensus        17 ~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c-------~~c~~C~~i~~~~~   89 (451)
T PRK06305         17 SEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPC-------NQCASCKEISSGTS   89 (451)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCC-------cccHHHHHHhcCCC
Confidence            4689999999999999987654 568899999999999999998876211000000000       000000000000  


Q ss_pred             ---hCCCCCCCCCCCHHHHHHHHHHH-----hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCC-hhHHh
Q 042645          225 ---IGLYNESWDNKSFDEKAQEIFKT-----MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTRE-FEVCG  293 (427)
Q Consensus       225 ---l~~~~~~~~~~~~~~~~~~l~~~-----L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~-~~v~~  293 (427)
                         +.....  .....++.. .+.+.     ..+++-++|+|+++...  ....+...+......+.+|++|.+ ..+..
T Consensus        90 ~d~~~i~g~--~~~gid~ir-~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~  166 (451)
T PRK06305         90 LDVLEIDGA--SHRGIEDIR-QINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPG  166 (451)
T ss_pred             CceEEeecc--ccCCHHHHH-HHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcch
Confidence               000000  011112211 11111     12567789999987542  233343444333345666666643 22221


Q ss_pred             -hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          294 -LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       294 -~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                       .......+++.++++++....+.+.+...+..   -..+.+..|++.++|.+.-+..
T Consensus       167 tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~---i~~~al~~L~~~s~gdlr~a~~  221 (451)
T PRK06305        167 TILSRCQKMHLKRIPEETIIDKLALIAKQEGIE---TSREALLPIARAAQGSLRDAES  221 (451)
T ss_pred             HHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHH
Confidence             22234578999999999999988876433212   2245688899999997754433

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.47  E-value=5.7e-06  Score=81.89  Aligned_cols=189  Identities=12%  Similarity=0.099  Sum_probs=106.4

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCC-C-CcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPN-D-FDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~-f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..++|.+..+..|.+++..+.. +.+.++|+.|+||||+|+.++........ . ..|..      .    .-...+...
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~------c----~nc~~i~~g   85 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGK------C----ENCVEIDKG   85 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCc------c----HHHHHHhcC
Confidence            4578999999999999987654 45678999999999999999887621000 0 00000      0    000000000


Q ss_pred             -----hCCCCCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEec-CChhH
Q 042645          225 -----IGLYNESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTT-REFEV  291 (427)
Q Consensus       225 -----l~~~~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTt-R~~~v  291 (427)
                           +.+...  .....++ ++.+.+..     .+++-++|+|+++...  ....+...+........+|++| +...+
T Consensus        86 ~~~d~~eidaa--s~~gvd~-ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl  162 (486)
T PRK14953         86 SFPDLIEIDAA--SNRGIDD-IRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKI  162 (486)
T ss_pred             CCCcEEEEeCc--cCCCHHH-HHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHH
Confidence                 000000  0111111 12222222     3566799999997552  2344433343333345555554 33333


Q ss_pred             Hh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          292 CG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       292 ~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .. .......+.+.+++.++....+.+.+...+...   ..+.+..|++.++|.+..+....
T Consensus       163 ~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~i---d~~al~~La~~s~G~lr~al~~L  221 (486)
T PRK14953        163 PPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEY---EEKALDLLAQASEGGMRDAASLL  221 (486)
T ss_pred             HHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHH
Confidence            22 223345789999999999999988775433222   23557889999999877554444

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.46  E-value=2.9e-06  Score=89.65  Aligned_cols=180  Identities=15%  Similarity=0.133  Sum_probs=100.4

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCC--CC-CCcEEEE-EEeCCCCCHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHT--PN-DFDFVIW-EVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~-~f~~~~w-v~~~~~~~~~~l~~~i~~  223 (427)
                      ..++||+++++++++.|.......+.++|++|+||||+|+.+++.....  .. .....+| +.++.      +      
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~------l------  254 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGL------L------  254 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhh------h------
Confidence            4589999999999999988776778899999999999999999876211  00 1112222 22211      0      


Q ss_pred             HhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc------ccc----cccCCCCCCCCcEEEEecCChhH
Q 042645          224 KIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD------LAQ----VGLPVPSRASASKVVFTTREFEV  291 (427)
Q Consensus       224 ~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~------~~~----~~~~l~~~~~gs~IivTtR~~~v  291 (427)
                        .. ... .....+..+..+.+.+.  +++.+|++|+++....      -.+    +.+.+.  ...-++|-||.....
T Consensus       255 --~a-g~~-~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~--~G~l~~IgaTT~~e~  328 (852)
T TIGR03345       255 --QA-GAS-VKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALA--RGELRTIAATTWAEY  328 (852)
T ss_pred             --hc-ccc-cchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHhh--CCCeEEEEecCHHHH
Confidence              00 000 01112222222332222  4789999999976421      111    222222  123456666665332


Q ss_pred             Hh-------hcCCCcceeccCCChHHHHHHHHHHhCCCCC-CCCCCHHHHHHHHHHHcCCCc
Q 042645          292 CG-------LMDAHKSFKVECLGYEDAWRLFEEKVGRDIL-DSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       292 ~~-------~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~-~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      ..       ...-...+.+++++.++..+++......-.. ..-.-..+....+++.+.+..
T Consensus       329 ~~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi  390 (852)
T TIGR03345       329 KKYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI  390 (852)
T ss_pred             hhhhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHccccc
Confidence            11       1122357899999999999997544321110 011122455667777776543

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.46  E-value=7.1e-06  Score=83.25  Aligned_cols=194  Identities=14%  Similarity=0.164  Sum_probs=108.4

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.|.+++..+.. +.+.++|+.|+||||+|+.+++.+..... ...       ..++.......|...-.
T Consensus        16 ~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~-~~~-------~~c~~c~~c~~i~~g~~   87 (576)
T PRK14965         16 SDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQG-LTA-------EPCNVCPPCVEITEGRS   87 (576)
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCC-CCC-------CCCCccHHHHHHhcCCC
Confidence            4689999999999999988765 45689999999999999999887621110 000       00011111111111000


Q ss_pred             CC---CCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEec-CChhHHh-h
Q 042645          227 LY---NESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTT-REFEVCG-L  294 (427)
Q Consensus       227 ~~---~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTt-R~~~v~~-~  294 (427)
                      ..   .+.......++. +.+.+.+     .+++-++|+|+++...  ....+...+......+.+|++| ....+.. .
T Consensus        88 ~d~~eid~~s~~~v~~i-r~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI  166 (576)
T PRK14965         88 VDVFEIDGASNTGVDDI-RELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITI  166 (576)
T ss_pred             CCeeeeeccCccCHHHH-HHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHH
Confidence            00   000001112222 2222222     2455689999997653  2444444443333455566555 4444432 2


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch-HHHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL-ALITVGR  353 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl-ai~~~~~  353 (427)
                      ......+++.+++.++....+...+...+...   ..+.+..|++.++|... ++..+-.
T Consensus       167 ~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i---~~~al~~la~~a~G~lr~al~~Ldq  223 (576)
T PRK14965        167 LSRCQRFDFRRIPLQKIVDRLRYIADQEGISI---SDAALALVARKGDGSMRDSLSTLDQ  223 (576)
T ss_pred             HHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCC---CHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            23345788999999999988887765433222   24557889999999764 4444433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.46  E-value=6.2e-06  Score=81.80  Aligned_cols=194  Identities=14%  Similarity=0.151  Sum_probs=110.4

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|-+.....|...+..+..+ ...++|+.|+||||+|+.+++....... .+.       .++..-.-...+.....
T Consensus        14 deiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~-~~~-------~pC~~C~~C~~~~~~~h   85 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQG-PSS-------TPCDTCIQCQSALENRH   85 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCC-CCC-------CCCcccHHHHHHhhcCC
Confidence            46899999999999999877655 5689999999999999998887621110 000       00000000001100000


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCCh-hHH-hhc
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREF-EVC-GLM  295 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~~  295 (427)
                      ...   ........+++.+.+...    ..+++-++|+|+++...  ....+...+......+.+|++|.+. .+. ...
T Consensus        86 ~dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~  165 (535)
T PRK08451         86 IDIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATIL  165 (535)
T ss_pred             CeEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHH
Confidence            000   000011123333222211    11455699999997653  2334433443334456677666553 221 122


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .-...+++.+++.++....+.+.+...+...   ..+.+..|++.++|.+.-+..+.
T Consensus       166 SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i---~~~Al~~Ia~~s~GdlR~alnlL  219 (535)
T PRK08451        166 SRTQHFRFKQIPQNSIISHLKTILEKEGVSY---EPEALEILARSGNGSLRDTLTLL  219 (535)
T ss_pred             hhceeEEcCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCcHHHHHHHH
Confidence            2346789999999999999988775443222   24568899999999986665543

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.45  E-value=2.2e-06  Score=78.46  Aligned_cols=155  Identities=16%  Similarity=0.121  Sum_probs=79.6

Q ss_pred             ccccchhhHHHHHHH---hc------------cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCC
Q 042645          149 TVVGMQSTLDRVWRC---LT------------EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ  213 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~---l~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~  213 (427)
                      .++|.+..+++|.+.   +.            .+....+.++|++|+||||+|+.+++.+... +......++.++..  
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~-~~~~~~~~v~~~~~--   83 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEM-NVLSKGHLIEVERA--   83 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhc-CcccCCceEEecHH--
Confidence            467877766655433   21            1244578899999999999999998765211 11111122332221  


Q ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc----------cccccccCCCCCCCCcEEE
Q 042645          214 LGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF----------DLAQVGLPVPSRASASKVV  283 (427)
Q Consensus       214 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~----------~~~~~~~~l~~~~~gs~Ii  283 (427)
                        ++..    ..       ...........+ +..  ...+|++|+++...          ....+...+........++
T Consensus        84 --~l~~----~~-------~g~~~~~~~~~~-~~a--~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vi  147 (261)
T TIGR02881        84 --DLVG----EY-------IGHTAQKTREVI-KKA--LGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLI  147 (261)
T ss_pred             --Hhhh----hh-------ccchHHHHHHHH-Hhc--cCCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEE
Confidence              1111    10       011111112222 211  23589999997532          1122222222223334555


Q ss_pred             EecCChhHHh-------hcC-CCcceeccCCChHHHHHHHHHHhCCC
Q 042645          284 FTTREFEVCG-------LMD-AHKSFKVECLGYEDAWRLFEEKVGRD  322 (427)
Q Consensus       284 vTtR~~~v~~-------~~~-~~~~~~l~~L~~~e~~~lf~~~~~~~  322 (427)
                      +++.......       ... ....+.+++++.++..+++.+.+...
T Consensus       148 la~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~~~  194 (261)
T TIGR02881       148 LAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKER  194 (261)
T ss_pred             ecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHHHHHc
Confidence            6654433211       111 12457899999999999999887543

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.45  E-value=5.6e-06  Score=84.29  Aligned_cols=176  Identities=14%  Similarity=0.189  Sum_probs=107.8

Q ss_pred             CccccchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCC--------------------CCCCcEEEEE
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHT--------------------PNDFDFVIWE  206 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~~f~~~~wv  206 (427)
                      ..++|.+..++.|.+++..+..+ .+.++|+.|+||||+|+.+.......                    ..+|+.. .+
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~-~l   95 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIH-EL   95 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceE-Ee
Confidence            46899999999999999887654 58899999999999999988765210                    0122211 11


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCcc--cccccccCCCCCCCCc
Q 042645          207 VVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASAS  280 (427)
Q Consensus       207 ~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs  280 (427)
                      ..+.                       ....+++...+.+.    ..+++=++|+|+++...  .+..+...+......+
T Consensus        96 d~~~-----------------------~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~t  152 (614)
T PRK14971         96 DAAS-----------------------NNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYA  152 (614)
T ss_pred             cccc-----------------------cCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCe
Confidence            1111                       11122222222111    12355588999997653  3444544444434456


Q ss_pred             EEEEec-CChhHHh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          281 KVVFTT-REFEVCG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       281 ~IivTt-R~~~v~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                      .+|++| ....+.. .......+++.+++.++....+.+.+...+...+   .+.+..|++.++|...-+..
T Consensus       153 ifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i~---~~al~~La~~s~gdlr~al~  221 (614)
T PRK14971        153 IFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAE---PEALNVIAQKADGGMRDALS  221 (614)
T ss_pred             EEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHH
Confidence            655544 4444432 2233467899999999999999887754432222   34578899999997765443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.44  E-value=7.5e-07  Score=83.76  Aligned_cols=99  Identities=17%  Similarity=0.192  Sum_probs=64.7

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC--CHHHHHHHHHHHhCCCCCCCCCCC
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL--QLGKIQESIAKKIGLYNESWDNKS  236 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~--~~~~l~~~i~~~l~~~~~~~~~~~  236 (427)
                      +++++.- +.....+|+|++|+|||||++.+++...  ..+|+.++|+.+....  .+.++++.+...+-...  .+...
T Consensus       159 vID~l~PIGkGQR~lIvgppGvGKTTLaK~Ian~I~--~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st--~d~~~  234 (416)
T PRK09376        159 IIDLIAPIGKGQRGLIVAPPKAGKTVLLQNIANSIT--TNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVAST--FDEPA  234 (416)
T ss_pred             eeeeecccccCceEEEeCCCCCChhHHHHHHHHHHH--hhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEEC--CCCCH
Confidence            3444432 3456789999999999999999999983  2389999999998876  67778887763221111  11111


Q ss_pred             HHH------HHHHHHHH-hcCCcEEEEEeccCC
Q 042645          237 FDE------KAQEIFKT-MRNRKIVLLLDDIWE  262 (427)
Q Consensus       237 ~~~------~~~~l~~~-L~~k~~LlVlDdv~~  262 (427)
                      ...      ..+.-... -.++++||++|++..
T Consensus       235 ~~~~~~a~~~ie~Ae~~~e~G~dVlL~iDsItR  267 (416)
T PRK09376        235 ERHVQVAEMVIEKAKRLVEHGKDVVILLDSITR  267 (416)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEEEEChHH
Confidence            111      11111111 357999999999964

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.42  E-value=2e-05  Score=77.04  Aligned_cols=181  Identities=19%  Similarity=0.173  Sum_probs=105.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.|+|++|+|||+|++.+++.... ...-..+++++      ..++...+...+...       ...    .+.+.+
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~-~~~~~~v~yi~------~~~~~~~~~~~~~~~-------~~~----~~~~~~  197 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILE-NNPNAKVVYVS------SEKFTNDFVNALRNN-------KME----EFKEKY  197 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHH-hCCCCcEEEEE------HHHHHHHHHHHHHcC-------CHH----HHHHHH
Confidence            346899999999999999999998732 11123455554      334455555554311       122    233333


Q ss_pred             cCCcEEEEEeccCCcccc----cccccCCCC-CCCCcEEEEecCChh---------HHhhcCCCcceeccCCChHHHHHH
Q 042645          249 RNRKIVLLLDDIWELFDL----AQVGLPVPS-RASASKVVFTTREFE---------VCGLMDAHKSFKVECLGYEDAWRL  314 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~~----~~~~~~l~~-~~~gs~IivTtR~~~---------v~~~~~~~~~~~l~~L~~~e~~~l  314 (427)
                      ++ .-+|+|||++.....    +.+...+.. ...+..+|+||....         +...+.....+.+++.+.++-..+
T Consensus       198 ~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~i  276 (405)
T TIGR00362       198 RS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAI  276 (405)
T ss_pred             Hh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHH
Confidence            32 348999999754221    112222211 123456888876532         122233345689999999999999


Q ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH-------cCCCChHHHHHHHHHH
Q 042645          315 FEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM-------ASKKAPREWAHAIEVL  371 (427)
Q Consensus       315 f~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L-------~~~~~~~~w~~~l~~l  371 (427)
                      +.+.+.......   ..++...|++.+.|.+-.+.-+...|       ...-+....+.++..+
T Consensus       277 l~~~~~~~~~~l---~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~~it~~~~~~~L~~~  337 (405)
T TIGR00362       277 LQKKAEEEGLEL---PDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGKPITLELAKEALKDL  337 (405)
T ss_pred             HHHHHHHcCCCC---CHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence            999886543222   25678889999998877544322222       1123555666666554

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).

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.42  E-value=5.4e-06  Score=80.21  Aligned_cols=170  Identities=18%  Similarity=0.239  Sum_probs=98.4

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|++..+++|.+.+..             ...+-|.++|++|+|||++|+.+++..   ...     |+.++.    
T Consensus       131 ~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~---~~~-----~i~v~~----  198 (389)
T PRK03992        131 EDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET---NAT-----FIRVVG----  198 (389)
T ss_pred             HHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHh---CCC-----EEEeeh----
Confidence            4678999999999887632             235679999999999999999999886   222     222211    


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCccc----------------ccccccCCC--C
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFD----------------LAQVGLPVP--S  275 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~  275 (427)
                      .++.    ...       .+. .......+.+.. ...+.+|+|||++....                ...+...+.  .
T Consensus       199 ~~l~----~~~-------~g~-~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~  266 (389)
T PRK03992        199 SELV----QKF-------IGE-GARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFD  266 (389)
T ss_pred             HHHh----Hhh-------ccc-hHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccC
Confidence            1111    111       011 122233333332 35678999999975410                011111111  1


Q ss_pred             CCCCcEEEEecCChhHHh--hc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          276 RASASKVVFTTREFEVCG--LM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       276 ~~~gs~IivTtR~~~v~~--~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      ...+..||.||.......  ..   .-...+.+++.+.++-.++|+.+..........+    ...+++.+.|.-
T Consensus       267 ~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~----~~~la~~t~g~s  337 (389)
T PRK03992        267 PRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVD----LEELAELTEGAS  337 (389)
T ss_pred             CCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCC----HHHHHHHcCCCC
Confidence            123456777776543211  11   1235689999999999999998775433222222    466777777754

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.42  E-value=5e-06  Score=76.81  Aligned_cols=132  Identities=11%  Similarity=0.081  Sum_probs=71.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcC
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRN  250 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~  250 (427)
                      .+.++|++|+|||++|+.+++.... .+......++.++.    .++.    ..+..       .+.......+.+ .  
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~-~g~~~~~~~v~v~~----~~l~----~~~~g-------~~~~~~~~~~~~-a--  120 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHR-LGYVRKGHLVSVTR----DDLV----GQYIG-------HTAPKTKEILKR-A--  120 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHH-cCCcccceEEEecH----HHHh----Hhhcc-------cchHHHHHHHHH-c--
Confidence            6889999999999999888776621 12211112333332    1222    11111       111112222222 2  


Q ss_pred             CcEEEEEeccCCcc------c-----ccccccCCCCCCCCcEEEEecCChhHHhhcC--------CCcceeccCCChHHH
Q 042645          251 RKIVLLLDDIWELF------D-----LAQVGLPVPSRASASKVVFTTREFEVCGLMD--------AHKSFKVECLGYEDA  311 (427)
Q Consensus       251 k~~LlVlDdv~~~~------~-----~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~--------~~~~~~l~~L~~~e~  311 (427)
                      ..-+|+||++....      +     ...+...+.....+.+||+++..........        ....+.+++++.+|.
T Consensus       121 ~~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl  200 (284)
T TIGR02880       121 MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAEL  200 (284)
T ss_pred             cCcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHH
Confidence            34689999997431      1     1223333333344566777765433222111        135689999999999


Q ss_pred             HHHHHHHhCC
Q 042645          312 WRLFEEKVGR  321 (427)
Q Consensus       312 ~~lf~~~~~~  321 (427)
                      ..++...+..
T Consensus       201 ~~I~~~~l~~  210 (284)
T TIGR02880       201 LVIAGLMLKE  210 (284)
T ss_pred             HHHHHHHHHH
Confidence            9999887743

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.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.42  E-value=5.7e-06  Score=84.38  Aligned_cols=186  Identities=11%  Similarity=0.126  Sum_probs=106.0

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.|.+++..++ .+.+.++|+.|+||||+|+.+++.+........+          .+-.-....   .+
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~----------~pC~~C~~~---~~   84 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLL----------EPCQECIEN---VN   84 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCC----------CchhHHHHh---hc
Confidence            457999999999999998765 4567899999999999999998876211100000          000000000   00


Q ss_pred             CCC-----CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEE-EecCChhHHh
Q 042645          227 LYN-----ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVV-FTTREFEVCG  293 (427)
Q Consensus       227 ~~~-----~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~Ii-vTtR~~~v~~  293 (427)
                      ...     ........++ ++.+.+.+     .+++-++|+|+++..  ..+..+...+-.....+.+| +|+....+..
T Consensus        85 ~~~Dvieidaasn~~vd~-IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~  163 (725)
T PRK07133         85 NSLDIIEMDAASNNGVDE-IRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPL  163 (725)
T ss_pred             CCCcEEEEeccccCCHHH-HHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhH
Confidence            000     0000112222 22222222     256679999999754  23444443333333344444 4544444432


Q ss_pred             -hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          294 -LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       294 -~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                       .......+.+.+++.++....+...+...+...   ..+.+..|++.++|.+.-+..
T Consensus       164 TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~i---d~eAl~~LA~lS~GslR~Als  218 (725)
T PRK07133        164 TILSRVQRFNFRRISEDEIVSRLEFILEKENISY---EKNALKLIAKLSSGSLRDALS  218 (725)
T ss_pred             HHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHH
Confidence             233346789999999999999988664333222   234578899999997754433

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.40  E-value=8.5e-06  Score=82.97  Aligned_cols=196  Identities=16%  Similarity=0.133  Sum_probs=111.4

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..+..|.+++..+. .+.+.++|+.|+||||+|+.+++.+...  ......    ...+..-...+.+.....
T Consensus        16 ~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~--~~~~~~----~~~Cg~C~~C~~i~~g~h   89 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCL--NSDKPT----PEPCGKCELCRAIAAGNA   89 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCC--CcCCCC----CCCCcccHHHHHHhcCCC
Confidence            457899999999999998764 3678899999999999999999887311  110000    011112223333332221


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCC-hhHH-hh
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTRE-FEVC-GL  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~-~~v~-~~  294 (427)
                      ...   ........+.+.+.+ +.+     .+++-++|+|+++...  ....+...+......+.+|++|.+ ..+. ..
T Consensus        90 ~D~~ei~~~~~~~vd~IReii-~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTI  168 (620)
T PRK14948         90 LDVIEIDAASNTGVDNIRELI-ERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTI  168 (620)
T ss_pred             ccEEEEeccccCCHHHHHHHH-HHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHH
Confidence            110   000112222222222 222     2455689999998653  344454444433344555555543 3332 22


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      ......+.+.+++.++....+...+...+...   ..+.+..|++.++|.+..+..+..
T Consensus       169 rSRc~~~~f~~l~~~ei~~~L~~ia~kegi~i---s~~al~~La~~s~G~lr~A~~lLe  224 (620)
T PRK14948        169 ISRCQRFDFRRIPLEAMVQHLSEIAEKESIEI---EPEALTLVAQRSQGGLRDAESLLD  224 (620)
T ss_pred             HhheeEEEecCCCHHHHHHHHHHHHHHhCCCC---CHHHHHHHHHHcCCCHHHHHHHHH
Confidence            22345678889999998888887765433122   234588899999998875544433

>CHL00181 cbbX CbbX; Provisional

Probab=98.38  E-value=9.5e-06  Score=74.97  Aligned_cols=133  Identities=14%  Similarity=0.124  Sum_probs=72.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      ..+.++|++|+||||+|+.+++.... .+.-...-|+.++    ..++....   .+        .........+.. . 
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~~-~g~~~~~~~~~v~----~~~l~~~~---~g--------~~~~~~~~~l~~-a-  121 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILYK-LGYIKKGHLLTVT----RDDLVGQY---IG--------HTAPKTKEVLKK-A-  121 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHH-cCCCCCCceEEec----HHHHHHHH---hc--------cchHHHHHHHHH-c-
Confidence            35889999999999999999886521 1111111233333    12222211   11        011111122222 1 


Q ss_pred             CCcEEEEEeccCCcc------cc-----cccccCCCCCCCCcEEEEecCChhHHhhc--------CCCcceeccCCChHH
Q 042645          250 NRKIVLLLDDIWELF------DL-----AQVGLPVPSRASASKVVFTTREFEVCGLM--------DAHKSFKVECLGYED  310 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~------~~-----~~~~~~l~~~~~gs~IivTtR~~~v~~~~--------~~~~~~~l~~L~~~e  310 (427)
                       ..-+|+||+++...      ++     ..+...+.+...+..||+++....+....        .....+.+++++.+|
T Consensus       122 -~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~e  200 (287)
T CHL00181        122 -MGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEE  200 (287)
T ss_pred             -cCCEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHH
Confidence             23599999997531      11     12222233334456777777654432211        123468999999999


Q ss_pred             HHHHHHHHhCC
Q 042645          311 AWRLFEEKVGR  321 (427)
Q Consensus       311 ~~~lf~~~~~~  321 (427)
                      ..+++...+..
T Consensus       201 l~~I~~~~l~~  211 (287)
T CHL00181        201 LLQIAKIMLEE  211 (287)
T ss_pred             HHHHHHHHHHH
Confidence            99999888743

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

Probab=98.38  E-value=5.4e-06  Score=76.56  Aligned_cols=199  Identities=16%  Similarity=0.130  Sum_probs=121.5

Q ss_pred             CCccccchhhHHHHHHHhccCC---CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTEEP---VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~~~---~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      .+.|.+|+.++..+...+....   +..|.|+|..|.|||.+.+++.+.. .     ...+|+++-+.++...++..|+.
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~-n-----~~~vw~n~~ecft~~~lle~IL~   78 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKL-N-----LENVWLNCVECFTYAILLEKILN   78 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhc-C-----CcceeeehHHhccHHHHHHHHHH
Confidence            4678899999999999997643   3456899999999999999999886 1     13589999999999999999999


Q ss_pred             HhC-CCCCCCCCC----CHHHHHHHHHH--Hhc--CCcEEEEEeccCCcccccccc--------cCCCCCCCCcEEEEec
Q 042645          224 KIG-LYNESWDNK----SFDEKAQEIFK--TMR--NRKIVLLLDDIWELFDLAQVG--------LPVPSRASASKVVFTT  286 (427)
Q Consensus       224 ~l~-~~~~~~~~~----~~~~~~~~l~~--~L~--~k~~LlVlDdv~~~~~~~~~~--------~~l~~~~~gs~IivTt  286 (427)
                      +.+ .+.++....    +....+..+.+  ...  ++.++||||+++...+.+.+.        ..++  .+.. +|+++
T Consensus        79 ~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~--~~~i-~iils  155 (438)
T KOG2543|consen   79 KSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLN--EPTI-VIILS  155 (438)
T ss_pred             HhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhC--CCce-EEEEe
Confidence            986 222211111    11122233333  111  468999999998765544321        1111  2223 33433


Q ss_pred             CChh---HHhhcCCC--cceeccCCChHHHHHHHHHHhCCCCCCC---CCCHHHHHHHHHHHcCCCchHHHHHHHHHc
Q 042645          287 REFE---VCGLMDAH--KSFKVECLGYEDAWRLFEEKVGRDILDS---HPDIPELAETVARECGGLPLALITVGRAMA  356 (427)
Q Consensus       287 R~~~---v~~~~~~~--~~~~l~~L~~~e~~~lf~~~~~~~~~~~---~~~~~~~~~~i~~~~~G~Plai~~~~~~L~  356 (427)
                      -...   ....++..  .++..+..+.+|...++.+.-.+.. ..   ..-+.-+..-....|+ -+-.+..+.....
T Consensus       156 ~~~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~r-~~~~ya~fl~v~l~vF~~~cr-d~~eL~~~~~~~w  231 (438)
T KOG2543|consen  156 APSCEKQYLINTGTLEIVVLHFPQYSVEETQVILSRDNPGKR-KLDVYAQFLHVLLQVFYMACR-DVNELRSLISLAW  231 (438)
T ss_pred             ccccHHHhhcccCCCCceEEecCCCCHHHHHHHHhcCCcccc-chHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHH
Confidence            3221   12212332  3457788999999998876532111 00   0112223445556676 6666666665544

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.38  E-value=1.2e-05  Score=80.90  Aligned_cols=193  Identities=15%  Similarity=0.134  Sum_probs=110.4

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|-+..+..|.+++..+.. +.+.++|+.|+||||+|+.+++.+... .....   ..+....    ..+.+...-.
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~-~~~~~---~pC~~C~----~C~~i~~~~~   87 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCV-NGPTP---MPCGECS----SCKSIDNDNS   87 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccc-cCCCC---CCCccch----HHHHHHcCCC
Confidence            4689999999999999987654 468899999999999999999886211 10000   0000000    0111111100


Q ss_pred             CC---CCCCCCCCHHHHHHHHHH----HhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCC-hhHHh-hc
Q 042645          227 LY---NESWDNKSFDEKAQEIFK----TMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTRE-FEVCG-LM  295 (427)
Q Consensus       227 ~~---~~~~~~~~~~~~~~~l~~----~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~-~~v~~-~~  295 (427)
                      ..   .........++..+....    -..+++-++|+|+++...  .+..+...+......+.+|++|.+ ..+.. ..
T Consensus        88 ~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~  167 (563)
T PRK06647         88 LDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIK  167 (563)
T ss_pred             CCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHH
Confidence            00   000011222232222111    123566689999998653  344554455444445666666543 33322 22


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .....+++.+++.++....+.+.+...+..   -..+.+..|++.++|.+..+...
T Consensus       168 SRc~~~~f~~l~~~el~~~L~~i~~~egi~---id~eAl~lLa~~s~GdlR~alsl  220 (563)
T PRK06647        168 SRCQHFNFRLLSLEKIYNMLKKVCLEDQIK---YEDEALKWIAYKSTGSVRDAYTL  220 (563)
T ss_pred             HhceEEEecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHH
Confidence            334568999999999999998877443322   22456788999999988655443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.35  E-value=1.7e-05  Score=80.18  Aligned_cols=192  Identities=14%  Similarity=0.144  Sum_probs=107.8

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+...+.|.+++..+. .+.+.++|+.|+||||+|+.+.+.+..... .+       ..+++.-.....+.....
T Consensus        16 ~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~-~~-------~~pC~~C~~C~~i~~g~~   87 (559)
T PRK05563         16 EDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNP-PD-------GEPCNECEICKAITNGSL   87 (559)
T ss_pred             HhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCC-CC-------CCCCCccHHHHHHhcCCC
Confidence            468999999999999998764 455778999999999999999877621110 00       001111112222211110


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHH-----hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEec-CChhHHh-h
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKT-----MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTT-REFEVCG-L  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~-----L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTt-R~~~v~~-~  294 (427)
                      .+.   +.......++.. .+.+.     ..++.-++|+|+++..  ..+..+...+........+|++| ....+.. .
T Consensus        88 ~dv~eidaas~~~vd~ir-~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI  166 (559)
T PRK05563         88 MDVIEIDAASNNGVDEIR-DIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATI  166 (559)
T ss_pred             CCeEEeeccccCCHHHHH-HHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHH
Confidence            000   000111222222 22222     1356678999999865  23444444443333344555444 3333322 2


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ......+.+.+++.++....+...+...+...   ..+.+..|++.++|.+..+...
T Consensus       167 ~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i---~~~al~~ia~~s~G~~R~al~~  220 (559)
T PRK05563        167 LSRCQRFDFKRISVEDIVERLKYILDKEGIEY---EDEALRLIARAAEGGMRDALSI  220 (559)
T ss_pred             HhHheEEecCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHH
Confidence            22345688999999999999988775433222   2355788899999987654433

>TIGR00767 rho transcription termination factor Rho

Probab=98.35  E-value=2e-06  Score=81.28  Aligned_cols=94  Identities=16%  Similarity=0.133  Sum_probs=63.6

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC--CCHHHHHHHHHHHhCCCCCCCCCCCHHHHHH--
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD--LQLGKIQESIAKKIGLYNESWDNKSFDEKAQ--  242 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~--~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~--  242 (427)
                      +....++|+|++|+|||||++.+++...  ..+|+..+|+.+...  .++.++++.+...+-...-.........+..  
T Consensus       166 g~Gq~~~IvG~~g~GKTtL~~~i~~~I~--~nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v  243 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVLLQKIAQAIT--RNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMV  243 (415)
T ss_pred             CCCCEEEEECCCCCChhHHHHHHHHhhc--ccCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHH
Confidence            3456899999999999999999999873  347999999998865  7899999998654332221101111111111  


Q ss_pred             --HHHHH-hcCCcEEEEEeccCC
Q 042645          243 --EIFKT-MRNRKIVLLLDDIWE  262 (427)
Q Consensus       243 --~l~~~-L~~k~~LlVlDdv~~  262 (427)
                        ..... -.+++++|++|++..
T Consensus       244 ~e~Ae~~~~~GkdVVLlIDEitR  266 (415)
T TIGR00767       244 IEKAKRLVEHKKDVVILLDSITR  266 (415)
T ss_pred             HHHHHHHHHcCCCeEEEEEChhH
Confidence              11121 358999999999964

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

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.34  E-value=4.5e-06  Score=81.94  Aligned_cols=182  Identities=16%  Similarity=0.126  Sum_probs=106.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.|+|++|+|||+|++.+++.... ...-..++|++.      .++...+...+...       ..+    .+.+.+
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~-~~~~~~v~yi~~------~~f~~~~~~~~~~~-------~~~----~f~~~~  191 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQ-NEPDLRVMYITS------EKFLNDLVDSMKEG-------KLN----EFREKY  191 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHH-hCCCCeEEEEEH------HHHHHHHHHHHhcc-------cHH----HHHHHH
Confidence            346999999999999999999998721 111124566643      45666666555311       112    233333


Q ss_pred             cCCcEEEEEeccCCccc---c-cccccCCCC-CCCCcEEEEecCChh---------HHhhcCCCcceeccCCChHHHHHH
Q 042645          249 RNRKIVLLLDDIWELFD---L-AQVGLPVPS-RASASKVVFTTREFE---------VCGLMDAHKSFKVECLGYEDAWRL  314 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~---~-~~~~~~l~~-~~~gs~IivTtR~~~---------v~~~~~~~~~~~l~~L~~~e~~~l  314 (427)
                      +.+.-+|++||++....   + ..+...+.. ...|..||+||....         +...+.....+.+++.+.+.-..+
T Consensus       192 ~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~I  271 (440)
T PRK14088        192 RKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKI  271 (440)
T ss_pred             HhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHH
Confidence            34566899999975421   1 122222211 122456888875321         122233445788999999999999


Q ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH------cC-CCChHHHHHHHHHH
Q 042645          315 FEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM------AS-KKAPREWAHAIEVL  371 (427)
Q Consensus       315 f~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L------~~-~~~~~~w~~~l~~l  371 (427)
                      +++.+.......   ..++...|++.+.|..-.+.-+...|      .. .-+...-+.++..+
T Consensus       272 L~~~~~~~~~~l---~~ev~~~Ia~~~~~~~R~L~g~l~~l~~~~~~~~~~it~~~a~~~L~~~  332 (440)
T PRK14088        272 ARKMLEIEHGEL---PEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGEEVDLKEAILLLKDF  332 (440)
T ss_pred             HHHHHHhcCCCC---CHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence            998875433222   25668889999888765553322222      11 24555666666544

>PRK06620 hypothetical protein; Validated

Probab=98.33  E-value=5.8e-06  Score=72.99  Aligned_cols=138  Identities=9%  Similarity=-0.011  Sum_probs=82.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      +.+.|+|++|+|||+|++.+++..   ..     .++.  ....                      . .       +.. 
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~---~~-----~~~~--~~~~----------------------~-~-------~~~-   83 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLS---NA-----YIIK--DIFF----------------------N-E-------EIL-   83 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhcc---CC-----EEcc--hhhh----------------------c-h-------hHH-
Confidence            568999999999999999987765   11     1111  0000                      0 0       011 


Q ss_pred             CCcEEEEEeccCCcccccccccCCCC-CCCCcEEEEecCChh-------HHhhcCCCcceeccCCChHHHHHHHHHHhCC
Q 042645          250 NRKIVLLLDDIWELFDLAQVGLPVPS-RASASKVVFTTREFE-------VCGLMDAHKSFKVECLGYEDAWRLFEEKVGR  321 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~~~~~~~~l~~-~~~gs~IivTtR~~~-------v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~  321 (427)
                      ...-+|++||++...+ ..+...+.. ...|..||+|++..+       +...+.....+++++++.++...++++.+..
T Consensus        84 ~~~d~lliDdi~~~~~-~~lf~l~N~~~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~  162 (214)
T PRK06620         84 EKYNAFIIEDIENWQE-PALLHIFNIINEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSI  162 (214)
T ss_pred             hcCCEEEEeccccchH-HHHHHHHHHHHhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHH
Confidence            1234788999974322 112111110 134668999988543       2333445568999999999988888887753


Q ss_pred             CCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          322 DILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       322 ~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      ....   -.+++.+-|++.+.|.--.+.-+.
T Consensus       163 ~~l~---l~~ev~~~L~~~~~~d~r~l~~~l  190 (214)
T PRK06620        163 SSVT---ISRQIIDFLLVNLPREYSKIIEIL  190 (214)
T ss_pred             cCCC---CCHHHHHHHHHHccCCHHHHHHHH
Confidence            3222   225668888888877655544433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.33  E-value=5.5e-06  Score=78.24  Aligned_cols=173  Identities=9%  Similarity=0.034  Sum_probs=95.8

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+...+.+..++..+.. .++.++|++|+||||+|+.+++..   ...   ...++.+. .... ..+..+..+.
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~---~~~---~~~i~~~~-~~~~-~i~~~l~~~~   92 (316)
T PHA02544         21 DECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV---GAE---VLFVNGSD-CRID-FVRNRLTRFA   92 (316)
T ss_pred             HHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh---Ccc---ceEeccCc-ccHH-HHHHHHHHHH
Confidence            4679999999999999987654 566669999999999999998875   111   23333333 1111 1111111110


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc--c-ccccccCCCCCCCCcEEEEecCChhH--HhhcCCCcce
Q 042645          227 LYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF--D-LAQVGLPVPSRASASKVVFTTREFEV--CGLMDAHKSF  301 (427)
Q Consensus       227 ~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~--~-~~~~~~~l~~~~~gs~IivTtR~~~v--~~~~~~~~~~  301 (427)
                      ..                 ..+.+.+-+||+||++...  + ...+...+.....++.+|+||.....  .........+
T Consensus        93 ~~-----------------~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i  155 (316)
T PHA02544         93 ST-----------------VSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVI  155 (316)
T ss_pred             Hh-----------------hcccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEE
Confidence            00                 0011345689999997651  1 12222223333456788888865431  1111222457


Q ss_pred             eccCCChHHHHHHHHHHh-------CCCCCCCCCCHHHHHHHHHHHcCCCchHH
Q 042645          302 KVECLGYEDAWRLFEEKV-------GRDILDSHPDIPELAETVARECGGLPLAL  348 (427)
Q Consensus       302 ~l~~L~~~e~~~lf~~~~-------~~~~~~~~~~~~~~~~~i~~~~~G~Plai  348 (427)
                      .++..+.++..+++....       ...+   .+-..+....+++..+|.-..+
T Consensus       156 ~~~~p~~~~~~~il~~~~~~~~~~~~~~~---~~i~~~al~~l~~~~~~d~r~~  206 (316)
T PHA02544        156 DFGVPTKEEQIEMMKQMIVRCKGILEAEG---VEVDMKVLAALVKKNFPDFRRT  206 (316)
T ss_pred             EeCCCCHHHHHHHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHhcCCCHHHH
Confidence            777888888776654321       1111   1122334577777776654433

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.32  E-value=1.1e-05  Score=79.96  Aligned_cols=181  Identities=19%  Similarity=0.181  Sum_probs=106.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.|+|++|+|||+|++.+++.... ...-..+++++.      .++...+...+..       ...    ..+.+.+
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~-~~~~~~v~yi~~------~~~~~~~~~~~~~-------~~~----~~~~~~~  209 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILE-KNPNAKVVYVTS------EKFTNDFVNALRN-------NTM----EEFKEKY  209 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHH-hCCCCeEEEEEH------HHHHHHHHHHHHc-------CcH----HHHHHHH
Confidence            356899999999999999999998732 111234455543      3344445444421       111    2233333


Q ss_pred             cCCcEEEEEeccCCccc---c-cccccCCCC-CCCCcEEEEecCChh---------HHhhcCCCcceeccCCChHHHHHH
Q 042645          249 RNRKIVLLLDDIWELFD---L-AQVGLPVPS-RASASKVVFTTREFE---------VCGLMDAHKSFKVECLGYEDAWRL  314 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~---~-~~~~~~l~~-~~~gs~IivTtR~~~---------v~~~~~~~~~~~l~~L~~~e~~~l  314 (427)
                      + +.-+|+|||++....   + +.+...+.. ...|..||+||...+         +...+.....+.+++.+.++-..+
T Consensus       210 ~-~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~i  288 (450)
T PRK00149        210 R-SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAI  288 (450)
T ss_pred             h-cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHH
Confidence            3 344899999975321   1 122221111 112455888876532         123334446789999999999999


Q ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH-------cCCCChHHHHHHHHHH
Q 042645          315 FEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM-------ASKKAPREWAHAIEVL  371 (427)
Q Consensus       315 f~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L-------~~~~~~~~w~~~l~~l  371 (427)
                      +++.+......   -..++...|++.+.|..-.+.-+...|       ...-+....+.++..+
T Consensus       289 l~~~~~~~~~~---l~~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~~~~it~~~~~~~l~~~  349 (450)
T PRK00149        289 LKKKAEEEGID---LPDEVLEFIAKNITSNVRELEGALNRLIAYASLTGKPITLELAKEALKDL  349 (450)
T ss_pred             HHHHHHHcCCC---CCHHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHh
Confidence            99988543222   235668999999999877543322222       1124566666666654

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

Probab=98.31  E-value=7.1e-06  Score=78.93  Aligned_cols=107  Identities=15%  Similarity=0.138  Sum_probs=71.1

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      .++++.+..++.+...|...  +.+.++|++|+|||++|+.+++.. .....+..+.||++++.++..++...+.-. +.
T Consensus       175 ~d~~i~e~~le~l~~~L~~~--~~iil~GppGtGKT~lA~~la~~l-~~~~~~~~v~~VtFHpsySYeDFI~G~rP~-~v  250 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK--KNIILQGPPGVGKTFVARRLAYLL-TGEKAPQRVNMVQFHQSYSYEDFIQGYRPN-GV  250 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC--CCEEEECCCCCCHHHHHHHHHHHh-cCCcccceeeEEeecccccHHHHhcccCCC-CC
Confidence            35678889999999998764  458889999999999999999887 444577888999999888766655422100 00


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCC
Q 042645          228 YNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWE  262 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~  262 (427)
                      .   .. ....-..+.+.....  +++++||+|++..
T Consensus       251 g---y~-~~~G~f~~~~~~A~~~p~~~~vliIDEINR  283 (459)
T PRK11331        251 G---FR-RKDGIFYNFCQQAKEQPEKKYVFIIDEINR  283 (459)
T ss_pred             C---eE-ecCchHHHHHHHHHhcccCCcEEEEehhhc
Confidence            0   00 000111122222222  4789999999964

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

Probab=98.30  E-value=7e-06  Score=85.99  Aligned_cols=155  Identities=15%  Similarity=0.251  Sum_probs=90.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC--CC-CcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP--ND-FDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~~-f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..++||+++++++++.|......-+.++|++|+|||++|+.+++......  .. ....+|. +    +...+.    ..
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~-~----~~~~l~----a~  252 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS-L----DMGSLL----AG  252 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE-e----cHHHHh----hh
Confidence            35899999999999999877666788999999999999999998863211  11 1233332 1    111111    10


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCccc----------ccc-cccCCCCCCCCcEEEEecCChhHH
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFD----------LAQ-VGLPVPSRASASKVVFTTREFEVC  292 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~----------~~~-~~~~l~~~~~gs~IivTtR~~~v~  292 (427)
                      ..      .....++.+..+.+.+ +.++.+|++|+++....          ... +...+..  ..-++|-+|...+..
T Consensus       253 ~~------~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~--g~i~~IgaTt~~e~~  324 (731)
T TIGR02639       253 TK------YRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSS--GKLRCIGSTTYEEYK  324 (731)
T ss_pred             cc------ccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhC--CCeEEEEecCHHHHH
Confidence            00      0112233444444443 34689999999974321          111 2222221  123455555432221


Q ss_pred             -------hhcCCCcceeccCCChHHHHHHHHHHh
Q 042645          293 -------GLMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       293 -------~~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                             ....-...+.+++++.++..++++...
T Consensus       325 ~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       325 NHFEKDRALSRRFQKIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             HHhhhhHHHHHhCceEEeCCCCHHHHHHHHHHHH
Confidence                   111123468999999999999999654

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

Probab=98.29  E-value=1.2e-05  Score=77.85  Aligned_cols=135  Identities=20%  Similarity=0.245  Sum_probs=85.4

Q ss_pred             cchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC
Q 042645          152 GMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE  230 (427)
Q Consensus       152 GR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~  230 (427)
                      .|...+.++.+.+..... ++.|.|+-++||||+++.+.....   ..   .++++..+.. +-..+ .           
T Consensus        21 ~~~~~~~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~---~~---~iy~~~~d~~~~~~~l-~-----------   81 (398)
T COG1373          21 ERRKLLPRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLL---EE---IIYINFDDLRLDRIEL-L-----------   81 (398)
T ss_pred             hHHhhhHHHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCC---cc---eEEEEecchhcchhhH-H-----------
Confidence            344555566666554443 999999999999999977776652   22   4554433221 11111 1           


Q ss_pred             CCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHh------hcCCCcceecc
Q 042645          231 SWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG------LMDAHKSFKVE  304 (427)
Q Consensus       231 ~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~------~~~~~~~~~l~  304 (427)
                              +....+...-..++..|+||.|....+|......+.+.... +|++|+.+.....      ..+-...+.+-
T Consensus        82 --------d~~~~~~~~~~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~  152 (398)
T COG1373          82 --------DLLRAYIELKEREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELY  152 (398)
T ss_pred             --------HHHHHHHHhhccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEEC
Confidence                    11111111111277899999999999999887777766555 8999888765421      12234578999


Q ss_pred             CCChHHHHHH
Q 042645          305 CLGYEDAWRL  314 (427)
Q Consensus       305 ~L~~~e~~~l  314 (427)
                      ||+..|-..+
T Consensus       153 PlSF~Efl~~  162 (398)
T COG1373         153 PLSFREFLKL  162 (398)
T ss_pred             CCCHHHHHhh
Confidence            9999888653

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.27  E-value=3.5e-05  Score=77.20  Aligned_cols=158  Identities=18%  Similarity=0.156  Sum_probs=96.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      ..+.|+|..|+|||.|++.+++.... ...-..++|++      ..++...+...+..       ..    ...+.+.++
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~-~~~g~~V~Yit------aeef~~el~~al~~-------~~----~~~f~~~y~  376 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARR-LYPGTRVRYVS------SEEFTNEFINSIRD-------GK----GDSFRRRYR  376 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHH-hCCCCeEEEee------HHHHHHHHHHHHHh-------cc----HHHHHHHhh
Confidence            45899999999999999999998721 11122445554      34455555544321       11    122333333


Q ss_pred             CCcEEEEEeccCCccc---cc-ccccCCCC-CCCCcEEEEecCCh---------hHHhhcCCCcceeccCCChHHHHHHH
Q 042645          250 NRKIVLLLDDIWELFD---LA-QVGLPVPS-RASASKVVFTTREF---------EVCGLMDAHKSFKVECLGYEDAWRLF  315 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~---~~-~~~~~l~~-~~~gs~IivTtR~~---------~v~~~~~~~~~~~l~~L~~~e~~~lf  315 (427)
                      + .=+|||||+.....   |. .+...+.. ...+..|||||...         .+...+.....+.+.+.+.+.-..++
T Consensus       377 ~-~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL  455 (617)
T PRK14086        377 E-MDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAIL  455 (617)
T ss_pred             c-CCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHH
Confidence            2 34788999975422   21 22222221 12345688888753         23344456678899999999999999


Q ss_pred             HHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          316 EEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      .+++.......   -.++++-|++.+.+..-.+.
T Consensus       456 ~kka~~r~l~l---~~eVi~yLa~r~~rnvR~Le  486 (617)
T PRK14086        456 RKKAVQEQLNA---PPEVLEFIASRISRNIRELE  486 (617)
T ss_pred             HHHHHhcCCCC---CHHHHHHHHHhccCCHHHHH
Confidence            99886544322   25668888888887655543

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=98.27  E-value=5.9e-05  Score=70.56  Aligned_cols=198  Identities=12%  Similarity=0.124  Sum_probs=110.2

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCC------------CCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTP------------NDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~------------~~f~~~~wv~~~~~~~~  214 (427)
                      ..++|.+..++.+.+.+..+. .+...++|+.|+||+++|..+++......            .......|+.-....+-
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~g   83 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQG   83 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccccc
Confidence            357899999999999998876 47899999999999999999887752111            11122233321100000


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecC
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTR  287 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR  287 (427)
                      ..+-..-+...+...........++ ++.+.+.+     .+++-++|+|+++....  ...+...+-... .+.+|++|.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~I~id~-ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~  161 (314)
T PRK07399         84 KLITASEAEEAGLKRKAPPQIRLEQ-IREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLILIAP  161 (314)
T ss_pred             cccchhhhhhccccccccccCcHHH-HHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEEC
Confidence            0000011111111111001122223 23344443     35667999999976532  333333332222 344555554


Q ss_pred             C-hhHHh-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          288 E-FEVCG-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       288 ~-~~v~~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      + ..+.. ..+-...+.+.+++.++..+.+.+......      .......++..++|.|..+..+..
T Consensus       162 ~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~------~~~~~~~l~~~a~Gs~~~al~~l~  223 (314)
T PRK07399        162 SPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEI------LNINFPELLALAQGSPGAAIANIE  223 (314)
T ss_pred             ChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhcccc------chhHHHHHHHHcCCCHHHHHHHHH
Confidence            4 33322 223346789999999999999998753211      111146789999999987655443

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.26  E-value=4.5e-05  Score=74.84  Aligned_cols=152  Identities=13%  Similarity=0.079  Sum_probs=90.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      ..+.|+|+.|+|||+|++.+++....   ....+++++      ...+...+...+...       .    ...++..++
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~---~~~~v~yi~------~~~f~~~~~~~l~~~-------~----~~~f~~~~~  201 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRE---SGGKILYVR------SELFTEHLVSAIRSG-------E----MQRFRQFYR  201 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHH---cCCCEEEee------HHHHHHHHHHHHhcc-------h----HHHHHHHcc
Confidence            56889999999999999999998732   123345543      334445555554311       1    123344343


Q ss_pred             CCcEEEEEeccCCcccc----cccccCCCC-CCCCcEEEEecCChh---------HHhhcCCCcceeccCCChHHHHHHH
Q 042645          250 NRKIVLLLDDIWELFDL----AQVGLPVPS-RASASKVVFTTREFE---------VCGLMDAHKSFKVECLGYEDAWRLF  315 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~~----~~~~~~l~~-~~~gs~IivTtR~~~---------v~~~~~~~~~~~l~~L~~~e~~~lf  315 (427)
                       ..-+|++||+......    +.+...+.. ...|..||+||....         +...+.....+.+.+++.++...++
T Consensus       202 -~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL  280 (445)
T PRK12422        202 -NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFL  280 (445)
T ss_pred             -cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHH
Confidence             3448889999754221    122222211 113456888886521         2233344567899999999999999


Q ss_pred             HHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          316 EEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      ++.+...+...   ..++..-|+..+.|.-
T Consensus       281 ~~k~~~~~~~l---~~evl~~la~~~~~di  307 (445)
T PRK12422        281 ERKAEALSIRI---EETALDFLIEALSSNV  307 (445)
T ss_pred             HHHHHHcCCCC---CHHHHHHHHHhcCCCH
Confidence            98875443222   2456777777777554

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

Probab=98.21  E-value=2.3e-05  Score=75.59  Aligned_cols=172  Identities=15%  Similarity=0.174  Sum_probs=97.4

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|.+..+++|.+.+..             ...+-+.++|++|+|||+||+.+++..   ...|     +.+..    
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l---~~~f-----i~i~~----  212 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHT---TATF-----IRVVG----  212 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc---CCCE-----EEEeh----
Confidence            3578988888888776531             245679999999999999999999876   2222     11111    


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCC--CC
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SR  276 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~  276 (427)
                      ..+.    ...       .......+...+.......+.+|+||+++....                +..+...+.  ..
T Consensus       213 s~l~----~k~-------~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~  281 (398)
T PTZ00454        213 SEFV----QKY-------LGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQ  281 (398)
T ss_pred             HHHH----HHh-------cchhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCC
Confidence            1111    111       011112222223333346889999999874310                111111111  12


Q ss_pred             CCCcEEEEecCChhHH-h-hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          277 ASASKVVFTTREFEVC-G-LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       277 ~~gs~IivTtR~~~v~-~-~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ..+..||.||...... . ...   -...+.++..+.++...+|+............+    ...+++.+.|..-
T Consensus       282 ~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd----~~~la~~t~g~sg  352 (398)
T PTZ00454        282 TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVD----LEDFVSRPEKISA  352 (398)
T ss_pred             CCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccC----HHHHHHHcCCCCH
Confidence            2356677777754332 1 111   235688999999998888887764433222223    4566677777544

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.20  E-value=6.1e-06  Score=87.50  Aligned_cols=154  Identities=19%  Similarity=0.277  Sum_probs=89.4

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC--CC-CcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP--ND-FDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~~-f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..++||+++++++++.|......-+.++|++|+|||++|..++.......  .. -...+|. +    +...++.     
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~-l----~~~~l~a-----  248 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT-L----DIGLLLA-----  248 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE-e----eHHHHhc-----
Confidence            35799999999999999877666778999999999999999988763211  11 1233442 1    2222211     


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCccc---------cccc-ccCCCCCCCCcEEEEecCChhHHh
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFD---------LAQV-GLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~---------~~~~-~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                       +..    .....++.+..+.+.+ ..++.+|++|+++....         ...+ .+.+.  ...-++|.+|.......
T Consensus       249 -g~~----~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~--rg~l~~IgaTt~~ey~~  321 (821)
T CHL00095        249 -GTK----YRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALA--RGELQCIGATTLDEYRK  321 (821)
T ss_pred             -cCC----CccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHh--CCCcEEEEeCCHHHHHH
Confidence             111    1112233333333333 35789999999974311         1111 11221  12245666666544321


Q ss_pred             -------hcCCCcceeccCCChHHHHHHHHHH
Q 042645          294 -------LMDAHKSFKVECLGYEDAWRLFEEK  318 (427)
Q Consensus       294 -------~~~~~~~~~l~~L~~~e~~~lf~~~  318 (427)
                             .......+.++..+.++...++...
T Consensus       322 ~ie~D~aL~rRf~~I~v~ep~~~e~~aILr~l  353 (821)
T CHL00095        322 HIEKDPALERRFQPVYVGEPSVEETIEILFGL  353 (821)
T ss_pred             HHhcCHHHHhcceEEecCCCCHHHHHHHHHHH
Confidence                   1122356788889999988888754

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

Probab=98.19  E-value=1.3e-05  Score=77.97  Aligned_cols=171  Identities=17%  Similarity=0.182  Sum_probs=96.9

Q ss_pred             ccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++.|.+..+++|.+.+.-             ...+.+.|+|++|+|||++|+.+++..   ...|     +.+...    
T Consensus       184 DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el---~~~f-----i~V~~s----  251 (438)
T PTZ00361        184 DIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET---SATF-----LRVVGS----  251 (438)
T ss_pred             HhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhh---CCCE-----EEEecc----
Confidence            467899988888877631             134578899999999999999999976   2333     222111    


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCC--CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~~  277 (427)
                      ++..    ..       .......+...+.....+.+.+|+||+++....                ...+...+.  ...
T Consensus       252 eL~~----k~-------~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~  320 (438)
T PTZ00361        252 ELIQ----KY-------LGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSR  320 (438)
T ss_pred             hhhh----hh-------cchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhccc
Confidence            1111    11       111111222222233346789999999864310                001111111  112


Q ss_pred             CCcEEEEecCChhHHhh--c---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          278 SASKVVFTTREFEVCGL--M---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       278 ~gs~IivTtR~~~v~~~--~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      .+..||.||........  +   .....+.++..+.++..++|..+..........+    ...++..+.|.--
T Consensus       321 ~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvd----l~~la~~t~g~sg  390 (438)
T PTZ00361        321 GDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVD----LEEFIMAKDELSG  390 (438)
T ss_pred             CCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcC----HHHHHHhcCCCCH
Confidence            35677878775443221  1   1235689999999999999998765433222223    4556666666544

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=98.16  E-value=0.00016  Score=63.58  Aligned_cols=182  Identities=16%  Similarity=0.183  Sum_probs=105.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS-RDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~-~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~  245 (427)
                      ++.+++.++|.-|+|||++.+.....+.   +  +.++-+.+. +..+...+...+...+.............+....+.
T Consensus        49 d~qg~~~vtGevGsGKTv~~Ral~~s~~---~--d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~  123 (269)
T COG3267          49 DGQGILAVTGEVGSGKTVLRRALLASLN---E--DQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELA  123 (269)
T ss_pred             cCCceEEEEecCCCchhHHHHHHHHhcC---C--CceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHH
Confidence            4556899999999999999996555541   1  112223433 445677788888888876321111112223333344


Q ss_pred             HHh-cCCc-EEEEEeccCCcc--cccccccCC---CCCCCCcEEEEecCCh--------hHHhhcCCCc-ceeccCCChH
Q 042645          246 KTM-RNRK-IVLLLDDIWELF--DLAQVGLPV---PSRASASKVVFTTREF--------EVCGLMDAHK-SFKVECLGYE  309 (427)
Q Consensus       246 ~~L-~~k~-~LlVlDdv~~~~--~~~~~~~~l---~~~~~gs~IivTtR~~--------~v~~~~~~~~-~~~l~~L~~~  309 (427)
                      +.. ++++ ..+++||.+...  ..+.++...   .+....-+|+..-..+        .....-.-.. .|.+.|++.+
T Consensus       124 al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~  203 (269)
T COG3267         124 ALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEA  203 (269)
T ss_pred             HHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChH
Confidence            433 4666 999999997542  222221111   1111112333333221        1111111112 3899999999


Q ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          310 DAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       310 e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      +...+++.+........+-...+....|.....|.|.+|..++.
T Consensus       204 ~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         204 ETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             HHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            99999998886554233333345688899999999999987764

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.14  E-value=0.0001  Score=73.97  Aligned_cols=177  Identities=16%  Similarity=0.142  Sum_probs=95.8

Q ss_pred             CccccchhhHHHHHHHh---cc---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCL---TE---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l---~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..+.++.+.+   ..         ...+-+.++|++|+|||+||+.+++..   ...|     +.++    ..
T Consensus        55 ~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~---~~~~-----~~i~----~~  122 (495)
T TIGR01241        55 KDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA---GVPF-----FSIS----GS  122 (495)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc---CCCe-----eecc----HH
Confidence            35788877666655443   21         234468999999999999999999876   2222     2222    11


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc------------c----cccccCCC--CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD------------L----AQVGLPVP--SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~------------~----~~~~~~l~--~~~  277 (427)
                      ++..    ..       .......+...+.......+.+|+|||++....            +    ..+...+.  ...
T Consensus       123 ~~~~----~~-------~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~  191 (495)
T TIGR01241       123 DFVE----MF-------VGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTN  191 (495)
T ss_pred             HHHH----HH-------hcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCC
Confidence            1111    11       011222333334444456789999999975311            0    01111111  112


Q ss_pred             CCcEEEEecCChhH-Hh-hc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc-hHHHHH
Q 042645          278 SASKVVFTTREFEV-CG-LM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP-LALITV  351 (427)
Q Consensus       278 ~gs~IivTtR~~~v-~~-~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P-lai~~~  351 (427)
                      .+..||.||..... -. ..   .-...+.++..+.++-.++|+..+........    .....+++.+.|.. --|..+
T Consensus       192 ~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~----~~l~~la~~t~G~sgadl~~l  267 (495)
T TIGR01241       192 TGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPD----VDLKAVARRTPGFSGADLANL  267 (495)
T ss_pred             CCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcc----hhHHHHHHhCCCCCHHHHHHH
Confidence            33445556654331 11 11   12356889999999999999887754321111    12557888888744 434433

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.14  E-value=1.7e-05  Score=78.36  Aligned_cols=158  Identities=16%  Similarity=0.254  Sum_probs=88.4

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCC--CCCcEEEEEEeCCCC
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTP--NDFDFVIWEVVSRDL  212 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~~f~~~~wv~~~~~~  212 (427)
                      .++.|.+..+++|.+.+..             ...+-+.++|++|+|||++|+.+++.+....  .......|+++... 
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~-  260 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGP-  260 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEeccch-
Confidence            3467899999988887631             2345699999999999999999999872110  01223344444331 


Q ss_pred             CHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCccc---------c-----cccccCC
Q 042645          213 QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELFD---------L-----AQVGLPV  273 (427)
Q Consensus       213 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~~---------~-----~~~~~~l  273 (427)
                         +++..    .       ... .+..+..+.+..     .+++++|+||+++....         .     ..+...+
T Consensus       261 ---eLl~k----y-------vGe-te~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~L  325 (512)
T TIGR03689       261 ---ELLNK----Y-------VGE-TERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSEL  325 (512)
T ss_pred             ---hhccc----c-------cch-HHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHh
Confidence               11110    0       001 112222222221     25799999999975311         1     1222222


Q ss_pred             CC--CCCCcEEEEecCChhHHh--hc---CCCcceeccCCChHHHHHHHHHHhCC
Q 042645          274 PS--RASASKVVFTTREFEVCG--LM---DAHKSFKVECLGYEDAWRLFEEKVGR  321 (427)
Q Consensus       274 ~~--~~~gs~IivTtR~~~v~~--~~---~~~~~~~l~~L~~~e~~~lf~~~~~~  321 (427)
                      ..  ...+..||.||.......  ..   .-...|.++..+.++..++|+.++..
T Consensus       326 Dgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~  380 (512)
T TIGR03689       326 DGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD  380 (512)
T ss_pred             cccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc
Confidence            21  112344555554433211  11   12345899999999999999998743

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

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.14  E-value=2.3e-05  Score=83.23  Aligned_cols=154  Identities=14%  Similarity=0.188  Sum_probs=87.0

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC--CC-Cc-EEEEEEeCCCCCHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP--ND-FD-FVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~~-f~-~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      ..++||+.+++++++.|.......+.++|++|+|||++|..++.......  .. .. .++++.++.      ++.    
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~------l~a----  247 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA------LVA----  247 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhh------hhh----
Confidence            35899999999999999887667788999999999999999998862110  00 11 222222221      110    


Q ss_pred             HhCCCCCCCCCCCHHHHHHHHHHHh--cCCcEEEEEeccCCccc---------ccc-cccCCCCCCCCcEEEEecCChhH
Q 042645          224 KIGLYNESWDNKSFDEKAQEIFKTM--RNRKIVLLLDDIWELFD---------LAQ-VGLPVPSRASASKVVFTTREFEV  291 (427)
Q Consensus       224 ~l~~~~~~~~~~~~~~~~~~l~~~L--~~k~~LlVlDdv~~~~~---------~~~-~~~~l~~~~~gs~IivTtR~~~v  291 (427)
                      ..  .    .....++....+...+  .+++.+|++|+++....         ... +.+.+.  ...-++|-+|...+.
T Consensus       248 g~--~----~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~--~g~l~~IgaTt~~e~  319 (857)
T PRK10865        248 GA--K----YRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEY  319 (857)
T ss_pred             cc--c----hhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchhh--cCCCeEEEcCCCHHH
Confidence            00  0    0111223333333322  25789999999975421         112 222222  123455655555443


Q ss_pred             Hhh-------cCCCcceeccCCChHHHHHHHHHHh
Q 042645          292 CGL-------MDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       292 ~~~-------~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      ...       ..-...+.+...+.++...+++...
T Consensus       320 r~~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~  354 (857)
T PRK10865        320 RQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLK  354 (857)
T ss_pred             HHHhhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHh
Confidence            111       1112356666668888888886554

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.13  E-value=0.00012  Score=68.98  Aligned_cols=167  Identities=11%  Similarity=0.093  Sum_probs=88.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC-----CC-CCCCCCCCHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG-----LY-NESWDNKSFDEKAQ  242 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~-----~~-~~~~~~~~~~~~~~  242 (427)
                      .+.+.++|+.|+|||++|..+++.+.-.... ..       ..+..-...+.+...-.     +. .........++..+
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~-~~-------~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~   93 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQ-GG-------GACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRE   93 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCC-CC-------CCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHH
Confidence            4568899999999999999998876321100 00       00000001111110000     00 00001122333332


Q ss_pred             HHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-HH-hhcCCCcceeccCCChHHHHH
Q 042645          243 EIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-VC-GLMDAHKSFKVECLGYEDAWR  313 (427)
Q Consensus       243 ~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v~-~~~~~~~~~~l~~L~~~e~~~  313 (427)
                       +.+.+     .+++-++|+|+++...  ....+...+.....++.+|+||.+.. +. ...+-...+.+.+++.+++.+
T Consensus        94 -l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~  172 (328)
T PRK05707         94 -LVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQ  172 (328)
T ss_pred             -HHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHH
Confidence             22222     2344566789998652  33344333433345677777777643 22 222334578999999999999


Q ss_pred             HHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          314 LFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       314 lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .+.......       ..+.+..++..++|.|+....+
T Consensus       173 ~L~~~~~~~-------~~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        173 WLQQALPES-------DERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             HHHHhcccC-------ChHHHHHHHHHcCCCHHHHHHH
Confidence            998764211       1233567789999999865443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.10  E-value=3.1e-05  Score=82.47  Aligned_cols=156  Identities=16%  Similarity=0.231  Sum_probs=88.9

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC--C-CCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP--N-DFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~-~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..++||+.+++++++.|.......+.++|++|+|||++|..+++......  . .....+|..     ++..++    . 
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l-----~~~~l~----a-  242 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLAL-----DMGALI----A-  242 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEe-----eHHHHh----h-
Confidence            34899999999999999877666778999999999999999988762110  0 012222211     111111    0 


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc---------ccccccCCCCCCCCcEEEEecCChhHHh
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD---------LAQVGLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~---------~~~~~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                       +..    .....+..+..+...+.  +++.+|++|+++....         ...+..+... ...-++|-+|...+...
T Consensus       243 -~~~----~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~-~g~i~~IgaTt~~e~r~  316 (852)
T TIGR03346       243 -GAK----YRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALA-RGELHCIGATTLDEYRK  316 (852)
T ss_pred             -cch----hhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhh-cCceEEEEeCcHHHHHH
Confidence             000    01122333333333332  4689999999985421         1112112111 12235555555444321


Q ss_pred             h-------cCCCcceeccCCChHHHHHHHHHHh
Q 042645          294 L-------MDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       294 ~-------~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      .       ..-...+.++..+.++...++....
T Consensus       317 ~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~  349 (852)
T TIGR03346       317 YIEKDAALERRFQPVFVDEPTVEDTISILRGLK  349 (852)
T ss_pred             HhhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHH
Confidence            1       1122467889999999999987654

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.

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

Probab=98.09  E-value=2e-05  Score=81.83  Aligned_cols=155  Identities=19%  Similarity=0.322  Sum_probs=89.1

Q ss_pred             ccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCC---CcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          149 TVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPND---FDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~---f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      .++||+.+++++++.|.......+.++|++|+|||++|+.+++......-.   .++.+|.     .++..+    +.  
T Consensus       187 ~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~-----l~~~~l----la--  255 (758)
T PRK11034        187 PLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYS-----LDIGSL----LA--  255 (758)
T ss_pred             cCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEe-----ccHHHH----hc--
Confidence            489999999999999987655667899999999999999998765221111   2333442     112111    10  


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCcc----------cccccccCCCCCCCCcEEEEecCChhHHh-
Q 042645          226 GLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELF----------DLAQVGLPVPSRASASKVVFTTREFEVCG-  293 (427)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~----------~~~~~~~~l~~~~~gs~IivTtR~~~v~~-  293 (427)
                      +..    .....+.....+...+ +.++.+|++|+++...          +...+..++.. ...-++|-+|...+... 
T Consensus       256 G~~----~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~-~g~i~vIgATt~~E~~~~  330 (758)
T PRK11034        256 GTK----YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS-SGKIRVIGSTTYQEFSNI  330 (758)
T ss_pred             ccc----hhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHh-CCCeEEEecCChHHHHHH
Confidence            000    0112233333333333 3567899999997531          11111112211 12344555555443211 


Q ss_pred             ------hcCCCcceeccCCChHHHHHHHHHHh
Q 042645          294 ------LMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       294 ------~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                            ...-...+.+++++.++..+++....
T Consensus       331 ~~~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        331 FEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             hhccHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence                  11122578999999999999998643

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.08  E-value=1.7e-05  Score=64.70  Aligned_cols=89  Identities=24%  Similarity=0.109  Sum_probs=49.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      ..+.|+|++|+||||+++.++....   .....++++..+........... .......   ............+....+
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~---~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~~~~~   75 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELG---PPGGGVIYIDGEDILEEVLDQLL-LIIVGGK---KASGSGELRLRLALALAR   75 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccC---CCCCCEEEECCEEccccCHHHHH-hhhhhcc---CCCCCHHHHHHHHHHHHH
Confidence            5789999999999999999998872   22233455554433222111111 0011110   122233333444444444


Q ss_pred             CC-cEEEEEeccCCccc
Q 042645          250 NR-KIVLLLDDIWELFD  265 (427)
Q Consensus       250 ~k-~~LlVlDdv~~~~~  265 (427)
                      .. ..+|++|++.....
T Consensus        76 ~~~~~viiiDei~~~~~   92 (148)
T smart00382       76 KLKPDVLILDEITSLLD   92 (148)
T ss_pred             hcCCCEEEEECCcccCC
Confidence            43 49999999987643

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.

>TIGR00763 lon ATP-dependent protease La

Probab=98.05  E-value=0.00079  Score=71.21  Aligned_cols=157  Identities=18%  Similarity=0.183  Sum_probs=84.7

Q ss_pred             CccccchhhHHHHHHHhcc------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      ..++|.+..++.|.+++..      ...+++.++|++|+|||++|+.+++..   ...|..   ++++...+..++..  
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l---~~~~~~---i~~~~~~~~~~i~g--  391 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKAL---NRKFVR---FSLGGVRDEAEIRG--  391 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHh---cCCeEE---EeCCCcccHHHHcC--
Confidence            4578999999998886631      244689999999999999999999987   233322   22232222222211  


Q ss_pred             HHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------cccccc-----CCCCC-------CCCc
Q 042645          222 AKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------LAQVGL-----PVPSR-------ASAS  280 (427)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~~~~~~-----~l~~~-------~~gs  280 (427)
                            ............+.+.+...-. ++-+|+||+++....         +-++..     .|.+.       ..+.
T Consensus       392 ------~~~~~~g~~~g~i~~~l~~~~~-~~~villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v  464 (775)
T TIGR00763       392 ------HRRTYVGAMPGRIIQGLKKAKT-KNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKV  464 (775)
T ss_pred             ------CCCceeCCCCchHHHHHHHhCc-CCCEEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCE
Confidence                  1111111222333344433322 334789999975421         111110     11111       1223


Q ss_pred             EEEEecCChh-H-HhhcCCCcceeccCCChHHHHHHHHHHh
Q 042645          281 KVVFTTREFE-V-CGLMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       281 ~IivTtR~~~-v-~~~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      -+|.||.... + .....-...+.+.+++.++-.+++++..
T Consensus       465 ~~I~TtN~~~~i~~~L~~R~~vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       465 IFIATANSIDTIPRPLLDRMEVIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             EEEEecCCchhCCHHHhCCeeEEecCCCCHHHHHHHHHHHH
Confidence            3444554322 1 1222233578999999999888887654

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.

>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=98.03  E-value=1.7e-05  Score=64.22  Aligned_cols=22  Identities=36%  Similarity=0.458  Sum_probs=20.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|++|+|||++|+.+++..
T Consensus         1 ill~G~~G~GKT~l~~~la~~l   22 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL   22 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT
T ss_pred             CEEECcCCCCeeHHHHHHHhhc
Confidence            5799999999999999999997

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 ....

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

Probab=98.02  E-value=0.00015  Score=63.96  Aligned_cols=46  Identities=22%  Similarity=0.434  Sum_probs=38.6

Q ss_pred             CccccchhhHHHHHHHh----ccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCL----TEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l----~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..++.|++-.    ......-+.++|..|+|||+|++.+.+.+
T Consensus        27 ~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y   76 (249)
T PF05673_consen   27 DDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEY   76 (249)
T ss_pred             HHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHH
Confidence            56899999988886643    33466779999999999999999999988

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

Probab=98.01  E-value=7.2e-05  Score=71.34  Aligned_cols=182  Identities=17%  Similarity=0.127  Sum_probs=105.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCc--EEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFD--FVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~--~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~  245 (427)
                      ....+.|||..|.|||.|++.+.+...   ....  .++++      +.......+...+.-           .....++
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~---~~~~~a~v~y~------~se~f~~~~v~a~~~-----------~~~~~Fk  171 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEAL---ANGPNARVVYL------TSEDFTNDFVKALRD-----------NEMEKFK  171 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHH---hhCCCceEEec------cHHHHHHHHHHHHHh-----------hhHHHHH
Confidence            367899999999999999999999872   2233  33333      234445555544421           2233445


Q ss_pred             HHhcCCcEEEEEeccCCcccc---c-ccccCCCC-CCCCcEEEEecCCh---------hHHhhcCCCcceeccCCChHHH
Q 042645          246 KTMRNRKIVLLLDDIWELFDL---A-QVGLPVPS-RASASKVVFTTREF---------EVCGLMDAHKSFKVECLGYEDA  311 (427)
Q Consensus       246 ~~L~~k~~LlVlDdv~~~~~~---~-~~~~~l~~-~~~gs~IivTtR~~---------~v~~~~~~~~~~~l~~L~~~e~  311 (427)
                      +..  .-=++++||++.....   + ++...|.. ...|..||+|++..         .+...+...-.+.+.+.+.+..
T Consensus       172 ~~y--~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r  249 (408)
T COG0593         172 EKY--SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETR  249 (408)
T ss_pred             Hhh--ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHH
Confidence            544  3348999999754222   1 22222221 12344899999653         2345556677899999999999


Q ss_pred             HHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCC----CchHHHHHHHHHcC---CCChHHHHHHHHHHhhc
Q 042645          312 WRLFEEKVGRDILDSHPDIPELAETVARECGG----LPLALITVGRAMAS---KKAPREWAHAIEVLRSS  374 (427)
Q Consensus       312 ~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G----~Plai~~~~~~L~~---~~~~~~w~~~l~~l~~~  374 (427)
                      ..++.+.+.......++   ++..-|++....    +.-|+..+..+-..   .-+...-+.++..+...
T Consensus       250 ~aiL~kka~~~~~~i~~---ev~~~la~~~~~nvReLegaL~~l~~~a~~~~~~iTi~~v~e~L~~~~~~  316 (408)
T COG0593         250 LAILRKKAEDRGIEIPD---EVLEFLAKRLDRNVRELEGALNRLDAFALFTKRAITIDLVKEILKDLLRA  316 (408)
T ss_pred             HHHHHHHHHhcCCCCCH---HHHHHHHHHhhccHHHHHHHHHHHHHHHHhcCccCcHHHHHHHHHHhhcc
Confidence            99999987655434433   334445554443    33333332222111   13555556666555444

>CHL00176 ftsH cell division protein; Validated

Probab=97.98  E-value=0.00021  Score=73.02  Aligned_cols=169  Identities=17%  Similarity=0.159  Sum_probs=94.8

Q ss_pred             CccccchhhHHHHHH---HhccC---------CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWR---CLTEE---------PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~---~l~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .++.|.++.++++.+   .+..+         ..+-+.++|++|+|||+||+.+++..   ...     ++.++.    .
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~---~~p-----~i~is~----s  250 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA---EVP-----FFSISG----S  250 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh---CCC-----eeeccH----H
Confidence            457788766555544   44332         24569999999999999999998876   111     222221    1


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc------------c----ccccccCCC--CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF------------D----LAQVGLPVP--SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~------------~----~~~~~~~l~--~~~  277 (427)
                      ++..    ..       .......+...+.......+++|+|||++...            .    +..+...+.  ...
T Consensus       251 ~f~~----~~-------~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~  319 (638)
T CHL00176        251 EFVE----MF-------VGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGN  319 (638)
T ss_pred             HHHH----Hh-------hhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCC
Confidence            1111    00       01111223334444556789999999997431            0    111111111  122


Q ss_pred             CCcEEEEecCChhHHh--hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCC
Q 042645          278 SASKVVFTTREFEVCG--LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGG  343 (427)
Q Consensus       278 ~gs~IivTtR~~~v~~--~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G  343 (427)
                      .+..||.||.......  ...   -...+.++..+.++-.++++.++.....    ........+++.+.|
T Consensus       320 ~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~----~~d~~l~~lA~~t~G  386 (638)
T CHL00176        320 KGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKL----SPDVSLELIARRTPG  386 (638)
T ss_pred             CCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhccc----chhHHHHHHHhcCCC
Confidence            3455666665533211  111   2356888999999999999988754221    112346778888887

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

Probab=97.98  E-value=9.1e-05  Score=64.00  Aligned_cols=46  Identities=24%  Similarity=0.307  Sum_probs=42.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++||-++.++.+.-...+++.+-+.|.||+|+||||-+..+++.+
T Consensus        27 ~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~L   72 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLAREL   72 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHH
Confidence            4689999999999888888999999999999999999999998887

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.95  E-value=5.4e-05  Score=76.81  Aligned_cols=201  Identities=14%  Similarity=0.160  Sum_probs=103.7

Q ss_pred             CccccchhhHHHHHHHhccC-----CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC---CCCCHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEE-----PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS---RDLQLGKIQE  219 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~-----~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~---~~~~~~~l~~  219 (427)
                      ..++|.++.+.++..++...     ..+++.|+|++|+||||+++.++....     ++..-|.+-.   ...+...+..
T Consensus        84 del~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~-----~~~~Ew~npv~~~~~~~~~~~~~  158 (637)
T TIGR00602        84 HELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELG-----IQVQEWSNPTLPDFQKNDHKVTL  158 (637)
T ss_pred             HHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhh-----hHHHHHhhhhhhcccccccccch
Confidence            46899999999999998652     345799999999999999999988761     1222232100   0001111111


Q ss_pred             HHHHHhCCCCCCCCCCCHHHHHHHHHH---H----hcCCcEEEEEeccCCcc-----ccccccc-CCCCCCCCcEEEEec
Q 042645          220 SIAKKIGLYNESWDNKSFDEKAQEIFK---T----MRNRKIVLLLDDIWELF-----DLAQVGL-PVPSRASASKVVFTT  286 (427)
Q Consensus       220 ~i~~~l~~~~~~~~~~~~~~~~~~l~~---~----L~~k~~LlVlDdv~~~~-----~~~~~~~-~l~~~~~gs~IivTt  286 (427)
                      .+..++.....  ..............   .    ..+++.+|+|||+.+..     .+..+.. .+...+.-.-|++||
T Consensus       159 s~~~~~~~~~s--~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~~~~lq~lLr~~~~e~~~~pLI~I~T  236 (637)
T TIGR00602       159 SLESCFSNFQS--QIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVFIIT  236 (637)
T ss_pred             hhhhccccccc--hHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhhHHHHHHHHHHHhhcCCCceEEEEec
Confidence            22222211100  00001111111111   1    13567899999996542     1222222 121222223344555


Q ss_pred             CChh---------HH-------hhcC--CCcceeccCCChHHHHHHHHHHhCCCCCCC-CC---CHHHHHHHHHHHcCCC
Q 042645          287 REFE---------VC-------GLMD--AHKSFKVECLGYEDAWRLFEEKVGRDILDS-HP---DIPELAETVARECGGL  344 (427)
Q Consensus       287 R~~~---------v~-------~~~~--~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~-~~---~~~~~~~~i~~~~~G~  344 (427)
                      -+..         ..       ....  ....|.++|++..+..+.+.+.+....... ..   ...+....|+..++|-
T Consensus       237 E~~~~~~~~~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~GD  316 (637)
T TIGR00602       237 ESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCSGD  316 (637)
T ss_pred             CCccccccccccccchhcccCHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCCCh
Confidence            2211         10       1111  123589999999998888877764321111 11   1235678888889887


Q ss_pred             chHHHHHHHHH
Q 042645          345 PLALITVGRAM  355 (427)
Q Consensus       345 Plai~~~~~~L  355 (427)
                      -..+.....++
T Consensus       317 iRsAIn~LQf~  327 (637)
T TIGR00602       317 IRSAINSLQFS  327 (637)
T ss_pred             HHHHHHHHHHH
Confidence            66665555554

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

>PRK10536 hypothetical protein; Provisional

Probab=97.94  E-value=0.00021  Score=63.82  Aligned_cols=132  Identities=15%  Similarity=0.165  Sum_probs=74.7

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC----CC--C---CHHH--
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS----RD--L---QLGK--  216 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~----~~--~---~~~~--  216 (427)
                      ..+.++......++.++.+.  ..+.+.|++|+|||+||..+..+... .+.|..++...-.    +.  +   +..+  
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~l~-~~~~~kIiI~RP~v~~ge~LGfLPG~~~eK~  131 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESK--QLIFATGEAGCGKTWISAAKAAEALI-HKDVDRIIVTRPVLQADEDLGFLPGDIAEKF  131 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHHHh-cCCeeEEEEeCCCCCchhhhCcCCCCHHHHH
Confidence            34567888888888888764  48999999999999999998875311 2334444332211    10  1   1111  


Q ss_pred             --HHHHHHHHhCCCCCCCCCCCHHHHHHHH-----------HHHhcCCcE---EEEEeccCCcccccccccCCCCCCCCc
Q 042645          217 --IQESIAKKIGLYNESWDNKSFDEKAQEI-----------FKTMRNRKI---VLLLDDIWELFDLAQVGLPVPSRASAS  280 (427)
Q Consensus       217 --l~~~i~~~l~~~~~~~~~~~~~~~~~~l-----------~~~L~~k~~---LlVlDdv~~~~~~~~~~~~l~~~~~gs  280 (427)
                        .+.-+...+..-.      +.......+           ..+++++.+   +||+|++.+... ..+...+...+.+|
T Consensus       132 ~p~~~pi~D~L~~~~------~~~~~~~~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~-~~~k~~ltR~g~~s  204 (262)
T PRK10536        132 APYFRPVYDVLVRRL------GASFMQYCLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTA-AQMKMFLTRLGENV  204 (262)
T ss_pred             HHHHHHHHHHHHHHh------ChHHHHHHHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCH-HHHHHHHhhcCCCC
Confidence              1111212221000      001111111           135667654   999999987643 33333444556889


Q ss_pred             EEEEecCCh
Q 042645          281 KVVFTTREF  289 (427)
Q Consensus       281 ~IivTtR~~  289 (427)
                      ++|+|--..
T Consensus       205 k~v~~GD~~  213 (262)
T PRK10536        205 TVIVNGDIT  213 (262)
T ss_pred             EEEEeCChh
Confidence            999987654

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.93  E-value=0.00033  Score=67.62  Aligned_cols=156  Identities=25%  Similarity=0.250  Sum_probs=94.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ....+.+.|++|+|||+||..++..     ..|..+--++      ++++               .+.++......+...
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~-----S~FPFvKiiS------pe~m---------------iG~sEsaKc~~i~k~  590 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALS-----SDFPFVKIIS------PEDM---------------IGLSESAKCAHIKKI  590 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhh-----cCCCeEEEeC------hHHc---------------cCccHHHHHHHHHHH
Confidence            4567889999999999999999765     4565543322      1111               233444445555544


Q ss_pred             h----cCCcEEEEEeccCCcccccccccCCCC-------------CCCCcEEE--EecCChhHHhhcCC----Ccceecc
Q 042645          248 M----RNRKIVLLLDDIWELFDLAQVGLPVPS-------------RASASKVV--FTTREFEVCGLMDA----HKSFKVE  304 (427)
Q Consensus       248 L----~~k~~LlVlDdv~~~~~~~~~~~~l~~-------------~~~gs~Ii--vTtR~~~v~~~~~~----~~~~~l~  304 (427)
                      +    +..=-+||+||++..-+|-.+++.+.+             ...|.|.+  -||....+...|+-    ...|.++
T Consensus       591 F~DAYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vp  670 (744)
T KOG0741|consen  591 FEDAYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVP  670 (744)
T ss_pred             HHHhhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecC
Confidence            4    445579999999988888766554421             12344443  46666667666552    3568899


Q ss_pred             CCCh-HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          305 CLGY-EDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       305 ~L~~-~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      .++. ++..+.++..-.    -.+...+.++++...+|  +-..|+-+..++
T Consensus       671 nl~~~~~~~~vl~~~n~----fsd~~~~~~~~~~~~~~--~~vgIKklL~li  716 (744)
T KOG0741|consen  671 NLTTGEQLLEVLEELNI----FSDDEVRAIAEQLLSKK--VNVGIKKLLMLI  716 (744)
T ss_pred             ccCchHHHHHHHHHccC----CCcchhHHHHHHHhccc--cchhHHHHHHHH
Confidence            9987 777777776531    12334455566666666  233344444433

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.93  E-value=0.00033  Score=66.31  Aligned_cols=162  Identities=8%  Similarity=0.022  Sum_probs=87.0

Q ss_pred             cccc-chhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          149 TVVG-MQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       149 ~~vG-R~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      .++| -+..++.+.+.+..++. +...++|+.|+||||+|..+.+..... ......   .+.    .-...+.+...-.
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~-~~~~~~---~cg----~C~~c~~~~~~~h   77 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCL-ERNGVE---PCG----TCTNCKRIDSGNH   77 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCC-CCCCCC---CCC----cCHHHHHHhcCCC
Confidence            3566 67778888888877654 456899999999999999998776211 100000   000    0001111100000


Q ss_pred             C----CCCCCCCCCHHHHHHHHHHH----hcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-HHh-h
Q 042645          227 L----YNESWDNKSFDEKAQEIFKT----MRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-VCG-L  294 (427)
Q Consensus       227 ~----~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v~~-~  294 (427)
                      .    ..........++..+.+...    ..+.+=++|+|+++....  ...+...+.....++.+|++|.+.. +.. .
T Consensus        78 pD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TI  157 (329)
T PRK08058         78 PDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTI  157 (329)
T ss_pred             CCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHH
Confidence            0    00000112223332222211    234556899999976532  3344444444455677777776533 222 2


Q ss_pred             cCCCcceeccCCChHHHHHHHHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEK  318 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~  318 (427)
                      .+-...+++.+++.++..+.+...
T Consensus       158 rSRc~~i~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        158 LSRCQVVEFRPLPPESLIQRLQEE  181 (329)
T ss_pred             HhhceeeeCCCCCHHHHHHHHHHc
Confidence            233467899999999998888754

>PRK08116 hypothetical protein; Validated

Probab=97.90  E-value=4e-05  Score=70.16  Aligned_cols=101  Identities=24%  Similarity=0.220  Sum_probs=58.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      ..+.|+|.+|+|||.||..+++.+..   ....+++++      ..+++..+.......    ...+..    .+.+.+.
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~---~~~~v~~~~------~~~ll~~i~~~~~~~----~~~~~~----~~~~~l~  177 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIE---KGVPVIFVN------FPQLLNRIKSTYKSS----GKEDEN----EIIRSLV  177 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHH---cCCeEEEEE------HHHHHHHHHHHHhcc----ccccHH----HHHHHhc
Confidence            45889999999999999999999832   223455554      445666665554321    111222    2334444


Q ss_pred             CCcEEEEEeccCC--cccccc--cccCCCC-CCCCcEEEEecCC
Q 042645          250 NRKIVLLLDDIWE--LFDLAQ--VGLPVPS-RASASKVVFTTRE  288 (427)
Q Consensus       250 ~k~~LlVlDdv~~--~~~~~~--~~~~l~~-~~~gs~IivTtR~  288 (427)
                      +-. ||||||+..  ..+|..  +...+.. ...+..+|+||..
T Consensus       178 ~~d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~  220 (268)
T PRK08116        178 NAD-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNL  220 (268)
T ss_pred             CCC-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            444 899999943  334432  2222211 1245568888875

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.89  E-value=0.00065  Score=63.45  Aligned_cols=182  Identities=11%  Similarity=0.064  Sum_probs=96.3

Q ss_pred             hhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCC-c-EE--EEEEeCCCCCHHHHHHHHHHHhCCC
Q 042645          154 QSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDF-D-FV--IWEVVSRDLQLGKIQESIAKKIGLY  228 (427)
Q Consensus       154 ~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f-~-~~--~wv~~~~~~~~~~l~~~i~~~l~~~  228 (427)
                      +...+++...+..+.. ..+.++|+.|+||+++|..+++.+.-....- . +.  -++..+..+|...+.       ..+
T Consensus        10 ~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~-------~~p   82 (319)
T PRK08769         10 QRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVS-------FIP   82 (319)
T ss_pred             HHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEe-------cCC
Confidence            3456677777766654 4688999999999999999887663211000 0 00  000000001100000       000


Q ss_pred             CCCC----CCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCCh-hHH-hhc
Q 042645          229 NESW----DNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREF-EVC-GLM  295 (427)
Q Consensus       229 ~~~~----~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~~  295 (427)
                      ....    .....++ ++.+.+.+     .+++-++|+|+++....  -..+...+-....++.+|++|.+. .+. ...
T Consensus        83 ~~~~~k~~~~I~idq-IR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIr  161 (319)
T PRK08769         83 NRTGDKLRTEIVIEQ-VREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIR  161 (319)
T ss_pred             CcccccccccccHHH-HHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHH
Confidence            0000    0111222 22233322     24566999999986532  223333333334466677776653 332 222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      +-...+.+.+++.+++.+.+... +     .+   ...+..++..++|.|+....+.
T Consensus       162 SRCq~i~~~~~~~~~~~~~L~~~-~-----~~---~~~a~~~~~l~~G~p~~A~~~~  209 (319)
T PRK08769        162 SRCQRLEFKLPPAHEALAWLLAQ-G-----VS---ERAAQEALDAARGHPGLAAQWL  209 (319)
T ss_pred             hhheEeeCCCcCHHHHHHHHHHc-C-----CC---hHHHHHHHHHcCCCHHHHHHHh
Confidence            23456889999999999888764 1     11   1226678999999998665443

>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=97.89  E-value=0.0005  Score=65.52  Aligned_cols=200  Identities=15%  Similarity=0.238  Sum_probs=123.0

Q ss_pred             chhhHHHHHHHhccCCCeEEEEEecCCCcHHHHH-HHHHhhccCCCCCCcEEEEEEeCCC---CCHHHHHHHHHHHhCCC
Q 042645          153 MQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLL-TQINNSFLHTPNDFDFVIWEVVSRD---LQLGKIQESIAKKIGLY  228 (427)
Q Consensus       153 R~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~~f~~~~wv~~~~~---~~~~~l~~~i~~~l~~~  228 (427)
                      |.+..++|..||.+..-..|.|.||-|+||+.|+ .++.++.       ..++.+.|.+-   .+-..++..++.++|.-
T Consensus         1 R~e~~~~L~~wL~e~~~TFIvV~GPrGSGK~elV~d~~L~~r-------~~vL~IDC~~i~~ar~D~~~I~~lA~qvGY~   73 (431)
T PF10443_consen    1 RKEAIEQLKSWLNENPNTFIVVQGPRGSGKRELVMDHVLKDR-------KNVLVIDCDQIVKARGDAAFIKNLASQVGYF   73 (431)
T ss_pred             CchHHHHHHHHHhcCCCeEEEEECCCCCCccHHHHHHHHhCC-------CCEEEEEChHhhhccChHHHHHHHHHhcCCC
Confidence            5677899999999987789999999999999999 7776654       12666665432   34455666666666542


Q ss_pred             C-----------------------CCCCCCCHHHHHHHHHH----Hh-----------------------c---CCcEEE
Q 042645          229 N-----------------------ESWDNKSFDEKAQEIFK----TM-----------------------R---NRKIVL  255 (427)
Q Consensus       229 ~-----------------------~~~~~~~~~~~~~~l~~----~L-----------------------~---~k~~Ll  255 (427)
                      .                       .++. .+.+.....+.+    .|                       .   .++=+|
T Consensus        74 PvFsw~nSiss~IDLa~qGltGqKaGfS-es~e~Ql~~IL~~t~~ALr~ial~~~~~~~~~~~l~e~~yl~~hPe~~PVV  152 (431)
T PF10443_consen   74 PVFSWMNSISSFIDLAVQGLTGQKAGFS-ESLETQLKKILQTTATALRDIALSNRKKDDKDANLKEEDYLEAHPERRPVV  152 (431)
T ss_pred             cchHHHHHHHHHHHHHHhhccccccCCC-CChHHHHHHHHHHHHHHHHHHHHHhhhccccccccCchhhhhhCCccCCEE
Confidence            1                       1111 222222222111    11                       1   125589


Q ss_pred             EEeccCCccc-----ccc---cccCCCCCCCCcEEEEecCChhHHh----hc--CCCcceeccCCChHHHHHHHHHHhCC
Q 042645          256 LLDDIWELFD-----LAQ---VGLPVPSRASASKVVFTTREFEVCG----LM--DAHKSFKVECLGYEDAWRLFEEKVGR  321 (427)
Q Consensus       256 VlDdv~~~~~-----~~~---~~~~l~~~~~gs~IivTtR~~~v~~----~~--~~~~~~~l~~L~~~e~~~lf~~~~~~  321 (427)
                      |+|++....+     |+.   +...+..+ +=.+||++|-+.....    .+  ...+.+.|...+++.|.++...+...
T Consensus       153 VIdnF~~k~~~~~~iy~~laeWAa~Lv~~-nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~~L~~  231 (431)
T PF10443_consen  153 VIDNFLHKAEENDFIYDKLAEWAASLVQN-NIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLSQLDE  231 (431)
T ss_pred             EEcchhccCcccchHHHHHHHHHHHHHhc-CccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHHHhcc
Confidence            9999864321     111   11122222 2346777776644422    22  23467899999999999999998854


Q ss_pred             CCCC------------CC-----CCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCCh
Q 042645          322 DILD------------SH-----PDIPELAETVARECGGLPLALITVGRAMASKKAP  361 (427)
Q Consensus       322 ~~~~------------~~-----~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~  361 (427)
                      ....            .+     .....-....+...||==.=+..+++.++...++
T Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~p  288 (431)
T PF10443_consen  232 DTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGESP  288 (431)
T ss_pred             cccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCCH
Confidence            3100            00     1233446677888999999999999999886544

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 [].

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

Probab=97.88  E-value=0.00043  Score=63.83  Aligned_cols=169  Identities=18%  Similarity=0.229  Sum_probs=101.2

Q ss_pred             cccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHH
Q 042645          150 VVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGK  216 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~  216 (427)
                      +=|-++.+++|.+.+.-             +.++-|.+||++|.|||-||+.|+++-   ...|     +.+..    .+
T Consensus       153 IGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T---~AtF-----Irvvg----SE  220 (406)
T COG1222         153 IGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQT---DATF-----IRVVG----SE  220 (406)
T ss_pred             ccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhcc---CceE-----EEecc----HH
Confidence            44678888888887642             256779999999999999999999986   2333     33322    12


Q ss_pred             HHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc-CCcEEEEEeccCCccc----------------ccccccCCCC--CC
Q 042645          217 IQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR-NRKIVLLLDDIWELFD----------------LAQVGLPVPS--RA  277 (427)
Q Consensus       217 l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~-~k~~LlVlDdv~~~~~----------------~~~~~~~l~~--~~  277 (427)
                          +.+..-.        .-..++..+.+.-+ ..+++|.+|+++....                .-++...+..  ..
T Consensus       221 ----lVqKYiG--------EGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~  288 (406)
T COG1222         221 ----LVQKYIG--------EGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPR  288 (406)
T ss_pred             ----HHHHHhc--------cchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCC
Confidence                2222111        11345556666554 5789999999975311                1122222221  23


Q ss_pred             CCcEEEEecCChhHHh--hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          278 SASKVVFTTREFEVCG--LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       278 ~gs~IivTtR~~~v~~--~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ...|||..|...+...  .+.   -...|+++.-+.+.-.++|+-+...-....+-+    .+.|++.|.|.--
T Consensus       289 ~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd----~e~la~~~~g~sG  358 (406)
T COG1222         289 GNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVD----LELLARLTEGFSG  358 (406)
T ss_pred             CCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcC----HHHHHHhcCCCch
Confidence            4568888887655421  222   235678886666666678877765544333344    4666777777654

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

Probab=97.88  E-value=0.00025  Score=69.57  Aligned_cols=169  Identities=17%  Similarity=0.175  Sum_probs=97.5

Q ss_pred             ccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHH
Q 042645          149 TVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGK  216 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~  216 (427)
                      ++=|.+..+.+|.+.+..            ...+-|.+||++|+|||.||+.++++. .       +-++.++..     
T Consensus       191 diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel-~-------vPf~~isAp-----  257 (802)
T KOG0733|consen  191 DIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL-G-------VPFLSISAP-----  257 (802)
T ss_pred             hccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhc-C-------CceEeecch-----
Confidence            456788888888777642            245678999999999999999999988 2       223333322     


Q ss_pred             HHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc---cc----------cccccCC---CCC-CCC
Q 042645          217 IQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF---DL----------AQVGLPV---PSR-ASA  279 (427)
Q Consensus       217 l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~---~~----------~~~~~~l---~~~-~~g  279 (427)
                         +|....       .+.++..+.+.+.+.-..-++++++|+++...   +|          .++...+   ... ..|
T Consensus       258 ---eivSGv-------SGESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g  327 (802)
T KOG0733|consen  258 ---EIVSGV-------SGESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKG  327 (802)
T ss_pred             ---hhhccc-------CcccHHHHHHHHHHHhccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCC
Confidence               122111       23444555555556666789999999997531   11          1221111   111 112


Q ss_pred             cEEE-E--ecCChhHHhhcC----CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC
Q 042645          280 SKVV-F--TTREFEVCGLMD----AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL  344 (427)
Q Consensus       280 s~Ii-v--TtR~~~v~~~~~----~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~  344 (427)
                      -.|| |  |+|...+-..+.    -.+.|.+.--++.+-.+++...+.+-....+-+    .++|++.+-|.
T Consensus       328 ~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d----~~qlA~lTPGf  395 (802)
T KOG0733|consen  328 DPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFD----FKQLAKLTPGF  395 (802)
T ss_pred             CCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcC----HHHHHhcCCCc
Confidence            2233 3  556554422221    235677877777777777777664333222223    56666666664

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.84  E-value=0.0012  Score=61.89  Aligned_cols=177  Identities=9%  Similarity=0.033  Sum_probs=96.7

Q ss_pred             hhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC-----CC
Q 042645          155 STLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG-----LY  228 (427)
Q Consensus       155 ~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~-----~~  228 (427)
                      ...+.|.+.+..+. .....++|+.|+||+++|..++....-... ...       ..++.-...+.+...-.     +.
T Consensus         9 ~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~-~~~-------~~Cg~C~sC~~~~~g~HPD~~~i~   80 (325)
T PRK06871          9 PTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTP-QGD-------QPCGQCHSCHLFQAGNHPDFHILE   80 (325)
T ss_pred             HHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCC-CCC-------CCCCCCHHHHHHhcCCCCCEEEEc
Confidence            34556777776654 457789999999999999999877632110 000       00000011111110000     00


Q ss_pred             CCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCCh-hHH-hhcCCCc
Q 042645          229 NESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREF-EVC-GLMDAHK  299 (427)
Q Consensus       229 ~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~~~~~~  299 (427)
                      .........++.. .+.+.+     .+++=++|+|+++...  ....+...+-....++.+|++|.+. .+. ...+-..
T Consensus        81 p~~~~~I~id~iR-~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~  159 (325)
T PRK06871         81 PIDNKDIGVDQVR-EINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQ  159 (325)
T ss_pred             cccCCCCCHHHHH-HHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhce
Confidence            0000112233332 233332     2566688999998653  2334433443344566777777654 333 2223346


Q ss_pred             ceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHH
Q 042645          300 SFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLAL  348 (427)
Q Consensus       300 ~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai  348 (427)
                      .+.+.+++.+++.+.+.......        ...+...+..++|.|+.+
T Consensus       160 ~~~~~~~~~~~~~~~L~~~~~~~--------~~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        160 TWLIHPPEEQQALDWLQAQSSAE--------ISEILTALRINYGRPLLA  200 (325)
T ss_pred             EEeCCCCCHHHHHHHHHHHhccC--------hHHHHHHHHHcCCCHHHH
Confidence            78999999999999998764211        112566788899999744

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.82  E-value=0.00014  Score=68.63  Aligned_cols=105  Identities=17%  Similarity=0.150  Sum_probs=65.6

Q ss_pred             hHHHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcE-EEEEEeCC-CCCHHHHHHHHHHHhCCCCCCC
Q 042645          156 TLDRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDF-VIWEVVSR-DLQLGKIQESIAKKIGLYNESW  232 (427)
Q Consensus       156 ~~~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~-~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~~  232 (427)
                      ...++++.+.. +....+.|+|.+|+|||||++.+++...  ..+-+. ++|+.+.+ ...+.++++.+...+.......
T Consensus       119 ~~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~--~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de  196 (380)
T PRK12608        119 LSMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVA--ANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDR  196 (380)
T ss_pred             hhHhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHH--hcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCC
Confidence            34457777653 3445689999999999999999988773  223333 46666654 4578888888888766543111


Q ss_pred             CCCC---HHHHHHHHHHHh--cCCcEEEEEeccCC
Q 042645          233 DNKS---FDEKAQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       233 ~~~~---~~~~~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                      ....   .......+-+++  ++++++||+|++..
T Consensus       197 ~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr  231 (380)
T PRK12608        197 PPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTR  231 (380)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHH
Confidence            1111   111111222222  47999999999853

>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=97.80  E-value=0.00026  Score=59.59  Aligned_cols=135  Identities=13%  Similarity=0.138  Sum_probs=72.3

Q ss_pred             cchhhHHHHHHHhccCCCe-EEEEEecCCCcHHHHHHHHHhhccCCCCC-----------------CcEEEEEEeCCCCC
Q 042645          152 GMQSTLDRVWRCLTEEPVG-IVGLYGMGGVGKTTLLTQINNSFLHTPND-----------------FDFVIWEVVSRDLQ  213 (427)
Q Consensus       152 GR~~~~~~l~~~l~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~~-----------------f~~~~wv~~~~~~~  213 (427)
                      |-+...+.|.+.+..+..+ .+.++|+.|+||+++|..+++........                 .....|+.-...  
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~--   78 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKK--   78 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTS--
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccc--
Confidence            5567778888888777654 57999999999999999998876321111                 111222221111  


Q ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEec
Q 042645          214 LGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTT  286 (427)
Q Consensus       214 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTt  286 (427)
                                        ......++.. .+.+.+     .++.=++|+||++..  .....+...+-....++.+|++|
T Consensus        79 ------------------~~~i~i~~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t  139 (162)
T PF13177_consen   79 ------------------KKSIKIDQIR-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILIT  139 (162)
T ss_dssp             ------------------SSSBSHHHHH-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEE
T ss_pred             ------------------cchhhHHHHH-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEE
Confidence                              0012222222 333332     235669999999865  33444444444445678888888


Q ss_pred             CChhH--HhhcCCCcceeccCCC
Q 042645          287 REFEV--CGLMDAHKSFKVECLG  307 (427)
Q Consensus       287 R~~~v--~~~~~~~~~~~l~~L~  307 (427)
                      .+..-  .....-...+.+.+++
T Consensus       140 ~~~~~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  140 NNPSKILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             S-GGGS-HHHHTTSEEEEE----
T ss_pred             CChHHChHHHHhhceEEecCCCC
Confidence            87542  2222233455666553

...

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.80  E-value=0.0013  Score=61.45  Aligned_cols=176  Identities=10%  Similarity=0.042  Sum_probs=96.5

Q ss_pred             hhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC-----C
Q 042645          155 STLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL-----Y  228 (427)
Q Consensus       155 ~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~-----~  228 (427)
                      ...+++.+.+..+. ...+.++|+.|+||+++|..+++...-......     .++..    ...+.+...-..     .
T Consensus        10 ~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~-----~Cg~C----~sC~~~~~g~HPD~~~i~   80 (319)
T PRK06090         10 PVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSE-----ACGFC----HSCELMQSGNHPDLHVIK   80 (319)
T ss_pred             HHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCC-----CCCCC----HHHHHHHcCCCCCEEEEe
Confidence            34566666666554 457889999999999999999876531110000     00000    011111100000     0


Q ss_pred             CC-CCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCCh-hHH-hhcCCC
Q 042645          229 NE-SWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREF-EVC-GLMDAH  298 (427)
Q Consensus       229 ~~-~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~~~~~  298 (427)
                      .. .......++.. .+.+.+     .++.=++|+|+++...  ....+...+-....++.+|++|.+. .+. ...+-.
T Consensus        81 p~~~~~~I~vdqiR-~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRC  159 (319)
T PRK06090         81 PEKEGKSITVEQIR-QCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRC  159 (319)
T ss_pred             cCcCCCcCCHHHHH-HHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcc
Confidence            00 00112333332 233333     2445689999998653  3444444443334566666666654 333 333334


Q ss_pred             cceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          299 KSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       299 ~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ..+.+.+++.+++.+.+....      .+     ....+++.++|.|+....+
T Consensus       160 q~~~~~~~~~~~~~~~L~~~~------~~-----~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        160 QQWVVTPPSTAQAMQWLKGQG------IT-----VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             eeEeCCCCCHHHHHHHHHHcC------Cc-----hHHHHHHHcCCCHHHHHHH
Confidence            678999999999999887642      11     1356788999999876544

>PRK08118 topology modulation protein; Reviewed

Probab=97.80  E-value=5.9e-05  Score=63.87  Aligned_cols=36  Identities=31%  Similarity=0.533  Sum_probs=28.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEE
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIW  205 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~w  205 (427)
                      +.|.|+|++|+||||||+.+++......-+|+..+|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            358999999999999999999987333356777666

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

Probab=97.77  E-value=9.9e-05  Score=72.56  Aligned_cols=187  Identities=16%  Similarity=0.194  Sum_probs=109.9

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ++++|.+.....|.+.+..+. .......|+-|+||||+|+.++..+--...        ....+++.-...++|...-.
T Consensus        16 ~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~--------~~~ePC~~C~~Ck~I~~g~~   87 (515)
T COG2812          16 DDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENG--------PTAEPCGKCISCKEINEGSL   87 (515)
T ss_pred             HHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCC--------CCCCcchhhhhhHhhhcCCc
Confidence            457999999999999998764 345677899999999999999887621110        00111111122222322200


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCChh-H-Hhh
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREFE-V-CGL  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~  294 (427)
                      .+.   +.......++.. .|.+..     +++.=+.|+|+|+-.  ..|..+...+-........|+.|++.+ + ...
T Consensus        88 ~DviEiDaASn~gVddiR-~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TI  166 (515)
T COG2812          88 IDVIEIDAASNTGVDDIR-EIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTI  166 (515)
T ss_pred             ccchhhhhhhccChHHHH-HHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhh
Confidence            000   000111222222 222222     345569999999744  456666555543344556666666543 3 233


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      .+-...|.+..++.++....+...+...+...+   .+....|++..+|...
T Consensus       167 lSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e---~~aL~~ia~~a~Gs~R  215 (515)
T COG2812         167 LSRCQRFDFKRLDLEEIAKHLAAILDKEGINIE---EDALSLIARAAEGSLR  215 (515)
T ss_pred             hhccccccccCCCHHHHHHHHHHHHHhcCCccC---HHHHHHHHHHcCCChh
Confidence            344567999999999999999988876554333   3446677777777554

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.76  E-value=0.00032  Score=69.43  Aligned_cols=174  Identities=16%  Similarity=0.095  Sum_probs=91.6

Q ss_pred             CccccchhhHHHHHHHh---cc-------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHH
Q 042645          148 PTVVGMQSTLDRVWRCL---TE-------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l---~~-------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l  217 (427)
                      .++.|.+..++.+.+..   ..       ...+-|.++|++|+|||.+|+.+++..   ...|   +-+..+      .+
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~---~~~~---~~l~~~------~l  295 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDW---QLPL---LRLDVG------KL  295 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh---CCCE---EEEEhH------Hh
Confidence            35677776666555422   11       235679999999999999999999987   2222   111111      11


Q ss_pred             HHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----c----------cccccCCCCCCCCcEEE
Q 042645          218 QESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----L----------AQVGLPVPSRASASKVV  283 (427)
Q Consensus       218 ~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----~----------~~~~~~l~~~~~gs~Ii  283 (427)
                      ..    .       ..+.+...+.+.+...-...+++|++|+++....    .          ..+...+.....+.-||
T Consensus       296 ~~----~-------~vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vI  364 (489)
T CHL00195        296 FG----G-------IVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVV  364 (489)
T ss_pred             cc----c-------ccChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEE
Confidence            11    0       0111222222222222235899999999974311    0          01111111122233455


Q ss_pred             EecCChhH-Hhhc----CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          284 FTTREFEV-CGLM----DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       284 vTtR~~~v-~~~~----~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      .||.+... ...+    .-...+.++.-+.++-.++|+.+..........  ......+++.+.|.--
T Consensus       365 aTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~--~~dl~~La~~T~GfSG  430 (489)
T CHL00195        365 ATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWK--KYDIKKLSKLSNKFSG  430 (489)
T ss_pred             EecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCccc--ccCHHHHHhhcCCCCH
Confidence            56654332 1111    223567888889999999999887543211101  1125677777777554

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

Probab=97.75  E-value=0.00029  Score=70.51  Aligned_cols=158  Identities=19%  Similarity=0.201  Sum_probs=90.4

Q ss_pred             CCccccchhhHHHHHHHhcc------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  220 (427)
                      ..+-+|-++.+++|++.|.-      -..++++++|+||+|||+|++.+++..   ...|-.   ++++.--|..++-  
T Consensus       322 d~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al---~RkfvR---~sLGGvrDEAEIR--  393 (782)
T COG0466         322 DKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKAL---GRKFVR---ISLGGVRDEAEIR--  393 (782)
T ss_pred             cccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHh---CCCEEE---EecCccccHHHhc--
Confidence            34569999999999998841      256899999999999999999999987   333322   2333322322221  


Q ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------ccccccC-----CCC-----CCCCcE
Q 042645          221 IAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------LAQVGLP-----VPS-----RASASK  281 (427)
Q Consensus       221 i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~~~~~~~-----l~~-----~~~gs~  281 (427)
                            .+....-+.=+..+++.+.+. ..+.=+++||+++....         +-++..+     |.+     .-.=|.
T Consensus       394 ------GHRRTYIGamPGrIiQ~mkka-~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~  466 (782)
T COG0466         394 ------GHRRTYIGAMPGKIIQGMKKA-GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSK  466 (782)
T ss_pred             ------cccccccccCChHHHHHHHHh-CCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhh
Confidence                  110000111122333333322 34667899999975411         1111111     100     001133


Q ss_pred             -EEEecCCh-h-H-HhhcCCCcceeccCCChHHHHHHHHHHh
Q 042645          282 -VVFTTREF-E-V-CGLMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       282 -IivTtR~~-~-v-~~~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                       +.|||-|. + + ..++.--..|++.+.+++|=.++-+++.
T Consensus       467 VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         467 VMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             eEEEeecCccccCChHHhcceeeeeecCCChHHHHHHHHHhc
Confidence             44555442 2 1 3444555789999999999988888765

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.73  E-value=0.00032  Score=73.84  Aligned_cols=171  Identities=16%  Similarity=0.149  Sum_probs=92.8

Q ss_pred             ccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++.|.+..+++|.+.+.-             ...+.+.|+|++|+|||+||+.+++..   ...|   +.++.+      
T Consensus       179 di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~---~~~~---i~i~~~------  246 (733)
T TIGR01243       179 DIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEA---GAYF---ISINGP------  246 (733)
T ss_pred             HhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHh---CCeE---EEEecH------
Confidence            478999998888777631             234578899999999999999999876   2222   222211      


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCCCCC-CCCcE
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPVPSR-ASASK  281 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l~~~-~~gs~  281 (427)
                      ++..    ..       .......+...+.......+.+|+|||++....             ...+...+... ..+..
T Consensus       247 ~i~~----~~-------~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~v  315 (733)
T TIGR01243       247 EIMS----KY-------YGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRV  315 (733)
T ss_pred             HHhc----cc-------ccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCE
Confidence            1110    00       111122233333344456788999999865311             11121112111 22333


Q ss_pred             EEE-ecCChh-HHhhcC----CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          282 VVF-TTREFE-VCGLMD----AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       282 Iiv-TtR~~~-v~~~~~----~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ++| ||.... +...+.    -...+.+...+.++-.++++..........+.    ....+++.+.|..-
T Consensus       316 ivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~----~l~~la~~t~G~~g  382 (733)
T TIGR01243       316 IVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDV----DLDKLAEVTHGFVG  382 (733)
T ss_pred             EEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCcccc----CHHHHHHhCCCCCH
Confidence            444 443322 211111    13457788888888888888655332211111    25667788888654

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.

>PRK07261 topology modulation protein; Provisional

Probab=97.72  E-value=0.0001  Score=62.75  Aligned_cols=66  Identities=17%  Similarity=0.384  Sum_probs=41.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcC
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRN  250 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~  250 (427)
                      .|.|+|++|+||||||+.+........-+.+...|-..                       ....+.++....+.+.+.+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~   58 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPN-----------------------WQERDDDDMIADISNFLLK   58 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccc-----------------------cccCCHHHHHHHHHHHHhC
Confidence            48999999999999999998775211223444444111                       1223345666666677766


Q ss_pred             CcEEEEEeccC
Q 042645          251 RKIVLLLDDIW  261 (427)
Q Consensus       251 k~~LlVlDdv~  261 (427)
                      .+  .|+|+..
T Consensus        59 ~~--wIidg~~   67 (171)
T PRK07261         59 HD--WIIDGNY   67 (171)
T ss_pred             CC--EEEcCcc
Confidence            65  6778763

>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=97.70  E-value=0.0016  Score=61.70  Aligned_cols=41  Identities=20%  Similarity=0.397  Sum_probs=33.3

Q ss_pred             hhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          154 QSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       154 ~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      +...+.|.+.+.+   ...-+|+|.|.=|+||||+.+.+.+.+.
T Consensus         2 ~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~   45 (325)
T PF07693_consen    2 KPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEELK   45 (325)
T ss_pred             hHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4455667777765   3677999999999999999999999883

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 [].

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

Probab=97.70  E-value=0.00029  Score=73.95  Aligned_cols=158  Identities=16%  Similarity=0.151  Sum_probs=86.8

Q ss_pred             CCccccchhhHHHHHHHhcc------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  220 (427)
                      ..+.+|.+..+++|++++..      ....++.++|++|+||||+++.++...   ...|..   ++.+...+...+...
T Consensus       321 ~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l---~~~~~~---i~~~~~~d~~~i~g~  394 (784)
T PRK10787        321 DTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKAT---GRKYVR---MALGGVRDEAEIRGH  394 (784)
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHh---CCCEEE---EEcCCCCCHHHhccc
Confidence            45579999999999988752      245689999999999999999999876   222322   333333333222111


Q ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-c-----cccccCCC---------------CCCCC
Q 042645          221 IAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-L-----AQVGLPVP---------------SRASA  279 (427)
Q Consensus       221 i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-~-----~~~~~~l~---------------~~~~g  279 (427)
                      -...        .+..+..+...+...- ...-+++||+++.... .     ..+...+.               ..-.+
T Consensus       395 ~~~~--------~g~~~G~~~~~l~~~~-~~~~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~  465 (784)
T PRK10787        395 RRTY--------IGSMPGKLIQKMAKVG-VKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSD  465 (784)
T ss_pred             hhcc--------CCCCCcHHHHHHHhcC-CCCCEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCc
Confidence            1000        1111223333333221 2334788999975421 0     11111111               01123


Q ss_pred             cEEEEecCChhHH-hhcCCCcceeccCCChHHHHHHHHHHh
Q 042645          280 SKVVFTTREFEVC-GLMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       280 s~IivTtR~~~v~-~~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      .-+|.|+.+..+. ...+-...+.+.+++.+|-.++.+++.
T Consensus       466 v~~i~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        466 VMFVATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             eEEEEcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHHHhh
Confidence            3344455433221 112223568999999999998888776

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.70  E-value=0.00081  Score=70.88  Aligned_cols=171  Identities=18%  Similarity=0.162  Sum_probs=94.6

Q ss_pred             ccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++.|.+..+++|.+.+.-             ...+-+.++|++|+|||+||+.+++..   ...|     +.+..    .
T Consensus       454 di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~---~~~f-----i~v~~----~  521 (733)
T TIGR01243       454 DIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATES---GANF-----IAVRG----P  521 (733)
T ss_pred             hcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc---CCCE-----EEEeh----H
Confidence            467888777777665531             134568999999999999999999886   2222     22221    1


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--------------ccccccCCCC--CCCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--------------LAQVGLPVPS--RASA  279 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--------------~~~~~~~l~~--~~~g  279 (427)
                      +++    ...       .+.+...+...+...-...+.+|++|+++....              ...+...+..  ...+
T Consensus       522 ~l~----~~~-------vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~  590 (733)
T TIGR01243       522 EIL----SKW-------VGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSN  590 (733)
T ss_pred             HHh----hcc-------cCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCC
Confidence            111    111       112222222333333346789999999974311              0111111211  1223


Q ss_pred             cEEEEecCChhHHh--hc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          280 SKVVFTTREFEVCG--LM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       280 s~IivTtR~~~v~~--~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      .-||.||.......  .+   .-...+.++..+.++-.++|+............+    ...+++.|.|.--
T Consensus       591 v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~----l~~la~~t~g~sg  658 (733)
T TIGR01243       591 VVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVD----LEELAEMTEGYTG  658 (733)
T ss_pred             EEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCC----HHHHHHHcCCCCH
Confidence            44555665443311  11   1245678899999999999987664333222222    4667778887653

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.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.69  E-value=0.0026  Score=60.02  Aligned_cols=91  Identities=16%  Similarity=0.224  Sum_probs=56.6

Q ss_pred             CCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCC-hhHH-hhcCCCcceeccCCChHHHHHHHHHHhCCCCCC
Q 042645          250 NRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTRE-FEVC-GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILD  325 (427)
Q Consensus       250 ~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~-~~v~-~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~  325 (427)
                      ++.=++|+|+++..  .....+...+-....++.+|++|.+ ..+. ...+-...+.+.+++.++..+.+... +.    
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~-~~----  205 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQ-GV----  205 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHc-CC----
Confidence            45568999999865  3344444444444556666655555 4443 22233467899999999999999775 11    


Q ss_pred             CCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          326 SHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       326 ~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .  .    ...++..++|.|+....+
T Consensus       206 ~--~----~~~~l~~~~Gsp~~Al~~  225 (342)
T PRK06964        206 A--D----ADALLAEAGGAPLAALAL  225 (342)
T ss_pred             C--h----HHHHHHHcCCCHHHHHHH
Confidence            1  1    233577889999755433

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.66  E-value=0.0023  Score=60.47  Aligned_cols=177  Identities=10%  Similarity=0.039  Sum_probs=96.9

Q ss_pred             hhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCC--CcEE-----EEEEeCCCCCHHHHHHHHHHHhC
Q 042645          155 STLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPND--FDFV-----IWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       155 ~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~--f~~~-----~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..-+++.+.+..+. ...+.++|+.|+||+++|..++..+.-....  -.|-     -++..+..+|+..+.        
T Consensus         9 ~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~--------   80 (334)
T PRK07993          9 PDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLT--------   80 (334)
T ss_pred             HHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEe--------
Confidence            34567777776654 5678899999999999999988776311100  0000     000001111110000        


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCCh-hHH-hhcCC
Q 042645          227 LYNESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREF-EVC-GLMDA  297 (427)
Q Consensus       227 ~~~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~-~v~-~~~~~  297 (427)
                       +.........++..+ +.+.+     .+++=++|+|+++...  ....+...+-....++.+|++|.+. .+. ...+-
T Consensus        81 -p~~~~~~I~idqiR~-l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSR  158 (334)
T PRK07993         81 -PEKGKSSLGVDAVRE-VTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSR  158 (334)
T ss_pred             -cccccccCCHHHHHH-HHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhc
Confidence             000001123333332 33322     2566799999998653  2333433343334566677666653 343 22233


Q ss_pred             CcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          298 HKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       298 ~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      ...+.+.+++.+++.+.+....+.     +   .+.+..++..++|.|....
T Consensus       159 Cq~~~~~~~~~~~~~~~L~~~~~~-----~---~~~a~~~~~la~G~~~~Al  202 (334)
T PRK07993        159 CRLHYLAPPPEQYALTWLSREVTM-----S---QDALLAALRLSAGAPGAAL  202 (334)
T ss_pred             cccccCCCCCHHHHHHHHHHccCC-----C---HHHHHHHHHHcCCCHHHHH
Confidence            456899999999999888764321     1   2236778999999997443

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.64  E-value=0.0013  Score=60.17  Aligned_cols=56  Identities=25%  Similarity=0.229  Sum_probs=36.4

Q ss_pred             hhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHH
Q 042645          155 STLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       155 ~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~  218 (427)
                      ..++++..++..+  ..|.|.|++|+|||+||+.+++..   ..   ..+.++++...+..+++
T Consensus         9 ~l~~~~l~~l~~g--~~vLL~G~~GtGKT~lA~~la~~l---g~---~~~~i~~~~~~~~~dll   64 (262)
T TIGR02640         9 RVTSRALRYLKSG--YPVHLRGPAGTGKTTLAMHVARKR---DR---PVMLINGDAELTTSDLV   64 (262)
T ss_pred             HHHHHHHHHHhcC--CeEEEEcCCCCCHHHHHHHHHHHh---CC---CEEEEeCCccCCHHHHh
Confidence            3445555555543  347799999999999999998754   22   23455666555555544

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).

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.64  E-value=0.0012  Score=65.69  Aligned_cols=170  Identities=18%  Similarity=0.193  Sum_probs=93.5

Q ss_pred             ccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++=|-++.+.+|.+.+.-             ...+-|.++|+||+|||++|+.+++..   .-.|     +++..    .
T Consensus       435 dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~---~~nF-----lsvkg----p  502 (693)
T KOG0730|consen  435 DIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEA---GMNF-----LSVKG----P  502 (693)
T ss_pred             hccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhh---cCCe-----eeccC----H
Confidence            334477766666655531             256789999999999999999999987   3333     22221    1


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCCCCCCCC-cE
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPVPSRASA-SK  281 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l~~~~~g-s~  281 (427)
                      +++...           -+.++..+.+.+.+.-+--+++|.||+++....             +..+...+...... ..
T Consensus       503 EL~sk~-----------vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V  571 (693)
T KOG0730|consen  503 ELFSKY-----------VGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNV  571 (693)
T ss_pred             HHHHHh-----------cCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcE
Confidence            111111           223334444444444445779999999875311             11121222221222 22


Q ss_pred             EEE--ecCChhH-HhhcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          282 VVF--TTREFEV-CGLMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       282 Iiv--TtR~~~v-~~~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      +||  |-|...+ ...+.   ....+.+++-+.+--.++|+.++........-++    .+|++++.|.-
T Consensus       572 ~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl----~~La~~T~g~S  637 (693)
T KOG0730|consen  572 LVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDL----EELAQATEGYS  637 (693)
T ss_pred             EEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccH----HHHHHHhccCC
Confidence            333  3333333 22233   3456777777888888999998865543333344    45555555544

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

Probab=97.63  E-value=0.00036  Score=73.34  Aligned_cols=46  Identities=28%  Similarity=0.502  Sum_probs=37.3

Q ss_pred             CccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..++.+.+.+..       +  ...++.++|++|+|||+||+.+++.+
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l  508 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL  508 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHh
Confidence            4578999888888888752       1  23468899999999999999999876

>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=97.63  E-value=0.0002  Score=62.26  Aligned_cols=89  Identities=19%  Similarity=0.200  Sum_probs=53.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCC-CCCCHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNESW-DNKSFDEKAQEIFK  246 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~~-~~~~~~~~~~~l~~  246 (427)
                      ++++.++|+.|+||||.+.+++..+. ..  -..+..++... .....+-++..++.++.+.... ...++.+......+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~-~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~   77 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLK-LK--GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALE   77 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHH-HT--T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHh-hc--cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHH
Confidence            36899999999999999999888872 22  44566676543 2345667778888888653211 22344444443333


Q ss_pred             HhcCCc-EEEEEecc
Q 042645          247 TMRNRK-IVLLLDDI  260 (427)
Q Consensus       247 ~L~~k~-~LlVlDdv  260 (427)
                      .++.++ =++++|=.
T Consensus        78 ~~~~~~~D~vlIDT~   92 (196)
T PF00448_consen   78 KFRKKGYDLVLIDTA   92 (196)
T ss_dssp             HHHHTTSSEEEEEE-
T ss_pred             HHhhcCCCEEEEecC
Confidence            333333 36777765

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 ....

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.63  E-value=0.0011  Score=60.59  Aligned_cols=170  Identities=17%  Similarity=0.207  Sum_probs=101.2

Q ss_pred             CccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH-HHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL-GKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~-~~l~~~i~  222 (427)
                      ..++|-.++...+-.++..    ++...+.|+|+.|.|||+|......+.   +..-+..+-|......-. .-.++.|.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~---q~~~E~~l~v~Lng~~~~dk~al~~I~  100 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDI---QENGENFLLVRLNGELQTDKIALKGIT  100 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhH---HhcCCeEEEEEECccchhhHHHHHHHH
Confidence            4578888888888888764    566779999999999999988887774   233334444555443322 23455666


Q ss_pred             HHhCCCCCC--CCCCCHHHHHHHHHHHhc------CCcEEEEEeccCCccc-------ccccccCCCCCCCCcEEEEecC
Q 042645          223 KKIGLYNES--WDNKSFDEKAQEIFKTMR------NRKIVLLLDDIWELFD-------LAQVGLPVPSRASASKVVFTTR  287 (427)
Q Consensus       223 ~~l~~~~~~--~~~~~~~~~~~~l~~~L~------~k~~LlVlDdv~~~~~-------~~~~~~~l~~~~~gs~IivTtR  287 (427)
                      .++......  ....+..+...++...|+      +.++++|+|+++-...       +.-+...-....+=|-|-+|||
T Consensus       101 rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttr  180 (408)
T KOG2228|consen  101 RQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTR  180 (408)
T ss_pred             HHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeecc
Confidence            555332111  012233444555555554      2468999998864211       1111111112344566778999


Q ss_pred             ChhH-------HhhcCCCcceeccCCChHHHHHHHHHHhC
Q 042645          288 EFEV-------CGLMDAHKSFKVECLGYEDAWRLFEEKVG  320 (427)
Q Consensus       288 ~~~v-------~~~~~~~~~~~l~~L~~~e~~~lf~~~~~  320 (427)
                      -.-.       -........+-+++++-++-..++++...
T Consensus       181 ld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  181 LDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             ccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHhc
Confidence            7432       22222223566788899999999998873

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

Probab=97.62  E-value=0.00015  Score=64.31  Aligned_cols=35  Identities=26%  Similarity=0.391  Sum_probs=29.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEe
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVV  208 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~  208 (427)
                      .++|.|..|+|||||+..+....   ...|.++++++-
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~---~~~f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYL---RHKFDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhh---cccCCEEEEEec
Confidence            57899999999999999998877   567877776654

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

>PRK08181 transposase; Validated

Probab=97.60  E-value=0.00011  Score=67.02  Aligned_cols=105  Identities=14%  Similarity=0.167  Sum_probs=57.1

Q ss_pred             HHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHH
Q 042645          162 RCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKA  241 (427)
Q Consensus       162 ~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~  241 (427)
                      +|+..  ...+.|+|++|+|||.||..+.+...   .....++|++      ..+++..+.....       ..+.....
T Consensus       101 ~~~~~--~~nlll~Gp~GtGKTHLa~Aia~~a~---~~g~~v~f~~------~~~L~~~l~~a~~-------~~~~~~~l  162 (269)
T PRK08181        101 SWLAK--GANLLLFGPPGGGKSHLAAAIGLALI---ENGWRVLFTR------TTDLVQKLQVARR-------ELQLESAI  162 (269)
T ss_pred             HHHhc--CceEEEEecCCCcHHHHHHHHHHHHH---HcCCceeeee------HHHHHHHHHHHHh-------CCcHHHHH
Confidence            45443  34599999999999999999998762   1223445543      3456655543321       11222222


Q ss_pred             HHHHHHhcCCcEEEEEeccCCc--ccc--cccccCCCCCCCCcEEEEecCCh
Q 042645          242 QEIFKTMRNRKIVLLLDDIWEL--FDL--AQVGLPVPSRASASKVVFTTREF  289 (427)
Q Consensus       242 ~~l~~~L~~k~~LlVlDdv~~~--~~~--~~~~~~l~~~~~gs~IivTtR~~  289 (427)
                      .    .+ .+.=||||||+...  ..+  ..+...+.....+..+||||...
T Consensus       163 ~----~l-~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        163 A----KL-DKFDLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             H----HH-hcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            2    22 23459999999643  111  12222222111123588888763

>PRK04296 thymidine kinase; Provisional

Probab=97.58  E-value=6.1e-05  Score=65.34  Aligned_cols=113  Identities=17%  Similarity=0.074  Sum_probs=64.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      .++.|+|+.|.||||++..++.+..   .+...++.+.  ..++.......++..++............+....+.+ ..
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~---~~g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~   76 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYE---ERGMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EG   76 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHH---HcCCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hC
Confidence            4788999999999999999988772   2223344342  1112222234455666543322112334555555555 33


Q ss_pred             CCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCChh
Q 042645          250 NRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       250 ~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                      ++.-+||+|++.-.  ++..++...+  ...|..|++|.++..
T Consensus        77 ~~~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~~  117 (190)
T PRK04296         77 EKIDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDTD  117 (190)
T ss_pred             CCCCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCcc
Confidence            45569999998543  1122222221  245778999998844

>PRK04132 replication factor C small subunit; Provisional

Probab=97.57  E-value=0.0013  Score=68.85  Aligned_cols=157  Identities=11%  Similarity=0.004  Sum_probs=94.3

Q ss_pred             cCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEE
Q 042645          177 MGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLL  256 (427)
Q Consensus       177 ~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlV  256 (427)
                      |.++||||+|..+++++. ..+.-..++-++.+....... .++++..+....+    .            -..+.-++|
T Consensus       574 Ph~lGKTT~A~ala~~l~-g~~~~~~~lElNASd~rgid~-IR~iIk~~a~~~~----~------------~~~~~KVvI  635 (846)
T PRK04132        574 PTVLHNTTAALALARELF-GENWRHNFLELNASDERGINV-IREKVKEFARTKP----I------------GGASFKIIF  635 (846)
T ss_pred             CCcccHHHHHHHHHHhhh-cccccCeEEEEeCCCcccHHH-HHHHHHHHHhcCC----c------------CCCCCEEEE
Confidence            788999999999999872 111122456666665444443 3333333211100    0            012457999


Q ss_pred             EeccCCcc--cccccccCCCCCCCCcEEEEecCChh-HH-hhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHH
Q 042645          257 LDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-VC-GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPE  332 (427)
Q Consensus       257 lDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v~-~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~  332 (427)
                      +|+++...  ....+...+......+++|++|.+.. +. ....-...+.+.+++.++....+...+...+...+   .+
T Consensus       636 IDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i~---~e  712 (846)
T PRK04132        636 LDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELT---EE  712 (846)
T ss_pred             EECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCCC---HH
Confidence            99998763  34444444433344566777666543 22 22233467899999999999888877654332222   45


Q ss_pred             HHHHHHHHcCCCchHHHHHHHH
Q 042645          333 LAETVARECGGLPLALITVGRA  354 (427)
Q Consensus       333 ~~~~i~~~~~G~Plai~~~~~~  354 (427)
                      ....|++.|+|.+..+..+...
T Consensus       713 ~L~~Ia~~s~GDlR~AIn~Lq~  734 (846)
T PRK04132        713 GLQAILYIAEGDMRRAINILQA  734 (846)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHH
Confidence            6889999999988766554443

>PRK06526 transposase; Provisional

Probab=97.53  E-value=9.9e-05  Score=66.85  Aligned_cols=74  Identities=19%  Similarity=0.240  Sum_probs=43.1

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.|+|++|+|||+||..+.+.... . .+ .+.|+      +..+++..+.....       .....   ..+.. +
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~~-~-g~-~v~f~------t~~~l~~~l~~~~~-------~~~~~---~~l~~-l  157 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRACQ-A-GH-RVLFA------TAAQWVARLAAAHH-------AGRLQ---AELVK-L  157 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHH-C-CC-chhhh------hHHHHHHHHHHHHh-------cCcHH---HHHHH-h
Confidence            456899999999999999999887621 1 12 23332      34455555543321       11111   22222 2


Q ss_pred             cCCcEEEEEeccCCc
Q 042645          249 RNRKIVLLLDDIWEL  263 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~  263 (427)
                       .+.-|||+||+...
T Consensus       158 -~~~dlLIIDD~g~~  171 (254)
T PRK06526        158 -GRYPLLIVDEVGYI  171 (254)
T ss_pred             -ccCCEEEEcccccC
Confidence             24568999999743

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.50  E-value=0.00049  Score=69.33  Aligned_cols=46  Identities=22%  Similarity=0.282  Sum_probs=39.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..++.+...+..+....+.|+|++|+|||++|+.+++..
T Consensus        65 ~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~  110 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEA  110 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999988776666678999999999999999997643

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.48  E-value=0.0005  Score=61.45  Aligned_cols=89  Identities=21%  Similarity=0.222  Sum_probs=52.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH----hCCCCCCCCCCCHHH---H
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK----IGLYNESWDNKSFDE---K  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~----l~~~~~~~~~~~~~~---~  240 (427)
                      ...++.|+|.+|+|||+++.+++....   .....++|++.. .++...+. ++...    +.....-....+..+   .
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~~~---~~~~~v~yi~~e-~~~~~r~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVEAA---KNGKKVIYIDTE-GLSPERFK-QIAGEDFEELLSNIIIFEPSSFEEQSEA   96 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---HCCCeEEEEECC-CCCHHHHH-HHHhhChHhHhhCeEEEeCCCHHHHHHH
Confidence            457999999999999999999987762   234677888877 45544432 23222    000000001122222   3


Q ss_pred             HHHHHHHhcCCcEEEEEeccC
Q 042645          241 AQEIFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       241 ~~~l~~~L~~k~~LlVlDdv~  261 (427)
                      +..+...+..+.-++|+|.+.
T Consensus        97 i~~~~~~~~~~~~lvVIDsi~  117 (225)
T PRK09361         97 IRKAEKLAKENVGLIVLDSAT  117 (225)
T ss_pred             HHHHHHHHHhcccEEEEeCcH
Confidence            334444444677799999974

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.44  E-value=0.0012  Score=70.39  Aligned_cols=47  Identities=26%  Similarity=0.398  Sum_probs=37.9

Q ss_pred             CCccccchhhHHHHHHHhcc-------CC--CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE-------EP--VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~-------~~--~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|.+..++.+.+.+..       ++  ..++.++|+.|+|||+||+.+++..
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l  622 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM  622 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            34688999998888888752       12  2478899999999999999998876

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.44  E-value=0.00048  Score=73.17  Aligned_cols=47  Identities=26%  Similarity=0.445  Sum_probs=38.7

Q ss_pred             CCccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|.+..+..+.+.+..       +  ...++.++|++|+|||.||+.++..+
T Consensus       565 ~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l  620 (852)
T TIGR03345       565 AERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELL  620 (852)
T ss_pred             cCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            35689999999999888742       2  23478999999999999999998877

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.

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

Probab=97.43  E-value=0.0045  Score=54.74  Aligned_cols=170  Identities=15%  Similarity=0.229  Sum_probs=94.8

Q ss_pred             CccccchhhHHH---HHHHhccC------CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHH
Q 042645          148 PTVVGMQSTLDR---VWRCLTEE------PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       148 ~~~vGR~~~~~~---l~~~l~~~------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~  218 (427)
                      ++++|.+..+.+   |++.|.++      -++.|..+|++|.|||.+|+.+++..   +-.|     +.+.    ..++ 
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~---kvp~-----l~vk----at~l-  187 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA---KVPL-----LLVK----ATEL-  187 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc---CCce-----EEec----hHHH-
Confidence            357888876544   46666553      46789999999999999999999987   2222     1111    1111 


Q ss_pred             HHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCc----------ccc----cccccCCC--CCCCCcE
Q 042645          219 ESIAKKIGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWEL----------FDL----AQVGLPVP--SRASASK  281 (427)
Q Consensus       219 ~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~----------~~~----~~~~~~l~--~~~~gs~  281 (427)
                        |.+..|         +....+..+.+.- +.-+|++.+|+++..          .+.    ..+...+.  ..+.|..
T Consensus       188 --iGehVG---------dgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVv  256 (368)
T COG1223         188 --IGEHVG---------DGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVV  256 (368)
T ss_pred             --HHHHhh---------hHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceE
Confidence              111111         2233334444333 347999999998743          111    11211221  1234554


Q ss_pred             EEEecCChhHHhh-c--CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          282 VVFTTREFEVCGL-M--DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       282 IivTtR~~~v~~~-~--~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      .|-.|.+.++... .  .-...|+...-+.+|-.+++...+..-.......    .+.++++.+|+.
T Consensus       257 tIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~----~~~~~~~t~g~S  319 (368)
T COG1223         257 TIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDAD----LRYLAAKTKGMS  319 (368)
T ss_pred             EEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCccccC----HHHHHHHhCCCC
Confidence            5555555443221 1  1234577777788999999888774322111112    566777777754

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.42  E-value=0.00067  Score=67.81  Aligned_cols=155  Identities=17%  Similarity=0.117  Sum_probs=87.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC--CHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL--QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~--~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~  245 (427)
                      ..+.|.|.|+.|+|||+||+.+++.+.  +++.-++.+++++.-.  ....+++.                   +...+.
T Consensus       430 ~~~~Ill~G~~GsGKT~L~kal~~~~~--k~~~~hv~~v~Cs~l~~~~~e~iQk~-------------------l~~vfs  488 (952)
T KOG0735|consen  430 RHGNILLNGPKGSGKTNLVKALFDYYS--KDLIAHVEIVSCSTLDGSSLEKIQKF-------------------LNNVFS  488 (952)
T ss_pred             ccccEEEeCCCCCCHhHHHHHHHHHhc--cccceEEEEEechhccchhHHHHHHH-------------------HHHHHH
Confidence            345789999999999999999999983  5566667777766431  12222111                   122334


Q ss_pred             HHhcCCcEEEEEeccCCcc--------ccc-----------ccccCCCCCCCCcE--EEEecCChhH-HhhcC----CCc
Q 042645          246 KTMRNRKIVLLLDDIWELF--------DLA-----------QVGLPVPSRASASK--VVFTTREFEV-CGLMD----AHK  299 (427)
Q Consensus       246 ~~L~~k~~LlVlDdv~~~~--------~~~-----------~~~~~l~~~~~gs~--IivTtR~~~v-~~~~~----~~~  299 (427)
                      +.+.-.+-+|||||++...        +|.           ++...+  ...+.+  +|.|.....- ...+.    ...
T Consensus       489 e~~~~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y--~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~  566 (952)
T KOG0735|consen  489 EALWYAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIY--LKRNRKIAVIATGQELQTLNPLLVSPLLFQI  566 (952)
T ss_pred             HHHhhCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHH--HccCcEEEEEEechhhhhcChhhcCccceEE
Confidence            4566789999999997431        121           111111  122333  3444443221 11111    224


Q ss_pred             ceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC-chHH
Q 042645          300 SFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL-PLAL  348 (427)
Q Consensus       300 ~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~-Plai  348 (427)
                      .+.|.++...+-.++++..+....   .........-+..+|+|. |.-+
T Consensus       567 ~~~L~ap~~~~R~~IL~~~~s~~~---~~~~~~dLd~ls~~TEGy~~~DL  613 (952)
T KOG0735|consen  567 VIALPAPAVTRRKEILTTIFSKNL---SDITMDDLDFLSVKTEGYLATDL  613 (952)
T ss_pred             EEecCCcchhHHHHHHHHHHHhhh---hhhhhHHHHHHHHhcCCccchhH
Confidence            568899988888787777653222   111223345588888883 4433

>PRK12377 putative replication protein; Provisional

Probab=97.41  E-value=0.00089  Score=60.27  Aligned_cols=75  Identities=21%  Similarity=0.221  Sum_probs=46.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      +...+.|+|++|+|||+||..+++.+.   .....++++++      .+++..+-....-      .....    .+.+.
T Consensus       100 ~~~~l~l~G~~GtGKThLa~AIa~~l~---~~g~~v~~i~~------~~l~~~l~~~~~~------~~~~~----~~l~~  160 (248)
T PRK12377        100 GCTNFVFSGKPGTGKNHLAAAIGNRLL---AKGRSVIVVTV------PDVMSRLHESYDN------GQSGE----KFLQE  160 (248)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHH---HcCCCeEEEEH------HHHHHHHHHHHhc------cchHH----HHHHH
Confidence            346789999999999999999999883   22233455543      3455555444321      11111    22222


Q ss_pred             hcCCcEEEEEeccCC
Q 042645          248 MRNRKIVLLLDDIWE  262 (427)
Q Consensus       248 L~~k~~LlVlDdv~~  262 (427)
                      + .+.-||||||+..
T Consensus       161 l-~~~dLLiIDDlg~  174 (248)
T PRK12377        161 L-CKVDLLVLDEIGI  174 (248)
T ss_pred             h-cCCCEEEEcCCCC
Confidence            2 3556999999943

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.40  E-value=0.01  Score=58.73  Aligned_cols=88  Identities=18%  Similarity=0.251  Sum_probs=46.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ..+++|+|++|+||||++..++..+. .......+..++... .....+.+......++....  ...+...+...+.. 
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la-~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~--~a~d~~~L~~aL~~-  425 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFA-AQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVH--EADSAESLLDLLER-  425 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHH-HhcCCCceEEEecccccccHHHHHHHhhcccCceeE--ecCcHHHHHHHHHH-
Confidence            47899999999999999999887652 122223444454322 11122233333333443221  12233344433333 


Q ss_pred             hcCCcEEEEEeccC
Q 042645          248 MRNRKIVLLLDDIW  261 (427)
Q Consensus       248 L~~k~~LlVlDdv~  261 (427)
                      +. ..=+|++|..-
T Consensus       426 l~-~~DLVLIDTaG  438 (559)
T PRK12727        426 LR-DYKLVLIDTAG  438 (559)
T ss_pred             hc-cCCEEEecCCC
Confidence            33 34488888874

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=97.40  E-value=0.0018  Score=62.84  Aligned_cols=45  Identities=27%  Similarity=0.300  Sum_probs=35.8

Q ss_pred             ccccch---hhHHHHHHHhccC---------CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQ---STLDRVWRCLTEE---------PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~---~~~~~l~~~l~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++-|-|   .++++|++.|.++         -++-|.++|++|.|||-||+.++-..
T Consensus       305 dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  305 DVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA  361 (752)
T ss_pred             cccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc
Confidence            345655   4778888888764         24578999999999999999998776

>PRK09183 transposase/IS protein; Provisional

Probab=97.39  E-value=0.00034  Score=63.72  Aligned_cols=25  Identities=32%  Similarity=0.352  Sum_probs=21.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+.|+|++|+|||+||..+++..
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a  126 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEA  126 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHH
Confidence            3468899999999999999998775

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.39  E-value=0.00081  Score=71.84  Aligned_cols=47  Identities=28%  Similarity=0.446  Sum_probs=38.9

Q ss_pred             CCccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|.+..++.+.+.+..       +  ...++.++|++|+|||++|+.+....
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l  619 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFL  619 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            35689999999999888853       1  23578899999999999999999876

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.

>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=97.39  E-value=0.00014  Score=57.99  Aligned_cols=23  Identities=26%  Similarity=0.499  Sum_probs=21.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|++|+||||+|+.+.+.+
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999886

...

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

Probab=97.39  E-value=0.00071  Score=60.16  Aligned_cols=208  Identities=12%  Similarity=0.129  Sum_probs=118.9

Q ss_pred             cccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCC----------C----
Q 042645          150 VVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRD----------L----  212 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~----------~----  212 (427)
                      +.++++....+......++.+-..++|+.|.||-|.+..+.++.-..   +-.-+..-|.+-+..          +    
T Consensus        15 l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEi   94 (351)
T KOG2035|consen   15 LIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEI   94 (351)
T ss_pred             cccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEe
Confidence            56777777788777776778999999999999999988887776210   112223344433222          0    


Q ss_pred             -------CHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcE-EEEEeccCCc--ccccccccCCCCCCCCcEE
Q 042645          213 -------QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKI-VLLLDDIWEL--FDLAQVGLPVPSRASASKV  282 (427)
Q Consensus       213 -------~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~-LlVlDdv~~~--~~~~~~~~~l~~~~~gs~I  282 (427)
                             .-.-+.+++++......+             + +.-..++| ++|+-.+++.  +.-..++.....-...+|+
T Consensus        95 tPSDaG~~DRvViQellKevAQt~q-------------i-e~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~Rl  160 (351)
T KOG2035|consen   95 TPSDAGNYDRVVIQELLKEVAQTQQ-------------I-ETQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNCRL  160 (351)
T ss_pred             ChhhcCcccHHHHHHHHHHHHhhcc-------------h-hhccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCceE
Confidence                   011222333332221110             0 00012344 5666666543  1111121111122345777


Q ss_pred             EEecCChh-H-HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCC--
Q 042645          283 VFTTREFE-V-CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASK--  358 (427)
Q Consensus       283 ivTtR~~~-v-~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~--  358 (427)
                      |+...+.+ + ...-.-.-.++++..+++|....+.+.+...+...+   .+++.+|+++++|+-.-...+...++-+  
T Consensus       161 Il~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp---~~~l~rIa~kS~~nLRrAllmlE~~~~~n~  237 (351)
T KOG2035|consen  161 ILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLP---KELLKRIAEKSNRNLRRALLMLEAVRVNNE  237 (351)
T ss_pred             EEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCc---HHHHHHHHHHhcccHHHHHHHHHHHHhccc
Confidence            77655422 1 111112235789999999999999998876654444   6779999999999776555555554432  


Q ss_pred             --------CChHHHHHHHHHHhhc
Q 042645          359 --------KAPREWAHAIEVLRSS  374 (427)
Q Consensus       359 --------~~~~~w~~~l~~l~~~  374 (427)
                              -..-+|+-++..+...
T Consensus       238 ~~~a~~~~i~~~dWe~~i~e~a~~  261 (351)
T KOG2035|consen  238 PFTANSQVIPKPDWEIYIQEIARV  261 (351)
T ss_pred             cccccCCCCCCccHHHHHHHHHHH
Confidence                    1245899888776554

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

Probab=97.39  E-value=0.0011  Score=62.76  Aligned_cols=44  Identities=27%  Similarity=0.330  Sum_probs=36.1

Q ss_pred             cccchhhHHHHHHHhcc-CCCeE-EEEEecCCCcHHHHHHHHHhhc
Q 042645          150 VVGMQSTLDRVWRCLTE-EPVGI-VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~-~~~~v-i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|-+....++..+..+ ++.+. +.++|++|+||||+|..+++.+
T Consensus         3 ~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l   48 (325)
T COG0470           3 LVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKEL   48 (325)
T ss_pred             cccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHH
Confidence            56777788888888774 44444 9999999999999999999887

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

Probab=97.38  E-value=0.00089  Score=60.73  Aligned_cols=75  Identities=21%  Similarity=0.254  Sum_probs=47.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ...-+.++|.+|+|||.||..+.+...  .. --.+.++      +..+++..+......          ......|...
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~--~~-g~sv~f~------~~~el~~~Lk~~~~~----------~~~~~~l~~~  164 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL--KA-GISVLFI------TAPDLLSKLKAAFDE----------GRLEEKLLRE  164 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH--Hc-CCeEEEE------EHHHHHHHHHHHHhc----------CchHHHHHHH
Confidence            556799999999999999999999983  22 2344454      345677777665542          1111222222


Q ss_pred             hcCCcEEEEEeccCC
Q 042645          248 MRNRKIVLLLDDIWE  262 (427)
Q Consensus       248 L~~k~~LlVlDdv~~  262 (427)
                      + .+-=||||||+-.
T Consensus       165 l-~~~dlLIiDDlG~  178 (254)
T COG1484         165 L-KKVDLLIIDDIGY  178 (254)
T ss_pred             h-hcCCEEEEecccC
Confidence            2 2334899999864

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.38  E-value=0.00021  Score=67.10  Aligned_cols=46  Identities=24%  Similarity=0.385  Sum_probs=40.6

Q ss_pred             ccccchhhHHHHHHHhcc------CCCeEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          149 TVVGMQSTLDRVWRCLTE------EPVGIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      .++|.++.++++++++..      ...+++.|+|++|+||||||..+.+.+.
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~  103 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLE  103 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            689999999999999864      2457899999999999999999998873

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

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

Probab=97.38  E-value=0.0034  Score=61.88  Aligned_cols=152  Identities=20%  Similarity=0.226  Sum_probs=85.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ..-|.+||++|+|||-||+.|+|..   .-+|     +++..+    +++...           .+.++......++..-
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEa---g~NF-----isVKGP----ELlNkY-----------VGESErAVR~vFqRAR  601 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEA---GANF-----ISVKGP----ELLNKY-----------VGESERAVRQVFQRAR  601 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhc---cCce-----EeecCH----HHHHHH-----------hhhHHHHHHHHHHHhh
Confidence            4568899999999999999999987   3343     333322    232221           1223333333444444


Q ss_pred             cCCcEEEEEeccCCcc-------c------ccccccCCCC--CCCCcEEEEecCChhHH--hhcCC---CcceeccCCCh
Q 042645          249 RNRKIVLLLDDIWELF-------D------LAQVGLPVPS--RASASKVVFTTREFEVC--GLMDA---HKSFKVECLGY  308 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~-------~------~~~~~~~l~~--~~~gs~IivTtR~~~v~--~~~~~---~~~~~l~~L~~  308 (427)
                      ..-+|+|.||+++...       .      ..++...+..  ...|--||-.|...++.  ..+.+   ....-++.-+.
T Consensus       602 ~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~  681 (802)
T KOG0733|consen  602 ASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNA  681 (802)
T ss_pred             cCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCH
Confidence            5689999999997531       1      1222222221  22344455555443331  11222   34566788888


Q ss_pred             HHHHHHHHHHhCC--CCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          309 EDAWRLFEEKVGR--DILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       309 ~e~~~lf~~~~~~--~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      +|-.++++.....  .....+-++.+++..  .+|.|..
T Consensus       682 ~eR~~ILK~~tkn~k~pl~~dVdl~eia~~--~~c~gft  718 (802)
T KOG0733|consen  682 EERVAILKTITKNTKPPLSSDVDLDEIARN--TKCEGFT  718 (802)
T ss_pred             HHHHHHHHHHhccCCCCCCcccCHHHHhhc--ccccCCc
Confidence            9999999988763  223344555555543  3566654

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.38  E-value=0.0011  Score=58.43  Aligned_cols=90  Identities=18%  Similarity=0.190  Sum_probs=54.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh-CCCCCC---CCCCCHHH---H
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI-GLYNES---WDNKSFDE---K  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l-~~~~~~---~~~~~~~~---~  240 (427)
                      ...++.|+|++|+|||+++.+++....   .....++|++... +++..+.+. +... ......   ....+..+   .
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~---~~g~~v~yi~~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~~~~~~~~   85 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAA---RQGKKVVYIDTEG-LSPERFKQI-AEDRPERALSNFIVFEVFDFDEQGVA   85 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---hCCCeEEEEECCC-CCHHHHHHH-HHhChHHHhcCEEEEECCCHHHHHHH
Confidence            457999999999999999999887662   2346789998865 555554443 2221 000000   01122222   3


Q ss_pred             HHHHHHHhcC-CcEEEEEeccCC
Q 042645          241 AQEIFKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       241 ~~~l~~~L~~-k~~LlVlDdv~~  262 (427)
                      ...+.+.+.. +.-+||+|.+..
T Consensus        86 ~~~l~~~~~~~~~~lvVIDSis~  108 (209)
T TIGR02237        86 IQKTSKFIDRDSASLVVVDSFTA  108 (209)
T ss_pred             HHHHHHHHhhcCccEEEEeCcHH
Confidence            4445555543 566999999853

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.37  E-value=0.00026  Score=61.44  Aligned_cols=129  Identities=17%  Similarity=0.210  Sum_probs=61.6

Q ss_pred             cchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC------CCHHHH-------H
Q 042645          152 GMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD------LQLGKI-------Q  218 (427)
Q Consensus       152 GR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~------~~~~~l-------~  218 (427)
                      .+..+....++.|.  +..++.+.|++|.|||.||...+-+. -..+.++.++++.-.-+      +-+.++       +
T Consensus         4 p~~~~Q~~~~~al~--~~~~v~~~G~AGTGKT~LA~a~Al~~-v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~   80 (205)
T PF02562_consen    4 PKNEEQKFALDALL--NNDLVIVNGPAGTGKTFLALAAALEL-VKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYL   80 (205)
T ss_dssp             --SHHHHHHHHHHH--H-SEEEEE--TTSSTTHHHHHHHHHH-HHTTS-SEEEEEE-S--TT----SS---------TTT
T ss_pred             CCCHHHHHHHHHHH--hCCeEEEECCCCCcHHHHHHHHHHHH-HHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHH
Confidence            34455566666666  45689999999999999998887665 23477887777652211      111111       1


Q ss_pred             HHHHHHhCCCCCCCCCCCHHHHHHHH------HHHhcCC---cEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecC
Q 042645          219 ESIAKKIGLYNESWDNKSFDEKAQEI------FKTMRNR---KIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTR  287 (427)
Q Consensus       219 ~~i~~~l~~~~~~~~~~~~~~~~~~l------~~~L~~k---~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR  287 (427)
                      .-+...+..-.   .....+.+.+.=      ..+++|+   ..+||+|++.+.  .++..+   +...+.+|++|++--
T Consensus        81 ~p~~d~l~~~~---~~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~i---lTR~g~~skii~~GD  154 (205)
T PF02562_consen   81 RPIYDALEELF---GKEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMI---LTRIGEGSKIIITGD  154 (205)
T ss_dssp             HHHHHHHTTTS----TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHH---HTTB-TT-EEEEEE-
T ss_pred             HHHHHHHHHHh---ChHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHH---HcccCCCcEEEEecC
Confidence            11112221110   111122221100      1244553   569999999775  334444   444578899999876


Q ss_pred             Ch
Q 042645          288 EF  289 (427)
Q Consensus       288 ~~  289 (427)
                      ..
T Consensus       155 ~~  156 (205)
T PF02562_consen  155 PS  156 (205)
T ss_dssp             --
T ss_pred             ce
Confidence            53

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

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

Probab=97.36  E-value=0.00022  Score=61.02  Aligned_cols=75  Identities=25%  Similarity=0.329  Sum_probs=43.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      +..-+.|+|++|+|||.||..+.+....   .-..+.|++      ..+++..+-..    .   .........    +.
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~~~~---~g~~v~f~~------~~~L~~~l~~~----~---~~~~~~~~~----~~  105 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANEAIR---KGYSVLFIT------ASDLLDELKQS----R---SDGSYEELL----KR  105 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHHHHH---TT--EEEEE------HHHHHHHHHCC----H---CCTTHCHHH----HH
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHHhcc---CCcceeEee------cCceecccccc----c---cccchhhhc----Cc
Confidence            3457999999999999999999987732   223455654      34555554321    1   111222222    22


Q ss_pred             hcCCcEEEEEeccCCc
Q 042645          248 MRNRKIVLLLDDIWEL  263 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~  263 (427)
                      +. +.=||||||+-..
T Consensus       106 l~-~~dlLilDDlG~~  120 (178)
T PF01695_consen  106 LK-RVDLLILDDLGYE  120 (178)
T ss_dssp             HH-TSSCEEEETCTSS
T ss_pred             cc-cccEeccccccee
Confidence            32 3347889999643

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=97.35  E-value=0.00054  Score=63.84  Aligned_cols=87  Identities=16%  Similarity=0.139  Sum_probs=57.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC---CCCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES---WDNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~~~l  244 (427)
                      ..+++.|+|++|+||||||.+++....   ..-..++|+.....+++.     .+++++.....   ....+.++....+
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~---~~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~  125 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQ---KAGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIA  125 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            557999999999999999999877762   234567788776655542     34555543211   1223455566666


Q ss_pred             HHHhc-CCcEEEEEeccCC
Q 042645          245 FKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~  262 (427)
                      ...++ +..-+||+|.+-.
T Consensus       126 ~~li~~~~~~lIVIDSv~a  144 (321)
T TIGR02012       126 ETLVRSGAVDIIVVDSVAA  144 (321)
T ss_pred             HHHhhccCCcEEEEcchhh
Confidence            55554 4567999999854

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.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.35  E-value=0.0022  Score=57.32  Aligned_cols=94  Identities=17%  Similarity=0.154  Sum_probs=57.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCC---CCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTP---NDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~~  237 (427)
                      ...++.|+|++|+|||+|+.+++.......   +.-..++|++....++...+. .+....+.....       ....+.
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~   96 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVARPYNG   96 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEeCCCH
Confidence            457999999999999999999876642110   112567888887766655443 333333221100       012345


Q ss_pred             HHHHHHHHHHhc----CCcEEEEEeccCC
Q 042645          238 DEKAQEIFKTMR----NRKIVLLLDDIWE  262 (427)
Q Consensus       238 ~~~~~~l~~~L~----~k~~LlVlDdv~~  262 (427)
                      +++...+.....    .+.-|+|+|.+..
T Consensus        97 ~~~~~~l~~~~~~~~~~~~~lvVIDsis~  125 (226)
T cd01393          97 EQQLEIVEELERIMSSGRVDLVVVDSVAA  125 (226)
T ss_pred             HHHHHHHHHHHHHhhcCCeeEEEEcCcch
Confidence            566655555543    3556999999854

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.

>PRK06921 hypothetical protein; Provisional

Probab=97.35  E-value=0.00049  Score=62.92  Aligned_cols=39  Identities=28%  Similarity=0.313  Sum_probs=28.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEe
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVV  208 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~  208 (427)
                      ....+.++|.+|+|||+|+..+++...  ......++|++.
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~--~~~g~~v~y~~~  154 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELM--RKKGVPVLYFPF  154 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHh--hhcCceEEEEEH
Confidence            456799999999999999999999872  111344566553

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.35  E-value=0.0004  Score=73.90  Aligned_cols=47  Identities=23%  Similarity=0.407  Sum_probs=38.0

Q ss_pred             CCccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|.+..+..+.+.+..       +  ....+.++|+.|+|||+||+.+++.+
T Consensus       508 ~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l  563 (821)
T CHL00095        508 HKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYF  563 (821)
T ss_pred             cCcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            35689999999999888752       2  23467789999999999999999876

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.34  E-value=0.00053  Score=63.94  Aligned_cols=87  Identities=18%  Similarity=0.133  Sum_probs=57.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC---CCCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES---WDNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~~~l  244 (427)
                      ..+++-|+|++|+||||||.+++-...   ..-..++|+.....+++.     .++.++...+.   ....+.++....+
T Consensus        54 ~G~iteI~Gp~GsGKTtLal~~~~~~~---~~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~  125 (325)
T cd00983          54 KGRIIEIYGPESSGKTTLALHAIAEAQ---KLGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIA  125 (325)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---HcCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHH
Confidence            467899999999999999999876652   234567888877665542     34445443211   1223456666666


Q ss_pred             HHHhc-CCcEEEEEeccCC
Q 042645          245 FKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~  262 (427)
                      ...++ +..-+||+|.+-.
T Consensus       126 ~~li~s~~~~lIVIDSvaa  144 (325)
T cd00983         126 DSLVRSGAVDLIVVDSVAA  144 (325)
T ss_pred             HHHHhccCCCEEEEcchHh
Confidence            55554 4567999999753

RecA couples ATP hydrolysis to DNA strand exchange.

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.34  E-value=0.011  Score=59.34  Aligned_cols=197  Identities=15%  Similarity=0.116  Sum_probs=116.9

Q ss_pred             CCccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccC--CC---CCCcEEEEEEeCCCCCHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLH--TP---NDFDFVIWEVVSRDLQLGK  216 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~---~~f~~~~wv~~~~~~~~~~  216 (427)
                      |..+-+|+.+..+|-..+..     +....+-|.|.+|.|||..+..|.+.+..  ..   ..|+. +.|+.-.-..+.+
T Consensus       395 p~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~y-veINgm~l~~~~~  473 (767)
T KOG1514|consen  395 PESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDY-VEINGLRLASPRE  473 (767)
T ss_pred             cccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccE-EEEcceeecCHHH
Confidence            44567899999999888753     23458889999999999999999886631  11   23332 2334334456899


Q ss_pred             HHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc-----CCcEEEEEeccCCccc--ccccccCCC-CCCCCcEEEEecC-
Q 042645          217 IQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR-----NRKIVLLLDDIWELFD--LAQVGLPVP-SRASASKVVFTTR-  287 (427)
Q Consensus       217 l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~-----~k~~LlVlDdv~~~~~--~~~~~~~l~-~~~~gs~IivTtR-  287 (427)
                      ++..|..++....     .......+.+..++.     .+.+++++|+++....  -+-+...|. ...++|+++|.+= 
T Consensus       474 ~Y~~I~~~lsg~~-----~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~Ia  548 (767)
T KOG1514|consen  474 IYEKIWEALSGER-----VTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIA  548 (767)
T ss_pred             HHHHHHHhcccCc-----ccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEec
Confidence            9999999987532     334455555555543     4678999999875421  011111121 1245666655332 


Q ss_pred             C-hh---------HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          288 E-FE---------VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       288 ~-~~---------v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                      + .+         ++..++ ...+.+.|.++++..++...++.....-.+...+-++++++.-.|-.-.|+..
T Consensus       549 NTmdlPEr~l~nrvsSRlg-~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGDaRraldi  620 (767)
T KOG1514|consen  549 NTMDLPERLLMNRVSSRLG-LTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGDARRALDI  620 (767)
T ss_pred             ccccCHHHHhccchhhhcc-ceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccccHHHHHHH
Confidence            1 11         122221 24678889999998888888775443222223333455555555544444443

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=97.34  E-value=0.004  Score=58.62  Aligned_cols=69  Identities=9%  Similarity=0.042  Sum_probs=39.0

Q ss_pred             CCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-HHhh-cCCCcceeccCCChHHHHHHHHHH
Q 042645          250 NRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-VCGL-MDAHKSFKVECLGYEDAWRLFEEK  318 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v~~~-~~~~~~~~l~~L~~~e~~~lf~~~  318 (427)
                      +++-++|+|+++....  -..+...+.....++.+|++|.+.. +... ..-...+.+.+++.+++.+.+.+.
T Consensus       112 ~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~  184 (325)
T PRK08699        112 GGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRER  184 (325)
T ss_pred             CCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhc
Confidence            3444556788875422  2222222222223465777777644 3322 223457889999999999888664

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.33  E-value=0.00063  Score=63.44  Aligned_cols=116  Identities=26%  Similarity=0.210  Sum_probs=64.9

Q ss_pred             cchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          152 GMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       152 GR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      +|........+++..    ...+-+.|+|..|+|||.||..+++.+.  ... ..+.++++      .+++..+.....-
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~--~~g-~~v~~~~~------~~l~~~lk~~~~~  205 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELA--KKG-VSSTLLHF------PEFIRELKNSISD  205 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHH--HcC-CCEEEEEH------HHHHHHHHHHHhc
Confidence            444445545555542    2346799999999999999999999983  222 23445543      3566666555421


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc--ccccc--cccCC-CCC-CCCcEEEEecCC
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL--FDLAQ--VGLPV-PSR-ASASKVVFTTRE  288 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~--~~~~~--~~~~l-~~~-~~gs~IivTtR~  288 (427)
                             .+..+.   + +.+ .+.=||||||+...  ..|..  +...+ ... ..+..+|+||.-
T Consensus       206 -------~~~~~~---l-~~l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        206 -------GSVKEK---I-DAV-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             -------CcHHHH---H-HHh-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence                   111222   2 222 24558999999643  44532  32222 211 234557777764

>cd01394 radB RadB

Probab=97.32  E-value=0.0019  Score=57.32  Aligned_cols=89  Identities=17%  Similarity=0.115  Sum_probs=50.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh----CCCCCCCCCCCHHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI----GLYNESWDNKSFDEK---  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l----~~~~~~~~~~~~~~~---  240 (427)
                      ...++.|+|.+|+||||++.+++....   ..-..++|++....+.  +-+.+++...    ....--....+..+.   
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~---~~g~~v~yi~~e~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVETA---GQGKKVAYIDTEGLSS--ERFRQIAGDRPERAASSIIVFEPMDFNEQGRA   92 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---hcCCeEEEEECCCCCH--HHHHHHHhHChHhhhcCEEEEeCCCHHHHHHH
Confidence            467899999999999999999987762   2334677877654443  2233333221    000000011222222   


Q ss_pred             HHHHHHHhcCCcEEEEEeccC
Q 042645          241 AQEIFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       241 ~~~l~~~L~~k~~LlVlDdv~  261 (427)
                      ...+...+..+.-++|+|.+-
T Consensus        93 ~~~~~~~~~~~~~lvvIDsi~  113 (218)
T cd01394          93 IQETETFADEKVDLVVVDSAT  113 (218)
T ss_pred             HHHHHHHHhcCCcEEEEechH
Confidence            233444444456688889874

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

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

Probab=97.31  E-value=0.0019  Score=64.81  Aligned_cols=157  Identities=19%  Similarity=0.219  Sum_probs=88.1

Q ss_pred             CCccccchhhHHHHHHHhcc------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  220 (427)
                      ..+-+|.++.+++|++.+.-      -+.+++..+|++|+|||++++.++..+.   ..|-   -++++.-.|..++-..
T Consensus       410 deDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALn---RkFf---RfSvGG~tDvAeIkGH  483 (906)
T KOG2004|consen  410 DEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALN---RKFF---RFSVGGMTDVAEIKGH  483 (906)
T ss_pred             cccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhC---CceE---EEeccccccHHhhccc
Confidence            34569999999999998842      2568999999999999999999999883   2221   2344444444433211


Q ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------ccccccC----------CCCCCCCcE
Q 042645          221 IAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------LAQVGLP----------VPSRASASK  281 (427)
Q Consensus       221 i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~~~~~~~----------l~~~~~gs~  281 (427)
                      =-...        +.=+..+++.++.. +-.+=|+.||+|+....         +-++..+          +.-.-.=|+
T Consensus       484 RRTYV--------GAMPGkiIq~LK~v-~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSk  554 (906)
T KOG2004|consen  484 RRTYV--------GAMPGKIIQCLKKV-KTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSK  554 (906)
T ss_pred             ceeee--------ccCChHHHHHHHhh-CCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhh
Confidence            00011        11112233333222 23455888999975311         1111111          110011256


Q ss_pred             EEE-ecCChhH----HhhcCCCcceeccCCChHHHHHHHHHHh
Q 042645          282 VVF-TTREFEV----CGLMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       282 Iiv-TtR~~~v----~~~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      |++ .|-| .+    ..+..--..|++.+...+|-.++-.+++
T Consensus       555 VLFicTAN-~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~yL  596 (906)
T KOG2004|consen  555 VLFICTAN-VIDTIPPPLLDRMEVIELSGYVAEEKVKIAERYL  596 (906)
T ss_pred             eEEEEecc-ccccCChhhhhhhheeeccCccHHHHHHHHHHhh
Confidence            654 3333 11    1222334678999999999888777665

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

Probab=97.30  E-value=0.0008  Score=69.12  Aligned_cols=104  Identities=23%  Similarity=0.365  Sum_probs=65.0

Q ss_pred             CCccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l  217 (427)
                      ...++|.++.+..+.+.+..       +  +..+....|+.|+|||-||+.++..+   .+.-+..+-+      |+.+.
T Consensus       490 ~~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~L---fg~e~aliR~------DMSEy  560 (786)
T COG0542         490 KKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEAL---FGDEQALIRI------DMSEY  560 (786)
T ss_pred             hcceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHh---cCCCccceee------chHHH
Confidence            35689999999999998852       2  34577789999999999999999887   2222333333      33333


Q ss_pred             HH--HHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcE-EEEEeccCCc
Q 042645          218 QE--SIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKI-VLLLDDIWEL  263 (427)
Q Consensus       218 ~~--~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~-LlVlDdv~~~  263 (427)
                      ..  .+.+-+|.+ ++.-+.+.   -..|-+..+.+|| +|+||+++..
T Consensus       561 ~EkHsVSrLIGaP-PGYVGyee---GG~LTEaVRr~PySViLlDEIEKA  605 (786)
T COG0542         561 MEKHSVSRLIGAP-PGYVGYEE---GGQLTEAVRRKPYSVILLDEIEKA  605 (786)
T ss_pred             HHHHHHHHHhCCC-CCCceecc---ccchhHhhhcCCCeEEEechhhhc
Confidence            32  222223332 22122221   2345566677887 8999999853

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=97.30  E-value=0.0028  Score=65.57  Aligned_cols=148  Identities=18%  Similarity=0.128  Sum_probs=79.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      +-|.|+|++|+|||++|+.+++..   ...|   +.++.+      ++..    ..       ...........+.....
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~---~~~f---~~is~~------~~~~----~~-------~g~~~~~~~~~f~~a~~  242 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEA---KVPF---FTISGS------DFVE----MF-------VGVGASRVRDMFEQAKK  242 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHc---CCCE---EEEehH------HhHH----hh-------hcccHHHHHHHHHHHHh
Confidence            459999999999999999998876   2222   122211      1111    00       11122233333333444


Q ss_pred             CCcEEEEEeccCCccc------------c----cccccCCCC--CCCCcEEEEecCChhHHh--hc---CCCcceeccCC
Q 042645          250 NRKIVLLLDDIWELFD------------L----AQVGLPVPS--RASASKVVFTTREFEVCG--LM---DAHKSFKVECL  306 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~------------~----~~~~~~l~~--~~~gs~IivTtR~~~v~~--~~---~~~~~~~l~~L  306 (427)
                      ..+++|++|+++....            .    ..+...+..  ...+.-+|.||...+...  ..   .-...+.++..
T Consensus       243 ~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~P  322 (644)
T PRK10733        243 AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLP  322 (644)
T ss_pred             cCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCC
Confidence            5789999999976411            0    111111111  123444555666544321  11   12356788888


Q ss_pred             ChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC
Q 042645          307 GYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL  344 (427)
Q Consensus       307 ~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~  344 (427)
                      +.++-.++++.+........+.+    ...+++.+.|.
T Consensus       323 d~~~R~~Il~~~~~~~~l~~~~d----~~~la~~t~G~  356 (644)
T PRK10733        323 DVRGREQILKVHMRRVPLAPDID----AAIIARGTPGF  356 (644)
T ss_pred             CHHHHHHHHHHHhhcCCCCCcCC----HHHHHhhCCCC
Confidence            88888888888775433222222    34466667663

>PRK09354 recA recombinase A; Provisional

Probab=97.29  E-value=0.00078  Score=63.35  Aligned_cols=87  Identities=18%  Similarity=0.144  Sum_probs=58.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC---CCCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES---WDNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~~~l  244 (427)
                      ..+++-|+|++|+|||||+.+++....   ..-..++|+.....+++     ..++.++.....   ....+.++....+
T Consensus        59 ~G~IteI~G~~GsGKTtLal~~~~~~~---~~G~~~~yId~E~s~~~-----~~a~~lGvdld~lli~qp~~~Eq~l~i~  130 (349)
T PRK09354         59 RGRIVEIYGPESSGKTTLALHAIAEAQ---KAGGTAAFIDAEHALDP-----VYAKKLGVDIDNLLVSQPDTGEQALEIA  130 (349)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEECCccchHH-----HHHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            467899999999999999999887662   23456789888776665     245555543211   1223455666666


Q ss_pred             HHHhc-CCcEEEEEeccCC
Q 042645          245 FKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~  262 (427)
                      ...++ +..-+||+|.+-.
T Consensus       131 ~~li~s~~~~lIVIDSvaa  149 (349)
T PRK09354        131 DTLVRSGAVDLIVVDSVAA  149 (349)
T ss_pred             HHHhhcCCCCEEEEeChhh
Confidence            66554 4567999999853

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=97.28  E-value=0.0042  Score=63.61  Aligned_cols=174  Identities=18%  Similarity=0.216  Sum_probs=100.1

Q ss_pred             ccccchh---hHHHHHHHhccC---------CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHH
Q 042645          149 TVVGMQS---TLDRVWRCLTEE---------PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGK  216 (427)
Q Consensus       149 ~~vGR~~---~~~~l~~~l~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~  216 (427)
                      ++.|-++   ++.++++.|..+         -++=+.++|++|+|||-||+.++-.. .       +-|++++.+     
T Consensus       312 DVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA-g-------VPF~svSGS-----  378 (774)
T KOG0731|consen  312 DVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA-G-------VPFFSVSGS-----  378 (774)
T ss_pred             cccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc-C-------CceeeechH-----
Confidence            4677775   455556666553         24568999999999999999998876 1       234444432     


Q ss_pred             HHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCccc-----------------ccccccCCCCCCC
Q 042645          217 IQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFD-----------------LAQVGLPVPSRAS  278 (427)
Q Consensus       217 l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~-----------------~~~~~~~l~~~~~  278 (427)
                         +..+.+..       .. ...+..+...- ...++++.+|+++...-                 +.++...+.....
T Consensus       379 ---EFvE~~~g-------~~-asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~  447 (774)
T KOG0731|consen  379 ---EFVEMFVG-------VG-ASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFET  447 (774)
T ss_pred             ---HHHHHhcc-------cc-hHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcC
Confidence               12222211       11 23333333333 35789999999875421                 1222111211112


Q ss_pred             -CcEEEE-ecCChhHH--hhcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          279 -ASKVVF-TTREFEVC--GLMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       279 -gs~Iiv-TtR~~~v~--~~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                       +..|++ +|...++.  .++.   -+..+.++.-+...-.++|..++......  .+..++.+ |+...-|.+=|..
T Consensus       448 ~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~--~e~~dl~~-~a~~t~gf~gadl  522 (774)
T KOG0731|consen  448 SKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLD--DEDVDLSK-LASLTPGFSGADL  522 (774)
T ss_pred             CCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCC--cchhhHHH-HHhcCCCCcHHHH
Confidence             223333 44443332  1222   24567888888889999999988654422  34455566 8999999887654

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.28  E-value=0.0019  Score=58.08  Aligned_cols=94  Identities=18%  Similarity=0.196  Sum_probs=56.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCC---CCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTP---NDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~~  237 (427)
                      ...++.|+|++|+|||+|+.+++-......   +....++|++....++...+. ++++..+.....       ....+.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~   96 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLV-QIAERFGLDPEEVLDNIYVARAYNS   96 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHH-HHHHHhccChHhHhcCEEEEecCCH
Confidence            457899999999999999999975431111   113578999987766655443 344443322110       011223


Q ss_pred             HH---HHHHHHHHhc-C-CcEEEEEeccCC
Q 042645          238 DE---KAQEIFKTMR-N-RKIVLLLDDIWE  262 (427)
Q Consensus       238 ~~---~~~~l~~~L~-~-k~~LlVlDdv~~  262 (427)
                      ++   ....+...+. . +.-+||+|.+..
T Consensus        97 ~~l~~~l~~l~~~l~~~~~~~liVIDSis~  126 (235)
T cd01123          97 DHQLQLLEELEAILIESSRIKLVIVDSVTA  126 (235)
T ss_pred             HHHHHHHHHHHHHHhhcCCeeEEEEeCcHH
Confidence            33   3344444443 3 667999999854

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 .

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=97.28  E-value=0.00058  Score=56.74  Aligned_cols=117  Identities=19%  Similarity=0.147  Sum_probs=62.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC---CCCHHHHHHHHHHHhCC---CC-CCCCCCCHHH---
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR---DLQLGKIQESIAKKIGL---YN-ESWDNKSFDE---  239 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~---~~~~~~l~~~i~~~l~~---~~-~~~~~~~~~~---  239 (427)
                      ..|-|++..|.||||+|...+-+..   .+-..+.++.+-+   ......++..+- .+..   .. ..+...+..+   
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~---~~g~~v~~vQFlKg~~~~gE~~~l~~l~-~v~~~~~g~~~~~~~~~~~~~~~   78 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRAL---GHGYRVGVVQFLKGGWKYGELKALERLP-NIEIHRMGRGFFWTTENDEEDIA   78 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH---HCCCeEEEEEEeCCCCccCHHHHHHhCC-CcEEEECCCCCccCCCChHHHHH
Confidence            4688999999999999988877652   2233455544322   334444443331 1100   00 0001111222   


Q ss_pred             ----HHHHHHHHhcC-CcEEEEEeccCCc-----ccccccccCCCCCCCCcEEEEecCChh
Q 042645          240 ----KAQEIFKTMRN-RKIVLLLDDIWEL-----FDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       240 ----~~~~l~~~L~~-k~~LlVlDdv~~~-----~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                          ..+..++.+.. .-=|||||++-..     .+.+++...+.....+..+|+|.|+.+
T Consensus        79 ~a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          79 AAAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence                22223344444 4459999998543     223444444555556778999999854

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

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

Probab=97.26  E-value=0.0015  Score=67.24  Aligned_cols=154  Identities=19%  Similarity=0.324  Sum_probs=87.2

Q ss_pred             ccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccC--CCCC-CcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          149 TVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLH--TPND-FDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~~-f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      .++||+++++++++-|....-.--.++|.+|+|||+++.-++.+...  +... -+..++ +    .++..+.       
T Consensus       171 PvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~-s----LD~g~Lv-------  238 (786)
T COG0542         171 PVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIY-S----LDLGSLV-------  238 (786)
T ss_pred             CCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEE-E----ecHHHHh-------
Confidence            47999999999999998654344557899999999999888877621  1111 111111 0    1111111       


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhc-CCcEEEEEeccCCccc--------c--cc-cccCCCCCCCCcEEEEecCChhH--
Q 042645          226 GLYNESWDNKSFDEKAQEIFKTMR-NRKIVLLLDDIWELFD--------L--AQ-VGLPVPSRASASKVVFTTREFEV--  291 (427)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~l~~~L~-~k~~LlVlDdv~~~~~--------~--~~-~~~~l~~~~~gs~IivTtR~~~v--  291 (427)
                      .  ... -..+.++..+.+.+.++ .++.+|++|.++..-.        .  .. +.+.|.. +.-..|-.||-++--  
T Consensus       239 A--Gak-yRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLAR-GeL~~IGATT~~EYRk~  314 (786)
T COG0542         239 A--GAK-YRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALAR-GELRCIGATTLDEYRKY  314 (786)
T ss_pred             c--ccc-ccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHhc-CCeEEEEeccHHHHHHH
Confidence            0  111 22344555555555554 4589999999975411        1  11 1222222 222235555554321  


Q ss_pred             ----HhhcCCCcceeccCCChHHHHHHHHHH
Q 042645          292 ----CGLMDAHKSFKVECLGYEDAWRLFEEK  318 (427)
Q Consensus       292 ----~~~~~~~~~~~l~~L~~~e~~~lf~~~  318 (427)
                          +.+-.-.+.+.++..+.+++..+++..
T Consensus       315 iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGl  345 (786)
T COG0542         315 IEKDAALERRFQKVLVDEPSVEDTIAILRGL  345 (786)
T ss_pred             hhhchHHHhcCceeeCCCCCHHHHHHHHHHH
Confidence                111123367889999999999988754

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.22  E-value=0.00085  Score=63.08  Aligned_cols=100  Identities=20%  Similarity=0.264  Sum_probs=53.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      ..+.++|++|+|||+||..+++...   ..-..+++++.      .+++..+...-. .    ...+...   . .+.+.
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~---~~g~~V~y~t~------~~l~~~l~~~~~-~----~~~~~~~---~-~~~l~  245 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELL---DRGKSVIYRTA------DELIEILREIRF-N----NDKELEE---V-YDLLI  245 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHH---HCCCeEEEEEH------HHHHHHHHHHHh-c----cchhHHH---H-HHHhc
Confidence            6799999999999999999999873   22234566543      344444433211 0    0111111   1 22232


Q ss_pred             CCcEEEEEeccCCc--ccc--cccccCCCCC-CCCcEEEEecCC
Q 042645          250 NRKIVLLLDDIWEL--FDL--AQVGLPVPSR-ASASKVVFTTRE  288 (427)
Q Consensus       250 ~k~~LlVlDdv~~~--~~~--~~~~~~l~~~-~~gs~IivTtR~  288 (427)
                       .-=||||||+...  ..|  ..+...+... ..+..+||||..
T Consensus       246 -~~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl  288 (329)
T PRK06835        246 -NCDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNL  288 (329)
T ss_pred             -cCCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence             2248999999543  222  2222222211 224558888875

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.20  E-value=0.15  Score=49.06  Aligned_cols=167  Identities=20%  Similarity=0.227  Sum_probs=86.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      |--.++||||.|||+++.++++.+     .|+.. =+.++...+-.+ ++.++.                       .. 
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L-----~ydIy-dLeLt~v~~n~d-Lr~LL~-----------------------~t-  284 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYL-----NYDIY-DLELTEVKLDSD-LRHLLL-----------------------AT-  284 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhc-----CCceE-EeeeccccCcHH-HHHHHH-----------------------hC-
Confidence            457899999999999999999987     23321 112221111111 222211                       11 


Q ss_pred             CCcEEEEEeccCCcccc-----------c---------ccccCCC---CCCCCcEEE-EecCChhH--HhhcCC---Ccc
Q 042645          250 NRKIVLLLDDIWELFDL-----------A---------QVGLPVP---SRASASKVV-FTTREFEV--CGLMDA---HKS  300 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~~-----------~---------~~~~~l~---~~~~gs~Ii-vTtR~~~v--~~~~~~---~~~  300 (427)
                      ..+-+||+.|++...+.           .         .+...+.   ..+.+-||| .||...+-  ..++.+   ...
T Consensus       285 ~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmh  364 (457)
T KOG0743|consen  285 PNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMH  364 (457)
T ss_pred             CCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeE
Confidence            34567778887643111           1         0111111   112223555 56655432  112222   245


Q ss_pred             eeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCC--ChHHHHHHHHHHhh
Q 042645          301 FKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKK--APREWAHAIEVLRS  373 (427)
Q Consensus       301 ~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~--~~~~w~~~l~~l~~  373 (427)
                      +.+.--+.+....|+.+..+.+.  .+    .+..+|.+...|.-+.=..++..|-.+.  .....+.+.+.|.+
T Consensus       365 I~mgyCtf~~fK~La~nYL~~~~--~h----~L~~eie~l~~~~~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~~  433 (457)
T KOG0743|consen  365 IYMGYCTFEAFKTLASNYLGIEE--DH----RLFDEIERLIEETEVTPAQVAEELMKNKNDADVALKGLVEALES  433 (457)
T ss_pred             EEcCCCCHHHHHHHHHHhcCCCC--Cc----chhHHHHHHhhcCccCHHHHHHHHhhccccHHHHHHHHHHHHHh
Confidence            78999999999999999987543  12    2356666655665554455554443333  22333344444433

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=97.20  E-value=0.0031  Score=62.93  Aligned_cols=53  Identities=26%  Similarity=0.417  Sum_probs=40.0

Q ss_pred             cccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEE
Q 042645          150 VVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEV  207 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~  207 (427)
                      ++--.+.++++.+||..     ...+++.++|++|+||||.++.+++.+     .|+..=|.+
T Consensus        21 LavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~el-----g~~v~Ew~n   78 (519)
T PF03215_consen   21 LAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKEL-----GFEVQEWIN   78 (519)
T ss_pred             hhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHh-----CCeeEEecC
Confidence            44445677888888864     235789999999999999999999886     355566754

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

Probab=97.19  E-value=0.0011  Score=66.46  Aligned_cols=73  Identities=26%  Similarity=0.290  Sum_probs=53.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      .-++..++|++|+||||||..++++.    +  ..++=++.|..-+...+-..|...+....                 .
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqa----G--YsVvEINASDeRt~~~v~~kI~~avq~~s-----------------~  381 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQA----G--YSVVEINASDERTAPMVKEKIENAVQNHS-----------------V  381 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhc----C--ceEEEecccccccHHHHHHHHHHHHhhcc-----------------c
Confidence            45799999999999999999999886    1  24567788877777766666665553221                 1


Q ss_pred             h--cCCcEEEEEeccCCc
Q 042645          248 M--RNRKIVLLLDDIWEL  263 (427)
Q Consensus       248 L--~~k~~LlVlDdv~~~  263 (427)
                      +  .+++.-||+|+++..
T Consensus       382 l~adsrP~CLViDEIDGa  399 (877)
T KOG1969|consen  382 LDADSRPVCLVIDEIDGA  399 (877)
T ss_pred             cccCCCcceEEEecccCC
Confidence            2  157888999999753

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.18  E-value=0.0025  Score=57.32  Aligned_cols=76  Identities=18%  Similarity=0.242  Sum_probs=46.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ...+.++|.+|+|||+|+..+++.+..   .-..+++++      ..+++..+-.....     ...+...    +.+.+
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~---~g~~v~~it------~~~l~~~l~~~~~~-----~~~~~~~----~l~~l  160 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLL---RGKSVLIIT------VADIMSAMKDTFSN-----SETSEEQ----LLNDL  160 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEE------HHHHHHHHHHHHhh-----ccccHHH----HHHHh
Confidence            357899999999999999999998832   223455553      45566555544321     1112222    33334


Q ss_pred             cCCcEEEEEeccCCc
Q 042645          249 RNRKIVLLLDDIWEL  263 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~  263 (427)
                      . +.=||||||+...
T Consensus       161 ~-~~dlLvIDDig~~  174 (244)
T PRK07952        161 S-NVDLLVIDEIGVQ  174 (244)
T ss_pred             c-cCCEEEEeCCCCC
Confidence            4 3448888999653

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.17  E-value=0.003  Score=52.87  Aligned_cols=39  Identities=23%  Similarity=0.376  Sum_probs=29.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL  212 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~  212 (427)
                      ++.|+|++|+||||++..+.....   ..-..++|+......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~---~~~~~v~~~~~e~~~   39 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIA---TKGGKVVYVDIEEEI   39 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHH---hcCCEEEEEECCcch
Confidence            368999999999999999988872   244567777765543

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.16  E-value=0.0027  Score=59.40  Aligned_cols=94  Identities=15%  Similarity=0.192  Sum_probs=58.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-------CCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW-------DNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~-------~~~~~  237 (427)
                      ...++-|+|++|+|||+|+.+++-.....   ...-..++|++....+++..+. ++++.++......       ...+.
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d~~~~l~~i~~~~~~~~  173 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVDPDAVLDNILYARAYTS  173 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCChHHhcCcEEEecCCCH
Confidence            45789999999999999998876433111   1223478999988888888765 4566666542210       11233


Q ss_pred             HHHHH---HHHHHhc-CCcEEEEEeccCC
Q 042645          238 DEKAQ---EIFKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       238 ~~~~~---~l~~~L~-~k~~LlVlDdv~~  262 (427)
                      ++..+   .+...+. .+.-|||+|.+-.
T Consensus       174 e~~~~~l~~l~~~i~~~~~~LvVIDSisa  202 (313)
T TIGR02238       174 EHQMELLDYLAAKFSEEPFRLLIVDSIMA  202 (313)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEEcchH
Confidence            43333   3333333 3555899999753

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.16  E-value=0.00056  Score=59.74  Aligned_cols=110  Identities=15%  Similarity=0.149  Sum_probs=59.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH-HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG-KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~-~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      .+|.|.|+.|+||||++..+.....   ......++. +..+.... .-...+..+-.      ...+.....+.+...+
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~---~~~~~~i~t-~e~~~E~~~~~~~~~i~q~~------vg~~~~~~~~~i~~aL   71 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYIN---KNKTHHILT-IEDPIEFVHESKRSLINQRE------VGLDTLSFENALKAAL   71 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhh---hcCCcEEEE-EcCCccccccCccceeeecc------cCCCccCHHHHHHHHh
Confidence            4789999999999999998887762   222323332 21111100 00000111100      1112233455667777


Q ss_pred             cCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHH
Q 042645          249 RNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVC  292 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~  292 (427)
                      +..+=++++|++.+.+.........   ..|..++.|+...+..
T Consensus        72 r~~pd~ii~gEird~e~~~~~l~~a---~~G~~v~~t~Ha~~~~  112 (198)
T cd01131          72 RQDPDVILVGEMRDLETIRLALTAA---ETGHLVMSTLHTNSAA  112 (198)
T ss_pred             cCCcCEEEEcCCCCHHHHHHHHHHH---HcCCEEEEEecCCcHH
Confidence            7778899999997665443322221   2355677777766554

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.

>PRK06696 uridine kinase; Validated

Probab=97.15  E-value=0.00061  Score=60.79  Aligned_cols=42  Identities=14%  Similarity=0.202  Sum_probs=35.3

Q ss_pred             cchhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          152 GMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       152 GR~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|++.+++|.+.+..   +...+|+|.|.+|+||||||+.+.+.+
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l   46 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEI   46 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            366777888887753   467899999999999999999999887

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

Probab=97.15  E-value=0.00069  Score=62.64  Aligned_cols=136  Identities=18%  Similarity=0.263  Sum_probs=73.1

Q ss_pred             ccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEE-E---EEeCCCC---------CHHHH
Q 042645          151 VGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVI-W---EVVSRDL---------QLGKI  217 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~-w---v~~~~~~---------~~~~l  217 (427)
                      -+|..+..--+++|.++....|.+.|.+|.|||-||....-..--.+..|..++ .   +.++++.         .+.-.
T Consensus       227 ~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG~eEeKm~PW  306 (436)
T COG1875         227 RPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPGTEEEKMGPW  306 (436)
T ss_pred             CcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCCchhhhccch
Confidence            456677777788999999999999999999999887654322111223333322 1   1122221         11112


Q ss_pred             HHHHHHHhCCCCCCCCCCCHHHHHHHHH----------HHhcCC---cEEEEEeccCCcccccccccCCCCCCCCcEEEE
Q 042645          218 QESIAKKIGLYNESWDNKSFDEKAQEIF----------KTMRNR---KIVLLLDDIWELFDLAQVGLPVPSRASASKVVF  284 (427)
Q Consensus       218 ~~~i~~~l~~~~~~~~~~~~~~~~~~l~----------~~L~~k---~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~Iiv  284 (427)
                      +..|...+..-... .... +..++.+.          .+.+|+   .-++|+|++.+..- .++...+...+.||||+.
T Consensus       307 mq~i~DnLE~L~~~-~~~~-~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTp-heikTiltR~G~GsKIVl  383 (436)
T COG1875         307 MQAIFDNLEVLFSP-NEPG-DRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTP-HELKTILTRAGEGSKIVL  383 (436)
T ss_pred             HHHHHhHHHHHhcc-cccc-hHHHHHHHhccceeeeeeeeecccccccceEEEehhhccCH-HHHHHHHHhccCCCEEEE
Confidence            22332222111100 1111 22222221          133443   45999999987522 233344556688999999


Q ss_pred             ecCCh
Q 042645          285 TTREF  289 (427)
Q Consensus       285 TtR~~  289 (427)
                      |.-..
T Consensus       384 ~gd~a  388 (436)
T COG1875         384 TGDPA  388 (436)
T ss_pred             cCCHH
Confidence            87543

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.15  E-value=0.0028  Score=57.05  Aligned_cols=89  Identities=17%  Similarity=0.169  Sum_probs=55.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------------
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES----------------  231 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~----------------  231 (427)
                      ...++.|.|++|+|||+++.++.....   ..-..++|++...  ++.++.+.+. +++.+...                
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~---~~ge~~lyvs~ee--~~~~i~~~~~-~~g~~~~~~~~~g~l~~~d~~~~~   93 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGL---QMGEPGIYVALEE--HPVQVRRNMA-QFGWDVRKYEEEGKFAIVDAFTGG   93 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH---HcCCcEEEEEeeC--CHHHHHHHHH-HhCCCHHHHhhcCCEEEEeccccc
Confidence            567899999999999999998765541   2345678888754  4555555533 33321100                


Q ss_pred             ------------CCCCCHHHHHHHHHHHhcC-CcEEEEEeccCC
Q 042645          232 ------------WDNKSFDEKAQEIFKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       232 ------------~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~~  262 (427)
                                  ....+.++....+.+.++. +.-++|+|.+..
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSls~  137 (237)
T TIGR03877        94 IGEAAEREKYVVKDPTDVRELIDVLRQAIRDINAKRVVIDSVTT  137 (237)
T ss_pred             cccccccccccccCcccHHHHHHHHHHHHHHhCCCEEEEcChhH
Confidence                        0123455666666666543 445799999854

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.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.12  E-value=0.0019  Score=58.84  Aligned_cols=83  Identities=18%  Similarity=0.192  Sum_probs=51.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccC-CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLH-TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      -++|.++||||.|||+|++.+++++.- ..+.+....-+.++.    ..++..-...        .+.-...+.++|.+.
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins----hsLFSKWFsE--------SgKlV~kmF~kI~EL  244 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS----HSLFSKWFSE--------SGKLVAKMFQKIQEL  244 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh----hHHHHHHHhh--------hhhHHHHHHHHHHHH
Confidence            478999999999999999999998831 123333333333322    2233222221        233445666777777


Q ss_pred             hcCCcE--EEEEeccCCc
Q 042645          248 MRNRKI--VLLLDDIWEL  263 (427)
Q Consensus       248 L~~k~~--LlVlDdv~~~  263 (427)
                      +.++..  .+.+|+|++.
T Consensus       245 v~d~~~lVfvLIDEVESL  262 (423)
T KOG0744|consen  245 VEDRGNLVFVLIDEVESL  262 (423)
T ss_pred             HhCCCcEEEEEeHHHHHH
Confidence            776553  5568998753

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

Probab=97.12  E-value=0.0011  Score=69.29  Aligned_cols=46  Identities=28%  Similarity=0.458  Sum_probs=37.8

Q ss_pred             CccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.++.++.|.+.+..       +  ....+.++|++|+|||++|+.++..+
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l  512 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999888752       1  24578999999999999999998876

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=97.11  E-value=0.0014  Score=61.42  Aligned_cols=27  Identities=22%  Similarity=0.327  Sum_probs=24.6

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+..++|||++|+|||.+|+.+++..
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~el  172 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKM  172 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHc
Confidence            356789999999999999999999998

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.10  E-value=0.0034  Score=61.28  Aligned_cols=89  Identities=24%  Similarity=0.215  Sum_probs=49.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCC-CCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNESW-DNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~~-~~~~~~~~~~~l~  245 (427)
                      ...+|.++|.+|+||||++..++..+. ..+ + .+..+++.. .+...+.+..++..++.+.... ...++........
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~-~~g-~-kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al  170 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFK-KKG-L-KVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGL  170 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH-HcC-C-eEEEecCCCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHH
Confidence            357899999999999999999998873 222 2 334444332 1223455666666666543211 1223333333333


Q ss_pred             HHhcCCcEEEEEecc
Q 042645          246 KTMRNRKIVLLLDDI  260 (427)
Q Consensus       246 ~~L~~k~~LlVlDdv  260 (427)
                      +.+.+. -+||+|..
T Consensus       171 ~~~~~~-DvVIIDTA  184 (437)
T PRK00771        171 EKFKKA-DVIIVDTA  184 (437)
T ss_pred             HHhhcC-CEEEEECC
Confidence            333333 45777765

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.09  E-value=0.0028  Score=60.69  Aligned_cols=86  Identities=20%  Similarity=0.300  Sum_probs=52.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ...++.|.|.+|+|||||+.+++....   .....++|++....  ..++ ..-+..++...+..   ...+.+.+.+.+
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~~a---~~g~~VlYvs~EEs--~~qi-~~Ra~rlg~~~~~l~l~~e~~le~I~~~i  154 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAARLA---KRGGKVLYVSGEES--PEQI-KLRADRLGISTENLYLLAETNLEDILASI  154 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH---hcCCeEEEEECCcC--HHHH-HHHHHHcCCCcccEEEEccCcHHHHHHHH
Confidence            456899999999999999999988762   22346777776433  3333 22244555433221   122334443333


Q ss_pred             HHHhcCCcEEEEEeccCC
Q 042645          245 FKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~~k~~LlVlDdv~~  262 (427)
                      .   ..++-+||+|.+..
T Consensus       155 ~---~~~~~lVVIDSIq~  169 (372)
T cd01121         155 E---ELKPDLVIIDSIQT  169 (372)
T ss_pred             H---hcCCcEEEEcchHH
Confidence            2   24677999999854

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.08  E-value=0.0042  Score=55.84  Aligned_cols=88  Identities=15%  Similarity=0.200  Sum_probs=57.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------------
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES----------------  231 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~----------------  231 (427)
                      ...++.|+|.+|+|||+|+.++.....   ..-..++|++..+.  +.++.+.+ .+++.....                
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~---~~g~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~   97 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGAL---KQGKKVYVITTENT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEG   97 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHH---hCCCEEEEEEcCCC--HHHHHHHH-HHCCCChhHHHhCCCceEEeccccc
Confidence            467899999999999999999865541   23457788887653  45555553 334322110                


Q ss_pred             --CCCCCHHHHHHHHHHHhcC-CcEEEEEeccC
Q 042645          232 --WDNKSFDEKAQEIFKTMRN-RKIVLLLDDIW  261 (427)
Q Consensus       232 --~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~  261 (427)
                        ....+.+.+...+.+.+.. +.-++|+|.+-
T Consensus        98 ~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         98 FEWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             cccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence              0122345666777776654 66689999975

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=97.07  E-value=0.013  Score=55.35  Aligned_cols=44  Identities=16%  Similarity=0.197  Sum_probs=33.4

Q ss_pred             cccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          150 VVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|+...+.++.+.+..  ....-|.|+|..|+||+++|+.+.+.-
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s   46 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLS   46 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhc
Confidence            46777777777666643  333458999999999999999997665

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

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

Probab=97.06  E-value=0.033  Score=52.21  Aligned_cols=49  Identities=27%  Similarity=0.235  Sum_probs=36.3

Q ss_pred             ceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHH
Q 042645          300 SFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLAL  348 (427)
Q Consensus       300 ~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai  348 (427)
                      .+++++++.+|+..++.-.....-.......+...+++.-..+|+|.-+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el  306 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPREL  306 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHh
Confidence            7899999999999999887754432332444556777777889999644

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).

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=97.06  E-value=0.061  Score=51.46  Aligned_cols=58  Identities=16%  Similarity=0.189  Sum_probs=39.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC-CCCCHHHHHHHHHHHhCCCC
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS-RDLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~-~~~~~~~l~~~i~~~l~~~~  229 (427)
                      +.+|..+|.-|+||||.+.++++.+.. .+  ..+.-|++. ..+...+-++.+..+.+.+.
T Consensus       100 P~vImmvGLQGsGKTTt~~KLA~~lkk-~~--~kvllVaaD~~RpAA~eQL~~La~q~~v~~  158 (451)
T COG0541         100 PTVILMVGLQGSGKTTTAGKLAKYLKK-KG--KKVLLVAADTYRPAAIEQLKQLAEQVGVPF  158 (451)
T ss_pred             CeEEEEEeccCCChHhHHHHHHHHHHH-cC--CceEEEecccCChHHHHHHHHHHHHcCCce
Confidence            468999999999999999999998832 22  223333322 22344556777778877654

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

Probab=97.06  E-value=0.0027  Score=55.43  Aligned_cols=46  Identities=26%  Similarity=0.456  Sum_probs=37.2

Q ss_pred             CccccchhhHHHHHHHh----ccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCL----TEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l----~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|-+...+.|++--    ......-|.+||.-|+|||+|++.+.+.+
T Consensus        60 ~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~  109 (287)
T COG2607          60 ADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEY  109 (287)
T ss_pred             HHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHH
Confidence            45789888888876543    33456679999999999999999999988

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=97.05  E-value=0.0041  Score=62.58  Aligned_cols=131  Identities=20%  Similarity=0.146  Sum_probs=75.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ..+.+.++|++|.|||.||+.+++..   ..+|-.+..     .    +++    ...       -..+...+...+...
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~---~~~fi~v~~-----~----~l~----sk~-------vGesek~ir~~F~~A  331 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALES---RSRFISVKG-----S----ELL----SKW-------VGESEKNIRELFEKA  331 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHhhC---CCeEEEeeC-----H----HHh----ccc-------cchHHHHHHHHHHHH
Confidence            45589999999999999999999965   333433221     1    111    110       122333344444455


Q ss_pred             hcCCcEEEEEeccCCccccc-------------ccccCCCC--CCCCcEEEEecCChhHHh---hc--CCCcceeccCCC
Q 042645          248 MRNRKIVLLLDDIWELFDLA-------------QVGLPVPS--RASASKVVFTTREFEVCG---LM--DAHKSFKVECLG  307 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~~~~~-------------~~~~~l~~--~~~gs~IivTtR~~~v~~---~~--~~~~~~~l~~L~  307 (427)
                      .+..+++|.+|+++....+.             ++...+..  ...+..||-||.......   ..  .-...+.+++-+
T Consensus       332 ~~~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd  411 (494)
T COG0464         332 RKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPD  411 (494)
T ss_pred             HcCCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCC
Confidence            56789999999997642221             11112221  122223344444332211   11  224578899999


Q ss_pred             hHHHHHHHHHHhCC
Q 042645          308 YEDAWRLFEEKVGR  321 (427)
Q Consensus       308 ~~e~~~lf~~~~~~  321 (427)
                      .++..+.|+.+...
T Consensus       412 ~~~r~~i~~~~~~~  425 (494)
T COG0464         412 LEERLEIFKIHLRD  425 (494)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999998864

>TIGR01817 nifA Nif-specific regulatory protein

Probab=97.05  E-value=0.012  Score=59.88  Aligned_cols=47  Identities=19%  Similarity=0.208  Sum_probs=38.7

Q ss_pred             CCccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|....+.++.+.+..  .....|.|+|..|+|||++|+.+.+..
T Consensus       195 ~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s  243 (534)
T TIGR01817       195 EDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLS  243 (534)
T ss_pred             cCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhC
Confidence            35789999999998887753  334468899999999999999998765

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.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.04  E-value=0.0013  Score=56.27  Aligned_cols=36  Identities=22%  Similarity=0.361  Sum_probs=27.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEE
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWE  206 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv  206 (427)
                      ...+|.+.|++|+||||+|+.+++.+   ...+...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l---~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERL---KLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHH---HHcCCcEEEE
Confidence            34689999999999999999999888   2334444444

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=97.03  E-value=0.0029  Score=57.54  Aligned_cols=93  Identities=20%  Similarity=0.219  Sum_probs=57.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~~  237 (427)
                      ...+.=|+|++|+|||.|+.+++-...-   ..+.-..++|++-...+....+. +|++..+.....       ....+.
T Consensus        37 ~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~  115 (256)
T PF08423_consen   37 TGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDL  115 (256)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSH
T ss_pred             CCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCH
Confidence            4568899999999999999887644311   12234578999988888877765 566665432110       012344


Q ss_pred             HHHHHHHH---HHhc-CCcEEEEEeccC
Q 042645          238 DEKAQEIF---KTMR-NRKIVLLLDDIW  261 (427)
Q Consensus       238 ~~~~~~l~---~~L~-~k~~LlVlDdv~  261 (427)
                      +++...+.   ..+. .+--|||+|.+-
T Consensus       116 ~~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  116 EELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHHhhccccceEEEEecchH
Confidence            44444333   3332 455599999974

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.02  E-value=0.00081  Score=56.88  Aligned_cols=81  Identities=15%  Similarity=0.175  Sum_probs=45.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcC
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRN  250 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~  250 (427)
                      ++.|.|.+|+|||++|.++....      ...++++.-...++. ++...|...-....   ......+....+.+.+..
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~~------~~~~~y~at~~~~d~-em~~rI~~H~~~R~---~~w~t~E~~~~l~~~l~~   70 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAEL------GGPVTYIATAEAFDD-EMAERIARHRKRRP---AHWRTIETPRDLVSALKE   70 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHhc------CCCeEEEEccCcCCH-HHHHHHHHHHHhCC---CCceEeecHHHHHHHHHh
Confidence            36899999999999999997542      235666666666554 34444443222112   122222333334444421


Q ss_pred             --CcEEEEEeccC
Q 042645          251 --RKIVLLLDDIW  261 (427)
Q Consensus       251 --k~~LlVlDdv~  261 (427)
                        +.-.+++|.+-
T Consensus        71 ~~~~~~VLIDclt   83 (169)
T cd00544          71 LDPGDVVLIDCLT   83 (169)
T ss_pred             cCCCCEEEEEcHh
Confidence              34479999873

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.

>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=97.02  E-value=0.0027  Score=54.10  Aligned_cols=89  Identities=17%  Similarity=0.111  Sum_probs=45.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCC-CCCCCCHHHHHH-HHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNE-SWDNKSFDEKAQ-EIFKT  247 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~-~~~~~~~~~~~~-~l~~~  247 (427)
                      ++.+.|++|+||||++..++..+..   .-..++.+..... ....+.+...+...+.+.. .....+...... .+...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~---~g~~v~~i~~D~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKK---KGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHA   78 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH---CCCcEEEEEcCCCChHHHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHHHH
Confidence            6789999999999999999887621   1123444443321 1223334334444443211 112234444433 33333


Q ss_pred             hcCCcEEEEEeccCC
Q 042645          248 MRNRKIVLLLDDIWE  262 (427)
Q Consensus       248 L~~k~~LlVlDdv~~  262 (427)
                      ..+..-++|+|..-.
T Consensus        79 ~~~~~d~viiDt~g~   93 (173)
T cd03115          79 REENFDVVIVDTAGR   93 (173)
T ss_pred             HhCCCCEEEEECccc
Confidence            343433566777543

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.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=97.00  E-value=0.0044  Score=58.11  Aligned_cols=94  Identities=18%  Similarity=0.172  Sum_probs=56.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-------CCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW-------DNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~-------~~~~~  237 (427)
                      ...++.|+|.+|+|||+|+..++.....   ....-..++|++....+.+.. +..+++.++......       ...+.
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R-l~~ia~~~~~~~~~~l~~i~~~~~~~~  173 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER-LLAIAERYGLNPEDVLDNVAYARAYNT  173 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH-HHHHHHHcCCChHHhhccEEEEecCCh
Confidence            4678999999999999999988754311   111224678998887777765 344555555432110       11233


Q ss_pred             HHHHHHH---HHHhc-CCcEEEEEeccCC
Q 042645          238 DEKAQEI---FKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       238 ~~~~~~l---~~~L~-~k~~LlVlDdv~~  262 (427)
                      ++....+   ...+. .+.-|||+|.+-.
T Consensus       174 ~~~~~~l~~~~~~~~~~~~~LvVIDSI~a  202 (316)
T TIGR02239       174 DHQLQLLQQAAAMMSESRFALLIVDSATA  202 (316)
T ss_pred             HHHHHHHHHHHHhhccCCccEEEEECcHH
Confidence            3333333   23333 3556899998743

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=96.99  E-value=0.0051  Score=58.07  Aligned_cols=96  Identities=20%  Similarity=0.312  Sum_probs=59.3

Q ss_pred             HHHHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--
Q 042645          157 LDRVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW--  232 (427)
Q Consensus       157 ~~~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~--  232 (427)
                      +.++-+.|..+  ...+|.|-|-+|+|||||..+++.++.   ..- .++||+-.++  +.+ .+--++.++...+..  
T Consensus        79 ~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA---~~~-~vLYVsGEES--~~Q-iklRA~RL~~~~~~l~l  151 (456)
T COG1066          79 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA---KRG-KVLYVSGEES--LQQ-IKLRADRLGLPTNNLYL  151 (456)
T ss_pred             hHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHH---hcC-cEEEEeCCcC--HHH-HHHHHHHhCCCccceEE
Confidence            33444445443  457899999999999999999999983   222 6777765543  222 233355666544321  


Q ss_pred             -CCCCHHHHHHHHHHHhcCCcEEEEEeccCC
Q 042645          233 -DNKSFDEKAQEIFKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       233 -~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~  262 (427)
                       ...+.+...+.+.+   .++-|+|+|-+..
T Consensus       152 ~aEt~~e~I~~~l~~---~~p~lvVIDSIQT  179 (456)
T COG1066         152 LAETNLEDIIAELEQ---EKPDLVVIDSIQT  179 (456)
T ss_pred             ehhcCHHHHHHHHHh---cCCCEEEEeccce
Confidence             12333433333333   6889999999854

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.99  E-value=0.00085  Score=66.48  Aligned_cols=45  Identities=24%  Similarity=0.414  Sum_probs=40.1

Q ss_pred             ccccchhhHHHHHHHhc------cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLT------EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +++|.++.+++|++.|.      +...+++.++|++|+||||||+.+.+.+
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHH
Confidence            57999999999999983      3466899999999999999999999877

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

Probab=96.97  E-value=0.0062  Score=51.43  Aligned_cols=58  Identities=19%  Similarity=0.202  Sum_probs=36.7

Q ss_pred             HHHHHHHHHhcCCcEEEEEecc----CCcccccccccCCCCCCCCcEEEEecCChhHHhhcC
Q 042645          239 EKAQEIFKTMRNRKIVLLLDDI----WELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMD  296 (427)
Q Consensus       239 ~~~~~l~~~L~~k~~LlVlDdv----~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~  296 (427)
                      +..-.|...+-+++-+|+-|+-    +....|+-+...-.-+..|+.|+++|.+.++...+.
T Consensus       143 QQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~  204 (223)
T COG2884         143 QQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMR  204 (223)
T ss_pred             HHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhcc
Confidence            3333455556678899999964    333345443222223466899999999988876653

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.95  E-value=0.0027  Score=55.22  Aligned_cols=79  Identities=14%  Similarity=0.171  Sum_probs=45.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      .+-+|+|.|.+|+||||+|+.++..+   ....-.+  ++...-+. ..-..................+.+-+.+.|...
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~~~---~~~~~~~--I~~D~YYk-~~~~~~~~~~~~~n~d~p~A~D~dLl~~~L~~L   80 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSEQL---GVEKVVV--ISLDDYYK-DQSHLPFEERNKINYDHPEAFDLDLLIEHLKDL   80 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHh---CcCcceE--eecccccc-chhhcCHhhcCCcCccChhhhcHHHHHHHHHHH
Confidence            34689999999999999999999988   2222111  11111010 001111111222222233455667778888888


Q ss_pred             hcCCc
Q 042645          248 MRNRK  252 (427)
Q Consensus       248 L~~k~  252 (427)
                      +++++
T Consensus        81 ~~g~~   85 (218)
T COG0572          81 KQGKP   85 (218)
T ss_pred             HcCCc
Confidence            88877

>PRK10867 signal recognition particle protein; Provisional

Probab=96.94  E-value=0.0041  Score=60.62  Aligned_cols=26  Identities=27%  Similarity=0.517  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.++|++|+||||++..++..+
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l  124 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYL  124 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHH
Confidence            35789999999999999988887766

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.94  E-value=0.0053  Score=52.60  Aligned_cols=26  Identities=31%  Similarity=0.494  Sum_probs=22.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.+....
T Consensus        27 ~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (178)
T cd03247          27 QGEKIALLGRSGSGKSTLLQLLTGDL   52 (178)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccC
Confidence            44689999999999999999998765

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.93  E-value=0.0016  Score=53.21  Aligned_cols=45  Identities=22%  Similarity=0.423  Sum_probs=35.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  229 (427)
                      +|.|-|++|+||||+|+.+++++.   -.+           .+...+++++++..+++.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~g---l~~-----------vsaG~iFR~~A~e~gmsl   46 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLG---LKL-----------VSAGTIFREMARERGMSL   46 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhC---Cce-----------eeccHHHHHHHHHcCCCH
Confidence            689999999999999999999871   111           134578999999988764

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.92  E-value=0.0035  Score=52.75  Aligned_cols=117  Identities=18%  Similarity=0.138  Sum_probs=62.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEE---EeCCCCCHHHHHHHHHHHhCCC--CC--CCCCCCHH---
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWE---VVSRDLQLGKIQESIAKKIGLY--NE--SWDNKSFD---  238 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv---~~~~~~~~~~l~~~i~~~l~~~--~~--~~~~~~~~---  238 (427)
                      ...|-|++..|.||||.|..++-+..   .+-..++.+   .-.........+..+  .+...  ..  .+...+.+   
T Consensus         5 ~Gli~v~~g~GkGKtt~a~g~a~ra~---~~g~~v~ivQFlKg~~~~GE~~~l~~~--~~~~~~~g~g~~~~~~~~~~~~   79 (173)
T TIGR00708         5 RGIIIVHTGNGKGKTTAAFGMALRAL---GHGKKVGVIQFIKGAWPNGERAAFEPH--GVEFQVMGTGFTWETQNREADT   79 (173)
T ss_pred             ccEEEEECCCCCChHHHHHHHHHHHH---HCCCeEEEEEEecCCcccChHHHHHhc--CcEEEECCCCCeecCCCcHHHH
Confidence            35788899999999999988877662   222233333   323233444444432  11100  00  01111111   


Q ss_pred             ----HHHHHHHHHhcCCc-EEEEEeccCCc-----ccccccccCCCCCCCCcEEEEecCChh
Q 042645          239 ----EKAQEIFKTMRNRK-IVLLLDDIWEL-----FDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       239 ----~~~~~l~~~L~~k~-~LlVlDdv~~~-----~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                          +..+..++.+...+ =|||||++-..     -+.+++...+.....+..||+|-|+.+
T Consensus        80 ~~~~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p  141 (173)
T TIGR00708        80 AIAKAAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCP  141 (173)
T ss_pred             HHHHHHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCC
Confidence                12233344444444 49999998532     223444445555556778999999863

Alternate name: corrinoid adenosyltransferase.

>TIGR00959 ffh signal recognition particle protein

Probab=96.92  E-value=0.0046  Score=60.23  Aligned_cols=26  Identities=27%  Similarity=0.460  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.++.++|++|+||||++..++..+
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l  123 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYL  123 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHH
Confidence            35689999999999999998888775

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.

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

Probab=96.92  E-value=0.007  Score=52.67  Aligned_cols=82  Identities=17%  Similarity=0.175  Sum_probs=45.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCc---EEEEEEeCCCCCHHHHHHHHHHHh--CCCCCCCCCCCHHHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFD---FVIWEVVSRDLQLGKIQESIAKKI--GLYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~---~~~wv~~~~~~~~~~l~~~i~~~l--~~~~~~~~~~~~~~~~~~l~  245 (427)
                      +|+|.|++|+||||+|+.+...+..  ....   ....++............. ....  ..........+.+.+.+.|.
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~--~~~~~~~~~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~~p~a~d~~~l~~~l~   77 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNK--RGIPAMEMDIILSLDDFYDDYHLRDR-KGRGENRYNFDHPDAFDFDLLKEDLK   77 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT--CTTTCCCSEEEEEGGGGBHHHHHHHH-HHHCTTTSSTTSGGGBSHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCc--cCcCccceeEEEeecccccccchhhH-hhccccccCCCCccccCHHHHHHHHH
Confidence            6999999999999999999998832  1222   2333333322222222221 1111  11111224556677777787


Q ss_pred             HHhcCCcEEE
Q 042645          246 KTMRNRKIVL  255 (427)
Q Consensus       246 ~~L~~k~~Ll  255 (427)
                      ...+++..-+
T Consensus        78 ~L~~g~~i~~   87 (194)
T PF00485_consen   78 ALKNGGSIEI   87 (194)
T ss_dssp             HHHTTSCEEE
T ss_pred             HHhCCCcccc
Confidence            7767776544

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

>PHA00729 NTP-binding motif containing protein

Probab=96.91  E-value=0.0012  Score=58.00  Aligned_cols=35  Identities=17%  Similarity=0.299  Sum_probs=29.1

Q ss_pred             HHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          159 RVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       159 ~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+++.+...+...|.|+|.+|+||||||..+.+..
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l   41 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDV   41 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHH
Confidence            45556666666789999999999999999998875

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.91  E-value=0.0016  Score=63.64  Aligned_cols=44  Identities=14%  Similarity=0.150  Sum_probs=39.0

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++||++.++.+...+..++  .|.|.|++|+|||+||+.+....
T Consensus        20 ~~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~   63 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAF   63 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHh
Confidence            468999999999999887764  48999999999999999999876

>PTZ00494 tuzin-like protein; Provisional

Probab=96.90  E-value=0.081  Score=50.92  Aligned_cols=165  Identities=15%  Similarity=0.069  Sum_probs=97.8

Q ss_pred             CCCCccccchhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          145 PLPPTVVGMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       145 ~~~~~~vGR~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      ..++.+|.|+.+-..+.+.|.+   .+++++.+.|.-|.||++|.+...... .     -..++|.+...   ++-++++
T Consensus       368 a~~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE-~-----~paV~VDVRg~---EDtLrsV  438 (664)
T PTZ00494        368 AAEAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVE-G-----VALVHVDVGGT---EDTLRSV  438 (664)
T ss_pred             cccccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHc-C-----CCeEEEEecCC---cchHHHH
Confidence            3456789998887766666654   478999999999999999999887765 1     13467777654   3457888


Q ss_pred             HHHhCCCCCCCCCCCHHHHHHHHHH---HhcCCcEEEEEeccCCccccccc---ccCCCCCCCCcEEEEecCChhHHhhc
Q 042645          222 AKKIGLYNESWDNKSFDEKAQEIFK---TMRNRKIVLLLDDIWELFDLAQV---GLPVPSRASASKVVFTTREFEVCGLM  295 (427)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~~~~l~~---~L~~k~~LlVlDdv~~~~~~~~~---~~~l~~~~~gs~IivTtR~~~v~~~~  295 (427)
                      .+.++.+.-+..+.-.+-+.+....   ...++.=+||+-==+ -.++..+   ...|.....-|.|++----+.+....
T Consensus       439 VKALgV~nve~CGDlLdFI~ea~~~A~~~~~g~~P~lVlkLRE-GssL~RVYnE~vaLacDrRlCHvv~EVplESLT~~n  517 (664)
T PTZ00494        439 VRALGVSNVEVCGDLLGFVEEAMRGATVKASDGVPFLVMRLRE-GSDLGRVYGEVVSLVSDCQACHIVLAVPMKALTPLN  517 (664)
T ss_pred             HHHhCCCChhhhccHHHHHHHHHHHHHHhcCCCCCEEEEEecc-CCcHHHHHHHHHHHHccchhheeeeechHhhhchhh
Confidence            9999887543333333333333332   234555566653211 1111111   01122233446666643333221110


Q ss_pred             ---CCCcceeccCCChHHHHHHHHHHh
Q 042645          296 ---DAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       296 ---~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                         .--..|.+++++.++|.++..+..
T Consensus       518 ~~LPRLDFy~VPnFSr~QAf~YtqH~l  544 (664)
T PTZ00494        518 VSSRRLDFYCIPPFSRRQAFAYAEHTL  544 (664)
T ss_pred             ccCccceeEecCCcCHHHHHHHHhccc
Confidence               111457899999999999888765

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.89  E-value=0.014  Score=55.26  Aligned_cols=93  Identities=15%  Similarity=0.165  Sum_probs=58.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~~  237 (427)
                      ...+.-|+|++|+|||+|+.+++-....   ..+.-..++|++....+++..+.. +++.++.....       ....+.
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~~~~~~~  203 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIYARAYTY  203 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEEecCCCH
Confidence            4578889999999999999988643311   112235789999998888887654 56666654321       012344


Q ss_pred             HHHHHH---HHHHhc-CCcEEEEEeccC
Q 042645          238 DEKAQE---IFKTMR-NRKIVLLLDDIW  261 (427)
Q Consensus       238 ~~~~~~---l~~~L~-~k~~LlVlDdv~  261 (427)
                      ++....   +...+. .+--|||+|.+-
T Consensus       204 e~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        204 EHQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence            443333   222332 345589999974

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.89  E-value=0.0043  Score=59.15  Aligned_cols=88  Identities=20%  Similarity=0.216  Sum_probs=51.3

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ..+++++|+.|+||||++.++...... ......+..++... .....+-+....+.++.+...  ..+..++...+ ..
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~-~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~--~~~~~~l~~~l-~~  212 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVM-RFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHA--VKDGGDLQLAL-AE  212 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH-hcCCCeEEEEecccccccHHHHHHHHHHHcCCceEe--cCCcccHHHHH-HH
Confidence            468999999999999999999887521 11123455555332 234455666666777665421  12222333333 33


Q ss_pred             hcCCcEEEEEeccC
Q 042645          248 MRNRKIVLLLDDIW  261 (427)
Q Consensus       248 L~~k~~LlVlDdv~  261 (427)
                      +.++ =++++|..-
T Consensus       213 l~~~-DlVLIDTaG  225 (374)
T PRK14722        213 LRNK-HMVLIDTIG  225 (374)
T ss_pred             hcCC-CEEEEcCCC
Confidence            4444 456689874

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.88  E-value=0.0098  Score=56.25  Aligned_cols=94  Identities=16%  Similarity=0.203  Sum_probs=58.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-------CCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW-------DNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~-------~~~~~  237 (427)
                      ...++-|+|.+|+|||+|+..++-....   ....-..++|++....+.+..+ .++++.++......       ...+.
T Consensus       122 ~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~~~~~~l~~i~~~~~~~~  200 (342)
T PLN03186        122 TGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGLNGADVLENVAYARAYNT  200 (342)
T ss_pred             CceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCCChhhhccceEEEecCCH
Confidence            4678889999999999999888754311   1112237899999988888776 45666666543110       12334


Q ss_pred             HHHHHHHH---HHh-cCCcEEEEEeccCC
Q 042645          238 DEKAQEIF---KTM-RNRKIVLLLDDIWE  262 (427)
Q Consensus       238 ~~~~~~l~---~~L-~~k~~LlVlDdv~~  262 (427)
                      +.....+.   ..+ ..+.-|||+|.+-.
T Consensus       201 e~~~~ll~~~~~~~~~~~~~LIVIDSI~a  229 (342)
T PLN03186        201 DHQSELLLEAASMMAETRFALMIVDSATA  229 (342)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEeCcHH
Confidence            44433332   223 34566899998743

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.88  E-value=0.012  Score=59.81  Aligned_cols=93  Identities=16%  Similarity=0.199  Sum_probs=60.9

Q ss_pred             CccccchhhHHHHHHHhcc----------C--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE----------E--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~----------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .++=|-++.+.+|.+.+.-          +  +..-|.+||++|.|||-||+.|+-.+   .     .-|++|..+    
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEc---s-----L~FlSVKGP----  739 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATEC---S-----LNFLSVKGP----  739 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhc---e-----eeEEeecCH----
Confidence            3456788888888887642          1  35578999999999999999998877   1     234444432    


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL  263 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~  263 (427)
                      +++...           -+.+++...+.+.+.-.-++|+|.||++++.
T Consensus       740 ELLNMY-----------VGqSE~NVR~VFerAR~A~PCVIFFDELDSl  776 (953)
T KOG0736|consen  740 ELLNMY-----------VGQSEENVREVFERARSAAPCVIFFDELDSL  776 (953)
T ss_pred             HHHHHH-----------hcchHHHHHHHHHHhhccCCeEEEecccccc
Confidence            222211           1223344444444444569999999999864

>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=96.88  E-value=0.0063  Score=51.87  Aligned_cols=124  Identities=15%  Similarity=0.127  Sum_probs=63.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC--CC---CCc--EEEEEEeCCCCCHHHHHHHHHHHhCCCCC----CCCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT--PN---DFD--FVIWEVVSRDLQLGKIQESIAKKIGLYNE----SWDNKS  236 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~---~f~--~~~wv~~~~~~~~~~l~~~i~~~l~~~~~----~~~~~~  236 (427)
                      ...+++|.|+.|+|||||.+.+..+...+  ..   .+.  .+.|+  .+        .+.+..+++...    .....+
T Consensus        20 ~G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~--~q--------~~~l~~~~L~~~~~~~~~~~LS   89 (176)
T cd03238          20 LNVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFI--DQ--------LQFLIDVGLGYLTLGQKLSTLS   89 (176)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEE--hH--------HHHHHHcCCCccccCCCcCcCC
Confidence            44689999999999999999886321110  00   110  12222  11        355666665321    111222


Q ss_pred             HHHH-HHHHHHHhcCC--cEEEEEeccCCccc---ccccccCCCC-CCCCcEEEEecCChhHHhhcCCCcceec
Q 042645          237 FDEK-AQEIFKTMRNR--KIVLLLDDIWELFD---LAQVGLPVPS-RASASKVVFTTREFEVCGLMDAHKSFKV  303 (427)
Q Consensus       237 ~~~~-~~~l~~~L~~k--~~LlVlDdv~~~~~---~~~~~~~l~~-~~~gs~IivTtR~~~v~~~~~~~~~~~l  303 (427)
                      ..+. .-.+...+-.+  +-+++||+.-+.-+   ...+...+.. ...|..||++|.+......  ....+.+
T Consensus        90 gGq~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~~--~d~i~~l  161 (176)
T cd03238          90 GGELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLSS--ADWIIDF  161 (176)
T ss_pred             HHHHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHh--CCEEEEE
Confidence            2222 22233444456  77889999754322   2222222221 1246678888888766532  3444444

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.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.88  E-value=0.019  Score=57.87  Aligned_cols=152  Identities=17%  Similarity=0.166  Sum_probs=83.3

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ..-|.++|++|+|||.||..++....        .-++++-.+    +++...   +|        .+++.....+.+.-
T Consensus       701 ~~giLLyGppGcGKT~la~a~a~~~~--------~~fisvKGP----ElL~Ky---IG--------aSEq~vR~lF~rA~  757 (952)
T KOG0735|consen  701 RTGILLYGPPGCGKTLLASAIASNSN--------LRFISVKGP----ELLSKY---IG--------ASEQNVRDLFERAQ  757 (952)
T ss_pred             ccceEEECCCCCcHHHHHHHHHhhCC--------eeEEEecCH----HHHHHH---hc--------ccHHHHHHHHHHhh
Confidence            34688999999999999999987761        224555432    233222   22        12233333333344


Q ss_pred             cCCcEEEEEeccCCccc-------------ccccccCCC--CCCCCcEEEE-ecCChhHH-hhcCC---CcceeccCCCh
Q 042645          249 RNRKIVLLLDDIWELFD-------------LAQVGLPVP--SRASASKVVF-TTREFEVC-GLMDA---HKSFKVECLGY  308 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~-------------~~~~~~~l~--~~~~gs~Iiv-TtR~~~v~-~~~~~---~~~~~l~~L~~  308 (427)
                      .-++|+|.+|++++..-             ..++...+.  .+-.|--|+- |||..-+- ..+.+   .+.+.-+.-++
T Consensus       758 ~a~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~  837 (952)
T KOG0735|consen  758 SAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDE  837 (952)
T ss_pred             ccCCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCc
Confidence            46999999999986411             222322222  1223444544 55543221 11222   23344455566


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          309 EDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       309 ~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      .+-.++|+............+    .+.++.+.+|..-|
T Consensus       838 ~eRl~il~~ls~s~~~~~~vd----l~~~a~~T~g~tgA  872 (952)
T KOG0735|consen  838 PERLEILQVLSNSLLKDTDVD----LECLAQKTDGFTGA  872 (952)
T ss_pred             HHHHHHHHHHhhccCCccccc----hHHHhhhcCCCchh
Confidence            777788877664322122222    67788888887654

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

Probab=96.88  E-value=0.006  Score=55.40  Aligned_cols=93  Identities=18%  Similarity=0.322  Sum_probs=55.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDE---  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~---  239 (427)
                      ....++|.|.+|+|||||+..+++....  .+-+.++++.+++.. ...++...+...-.....    .....+...   
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~~i~~--~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~  145 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELINNIAK--AHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARAR  145 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHHHHHh--cCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            4567999999999999999999988721  222455666676554 455666666543211100    001111111   


Q ss_pred             ---HHHHHHHHh---cCCcEEEEEeccCC
Q 042645          240 ---KAQEIFKTM---RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ---~~~~l~~~L---~~k~~LlVlDdv~~  262 (427)
                         ..-.+-+++   +++.+||++||+-.
T Consensus       146 ~~~~a~~~AEyfr~~~g~~Vl~~~Dsltr  174 (274)
T cd01133         146 VALTGLTMAEYFRDEEGQDVLLFIDNIFR  174 (274)
T ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEeChhH
Confidence               111233444   38999999999843

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

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.87  E-value=0.0089  Score=56.22  Aligned_cols=59  Identities=19%  Similarity=0.210  Sum_probs=41.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      ...++-|+|++|+|||+++.+++-.....   ...-..++|++....+++..+. ++++.++.
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl  155 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGL  155 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCC
Confidence            46788999999999999999997665211   1112378999988888877654 44555543

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.87  E-value=0.0055  Score=56.61  Aligned_cols=87  Identities=23%  Similarity=0.303  Sum_probs=47.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      .++++|+|++|+||||++..++..+. ....-..+..++.... ....+.+......++.+..  ...+...+...+.. 
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~-~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~--~~~~~~~l~~~l~~-  269 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFV-LEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVK--VARDPKELRKALDR-  269 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-HHcCCCeEEEEECCccchhHHHHHHHHHHHhCCcee--ccCCHHHHHHHHHH-
Confidence            46899999999999999999987762 1111134555554331 1223333344444554332  22344444444433 


Q ss_pred             hcCCcEEEEEecc
Q 042645          248 MRNRKIVLLLDDI  260 (427)
Q Consensus       248 L~~k~~LlVlDdv  260 (427)
                      +.+ .=+|++|..
T Consensus       270 ~~~-~d~vliDt~  281 (282)
T TIGR03499       270 LRD-KDLILIDTA  281 (282)
T ss_pred             ccC-CCEEEEeCC
Confidence            333 347777753

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.86  E-value=0.025  Score=59.29  Aligned_cols=46  Identities=20%  Similarity=0.273  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|+...+..+.+.+..  .....|.|+|..|+|||++|+.+.+..
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s  423 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLS  423 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            3589999888888776653  334568999999999999999998765

>PRK04328 hypothetical protein; Provisional

Probab=96.86  E-value=0.0047  Score=55.99  Aligned_cols=88  Identities=14%  Similarity=0.130  Sum_probs=53.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------------
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES----------------  231 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~----------------  231 (427)
                      ...++.|.|.+|+|||+|+.++.....   ..-..++|++....  +.++.+ .+++++.....                
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~---~~ge~~lyis~ee~--~~~i~~-~~~~~g~d~~~~~~~~~l~iid~~~~~   95 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGL---QMGEPGVYVALEEH--PVQVRR-NMRQFGWDVRKYEEEGKFAIVDAFTGG   95 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH---hcCCcEEEEEeeCC--HHHHHH-HHHHcCCCHHHHhhcCCEEEEeccccc
Confidence            467899999999999999999766541   22456778877653  344333 33444331100                


Q ss_pred             ------------CCCCCHHHHHHHHHHHhcC-CcEEEEEeccC
Q 042645          232 ------------WDNKSFDEKAQEIFKTMRN-RKIVLLLDDIW  261 (427)
Q Consensus       232 ------------~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~  261 (427)
                                  ....+.+.....+.+.++. +.-++|+|.+-
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSlt  138 (249)
T PRK04328         96 IGSAAKREKYVVKDPDDVRELIDVLRQAIKDIGAKRVVIDSVS  138 (249)
T ss_pred             cccccccccccccCcccHHHHHHHHHHHHHhhCCCEEEEeChh
Confidence                        0112345555666665543 45589999984

>PRK06547 hypothetical protein; Provisional

Probab=96.85  E-value=0.0017  Score=55.12  Aligned_cols=34  Identities=26%  Similarity=0.193  Sum_probs=28.0

Q ss_pred             HHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          160 VWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       160 l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+......+|+|.|++|+||||+|+.+.+..
T Consensus         6 ~~~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547          6 IAARLCGGGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             HHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3444555677899999999999999999998875

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.84  E-value=0.023  Score=51.42  Aligned_cols=92  Identities=22%  Similarity=0.376  Sum_probs=60.9

Q ss_pred             CccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      +++.|-+..++.|.+++.-            ...+-|.++|++|.||+.||+.|+-..   ..     -|.++|.+    
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEA---nS-----TFFSvSSS----  200 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEA---NS-----TFFSVSSS----  200 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhc---CC-----ceEEeehH----
Confidence            4567888888888887642            146789999999999999999998775   12     22334332    


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc-CCcEEEEEeccCCc
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR-NRKIVLLLDDIWEL  263 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~-~k~~LlVlDdv~~~  263 (427)
                      ++..   +.++         .-+.++..|.+.-+ .|+-+|.+|+++..
T Consensus       201 DLvS---KWmG---------ESEkLVknLFemARe~kPSIIFiDEiDsl  237 (439)
T KOG0739|consen  201 DLVS---KWMG---------ESEKLVKNLFEMARENKPSIIFIDEIDSL  237 (439)
T ss_pred             HHHH---HHhc---------cHHHHHHHHHHHHHhcCCcEEEeehhhhh
Confidence            1111   1111         11455556665543 69999999999753

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.84  E-value=0.0012  Score=53.91  Aligned_cols=24  Identities=38%  Similarity=0.473  Sum_probs=22.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|.|++|+||||+++.+.+.+
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHH
Confidence            468999999999999999999888

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.82  E-value=0.0015  Score=56.33  Aligned_cols=23  Identities=35%  Similarity=0.450  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|.|+|++|+||||+|+.+++.+
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58899999999999999998876

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.

>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=96.81  E-value=0.0031  Score=51.53  Aligned_cols=42  Identities=31%  Similarity=0.239  Sum_probs=32.0

Q ss_pred             EEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHH
Q 042645          172 VGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQE  219 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~  219 (427)
                      |.|+|++|+|||+||+.+++..   .   ....-+.++...+..+++.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~---~---~~~~~i~~~~~~~~~dl~g   43 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL---G---RPVIRINCSSDTTEEDLIG   43 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH---T---CEEEEEE-TTTSTHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHh---h---cceEEEEecccccccccee
Confidence            6799999999999999999887   1   2344567777777777664

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.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=96.79  E-value=0.00038  Score=58.99  Aligned_cols=83  Identities=12%  Similarity=0.108  Sum_probs=44.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC-CCCHHHHHHHHHHHhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWD-NKSFDEKAQEIFKTMR  249 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~-~~~~~~~~~~l~~~L~  249 (427)
                      ++.|.|.+|+||||+|..+.....   .   .++++.-.... ..+....|..........+. ...+..+...+.....
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~---~---~~~~iat~~~~-~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~   75 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSG---L---QVLYIATAQPF-DDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAA   75 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcC---C---CcEeCcCCCCC-hHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcC
Confidence            689999999999999999987651   1   12344333332 33455555443322222221 1112234444444333


Q ss_pred             CCcEEEEEeccC
Q 042645          250 NRKIVLLLDDIW  261 (427)
Q Consensus       250 ~k~~LlVlDdv~  261 (427)
                      + .-++++|.+.
T Consensus        76 ~-~~~VlID~Lt   86 (170)
T PRK05800         76 P-GRCVLVDCLT   86 (170)
T ss_pred             C-CCEEEehhHH
Confidence            2 3378899873

>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=96.79  E-value=0.0012  Score=60.59  Aligned_cols=56  Identities=23%  Similarity=0.259  Sum_probs=34.9

Q ss_pred             HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHH
Q 042645          158 DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       158 ~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l  217 (427)
                      ..+++.+...+ +-+.++|+.|+|||++++.......  ...+ ...-++.+...+...+
T Consensus        23 ~~ll~~l~~~~-~pvLl~G~~GtGKT~li~~~l~~l~--~~~~-~~~~~~~s~~Tts~~~   78 (272)
T PF12775_consen   23 SYLLDLLLSNG-RPVLLVGPSGTGKTSLIQNFLSSLD--SDKY-LVITINFSAQTTSNQL   78 (272)
T ss_dssp             HHHHHHHHHCT-EEEEEESSTTSSHHHHHHHHHHCST--TCCE-EEEEEES-TTHHHHHH
T ss_pred             HHHHHHHHHcC-CcEEEECCCCCchhHHHHhhhccCC--cccc-ceeEeeccCCCCHHHH
Confidence            44555555544 4578999999999999999887662  1221 2344556655444433

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.79  E-value=0.016  Score=54.37  Aligned_cols=44  Identities=20%  Similarity=0.268  Sum_probs=33.3

Q ss_pred             cccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          150 VVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|-++.++-|.+++.-            ...+-|.++|++|.|||-||+.|+...
T Consensus       214 Iagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc  269 (491)
T KOG0738|consen  214 IAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATEC  269 (491)
T ss_pred             hcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHhh
Confidence            45666666666555432            245679999999999999999999887

>PRK14527 adenylate kinase; Provisional

Probab=96.79  E-value=0.0022  Score=55.70  Aligned_cols=26  Identities=23%  Similarity=0.317  Sum_probs=23.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|+|++|+||||+|+.+++.+
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998876

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.78  E-value=0.0083  Score=51.01  Aligned_cols=26  Identities=35%  Similarity=0.521  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|.|||||.+.++.-.
T Consensus        27 ~G~~~~l~G~nGsGKstLl~~i~G~~   52 (171)
T cd03228          27 PGEKVAIVGPSGSGKSTLLKLLLRLY   52 (171)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            45689999999999999999998765

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PTZ00035 Rad51 protein; Provisional

Probab=96.78  E-value=0.019  Score=54.38  Aligned_cols=94  Identities=19%  Similarity=0.181  Sum_probs=56.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~~  237 (427)
                      ...++.|+|.+|+|||+|+..++-....   ....-..++|+.....+++.. +..+++.++.....       ....+.
T Consensus       117 ~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er-i~~ia~~~g~~~~~~l~nI~~~~~~~~  195 (337)
T PTZ00035        117 TGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERFGLDPEDVLDNIAYARAYNH  195 (337)
T ss_pred             CCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH-HHHHHHHhCCChHhHhhceEEEccCCH
Confidence            4678999999999999999988754411   111234667888877777766 34455665543210       012333


Q ss_pred             HHHHHHHH---HHhc-CCcEEEEEeccCC
Q 042645          238 DEKAQEIF---KTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       238 ~~~~~~l~---~~L~-~k~~LlVlDdv~~  262 (427)
                      ++....+.   ..+. .+.-|||+|.+-.
T Consensus       196 e~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        196 EHQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             HHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence            44443332   2332 4556999999853

>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=96.78  E-value=0.0011  Score=53.14  Aligned_cols=22  Identities=32%  Similarity=0.714  Sum_probs=20.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+|.|++|+||||+|+.+.+..
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            6899999999999999998874

...

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.78  E-value=0.014  Score=53.32  Aligned_cols=126  Identities=17%  Similarity=0.050  Sum_probs=67.4

Q ss_pred             hHHHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEE---eCCCCCHHHHHHHHHHHhCC-CCC
Q 042645          156 TLDRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEV---VSRDLQLGKIQESIAKKIGL-YNE  230 (427)
Q Consensus       156 ~~~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~---~~~~~~~~~l~~~i~~~l~~-~~~  230 (427)
                      ..+.++..+.+ +....++|.|+.|+|||||.+.+.....    .....+++.   +......    .++...... +..
T Consensus        97 ~~~~~l~~l~~~~~~~~~~i~g~~g~GKttl~~~l~~~~~----~~~G~i~~~g~~v~~~d~~----~ei~~~~~~~~q~  168 (270)
T TIGR02858        97 AADKLLPYLVRNNRVLNTLIISPPQCGKTTLLRDLARILS----TGISQLGLRGKKVGIVDER----SEIAGCVNGVPQH  168 (270)
T ss_pred             cHHHHHHHHHhCCCeeEEEEEcCCCCCHHHHHHHHhCccC----CCCceEEECCEEeecchhH----HHHHHHhcccccc
Confidence            34444444443 4457899999999999999999998762    112222221   1111111    233322221 111


Q ss_pred             CC----CCCCHHHHHHHHHHHhc-CCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHH
Q 042645          231 SW----DNKSFDEKAQEIFKTMR-NRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVC  292 (427)
Q Consensus       231 ~~----~~~~~~~~~~~l~~~L~-~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~  292 (427)
                      ..    +..+.......+...+. ..+=++++|++-....+..+...+   ..|..+|+||.+..+.
T Consensus       169 ~~~~r~~v~~~~~k~~~~~~~i~~~~P~villDE~~~~e~~~~l~~~~---~~G~~vI~ttH~~~~~  232 (270)
T TIGR02858       169 DVGIRTDVLDGCPKAEGMMMLIRSMSPDVIVVDEIGREEDVEALLEAL---HAGVSIIATAHGRDVE  232 (270)
T ss_pred             cccccccccccchHHHHHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHH---hCCCEEEEEechhHHH
Confidence            00    01111111222333333 578899999987665555554443   2467899999876553

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

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.78  E-value=0.012  Score=55.47  Aligned_cols=94  Identities=16%  Similarity=0.202  Sum_probs=56.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-------CCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW-------DNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~-------~~~~~  237 (427)
                      ...++-|+|++|+|||+++.+++-.....   ...-..++|++....+++..+.+ +++.++......       ...+.
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g~~~~~~l~~i~~~~~~~~  179 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALGLDPDEVLDNIHVARAYNS  179 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcCCChHhhhccEEEEeCCCH
Confidence            46789999999999999999998654211   11124789999988888776654 445554322110       01111


Q ss_pred             H---HHHHHHHHHhcC--CcEEEEEeccCC
Q 042645          238 D---EKAQEIFKTMRN--RKIVLLLDDIWE  262 (427)
Q Consensus       238 ~---~~~~~l~~~L~~--k~~LlVlDdv~~  262 (427)
                      +   .....+...+..  +.-|||+|.+-.
T Consensus       180 ~~~~~~~~~l~~~i~~~~~~~lvVIDSisa  209 (317)
T PRK04301        180 DHQMLLAEKAEELIKEGENIKLVIVDSLTA  209 (317)
T ss_pred             HHHHHHHHHHHHHHhccCceeEEEEECchH
Confidence            1   233444455543  344899998743

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.77  E-value=0.011  Score=52.89  Aligned_cols=89  Identities=22%  Similarity=0.233  Sum_probs=52.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC-----------------
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE-----------------  230 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~-----------------  230 (427)
                      ....+.|.|.+|+|||||+.++......   .-..++|++...  +..++... +++++....                 
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~---~g~~~~~is~e~--~~~~i~~~-~~~~g~~~~~~~~~~~l~i~d~~~~~   92 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLR---DGDPVIYVTTEE--SRESIIRQ-AAQFGMDFEKAIEEGKLVIIDALMKE   92 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHh---cCCeEEEEEccC--CHHHHHHH-HHHhCCCHHHHhhcCCEEEEEccccc
Confidence            4578999999999999999987755421   234678887643  33444333 333332110                 


Q ss_pred             -----CCCCCCHHHHHHHHHHHhcC---CcEEEEEeccCC
Q 042645          231 -----SWDNKSFDEKAQEIFKTMRN---RKIVLLLDDIWE  262 (427)
Q Consensus       231 -----~~~~~~~~~~~~~l~~~L~~---k~~LlVlDdv~~  262 (427)
                           .....+.+++...+.+.++.   +.-++|+|.+..
T Consensus        93 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~vvIDsl~~  132 (229)
T TIGR03881        93 KEDEWSLRELSIEELLNKVIEAKKYLGYGHARLVIDSMSA  132 (229)
T ss_pred             cccccccccCCHHHHHHHHHHHHHhhccCceEEEecCchh
Confidence                 00123455666666655543   345788888753

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK07667 uridine kinase; Provisional

Probab=96.76  E-value=0.002  Score=56.03  Aligned_cols=37  Identities=22%  Similarity=0.426  Sum_probs=29.6

Q ss_pred             HHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          157 LDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       157 ~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|.+.+..  +...+|+|.|.+|+||||+|..+...+
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l   41 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENM   41 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4556666643  345799999999999999999999877

>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=96.75  E-value=0.0049  Score=53.13  Aligned_cols=45  Identities=22%  Similarity=0.138  Sum_probs=31.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  220 (427)
                      ++.|.|++|+|||+|+.++.....   ..-..++|++...  +..++...
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~---~~g~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGL---ARGEPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH---HCCCcEEEEECCC--CHHHHHHH
Confidence            367999999999999999877652   2234567777654  34555444

A related protein is found in archaea.

>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=96.75  E-value=0.01  Score=50.26  Aligned_cols=115  Identities=14%  Similarity=0.212  Sum_probs=58.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCC--C---cEEEEEEeCCCCC--HHHHHHHHHHHhCCCCCCCCCCCHHH-
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPND--F---DFVIWEVVSRDLQ--LGKIQESIAKKIGLYNESWDNKSFDE-  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~--f---~~~~wv~~~~~~~--~~~l~~~i~~~l~~~~~~~~~~~~~~-  239 (427)
                      ...+++|.|+.|.|||||++.+........+.  +   ..+.+  +.+...  ...+...+...   ..   ...+..+ 
T Consensus        26 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~--~~q~~~~~~~tv~~nl~~~---~~---~~LS~G~~   97 (166)
T cd03223          26 PGDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLF--LPQRPYLPLGTLREQLIYP---WD---DVLSGGEQ   97 (166)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEE--ECCCCccccccHHHHhhcc---CC---CCCCHHHH
Confidence            44689999999999999999998765211111  1   11222  222221  11233333210   11   1222222 


Q ss_pred             HHHHHHHHhcCCcEEEEEeccCCccc---ccccccCCCCCCCCcEEEEecCChhHH
Q 042645          240 KAQEIFKTMRNRKIVLLLDDIWELFD---LAQVGLPVPSRASASKVVFTTREFEVC  292 (427)
Q Consensus       240 ~~~~l~~~L~~k~~LlVlDdv~~~~~---~~~~~~~l~~~~~gs~IivTtR~~~v~  292 (427)
                      ..-.+...+-.++=+++||+.-+.-+   ...+...+...  +..||++|.+....
T Consensus        98 ~rv~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~  151 (166)
T cd03223          98 QRLAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLW  151 (166)
T ss_pred             HHHHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHH
Confidence            22233444556778889998754322   12222222211  35688888876654

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

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.74  E-value=0.012  Score=52.57  Aligned_cols=27  Identities=33%  Similarity=0.480  Sum_probs=24.5

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+++|.|+.|+|||||++.+...+
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l   57 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALL   57 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            457799999999999999999999877

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=96.74  E-value=0.0039  Score=50.26  Aligned_cols=72  Identities=15%  Similarity=0.104  Sum_probs=43.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      .+-|.|.|.||+|||||+..++...     .   .-|+++++-..-.+++...-+...     ....+.+.+.+.|...+
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~-----~---~~~i~isd~vkEn~l~~gyDE~y~-----c~i~DEdkv~D~Le~~m   73 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKT-----G---LEYIEISDLVKENNLYEGYDEEYK-----CHILDEDKVLDELEPLM   73 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHh-----C---CceEehhhHHhhhcchhccccccc-----CccccHHHHHHHHHHHH
Confidence            4569999999999999999998654     1   235666543333333222211111     13456677777777766


Q ss_pred             cCCcE
Q 042645          249 RNRKI  253 (427)
Q Consensus       249 ~~k~~  253 (427)
                      .+..+
T Consensus        74 ~~Gg~   78 (176)
T KOG3347|consen   74 IEGGN   78 (176)
T ss_pred             hcCCc
Confidence            55433

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.73  E-value=0.0051  Score=60.61  Aligned_cols=86  Identities=21%  Similarity=0.313  Sum_probs=52.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ...++.|.|.+|+|||||+.+++....   ..-..++|++....  ..++... ++.++......   ...+.+.+.+.+
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~~a---~~g~~vlYvs~Ees--~~qi~~r-a~rlg~~~~~l~~~~e~~l~~i~~~i  152 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAARLA---AAGGKVLYVSGEES--ASQIKLR-AERLGLPSDNLYLLAETNLEAILATI  152 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHH---hcCCeEEEEEcccc--HHHHHHH-HHHcCCChhcEEEeCCCCHHHHHHHH
Confidence            456899999999999999999988762   22346778776543  3343322 45555432211   122334443333


Q ss_pred             HHHhcCCcEEEEEeccCC
Q 042645          245 FKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~~k~~LlVlDdv~~  262 (427)
                      .   +.+.-++|+|.+..
T Consensus       153 ~---~~~~~lVVIDSIq~  167 (446)
T PRK11823        153 E---EEKPDLVVIDSIQT  167 (446)
T ss_pred             H---hhCCCEEEEechhh
Confidence            2   24667999999853

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=96.72  E-value=0.061  Score=47.42  Aligned_cols=165  Identities=15%  Similarity=0.211  Sum_probs=90.0

Q ss_pred             ccc-chhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          150 VVG-MQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       150 ~vG-R~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++| -+..+.+|.+.+.-             .+++-+.++|++|.|||-||+.++++-        ...|+.+|.+    
T Consensus       148 MiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht--------~c~firvsgs----  215 (404)
T KOG0728|consen  148 MIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT--------DCTFIRVSGS----  215 (404)
T ss_pred             HhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc--------ceEEEEechH----
Confidence            455 45566666555431             246678999999999999999998875        2345666543    


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCcccc----------------cccccCCC--CC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFDL----------------AQVGLPVP--SR  276 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~~----------------~~~~~~l~--~~  276 (427)
                      ++.+..+   + .        .......+.-.- ..-+.+|.+|++++...-                -++...+.  ..
T Consensus       216 elvqk~i---g-e--------gsrmvrelfvmarehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfea  283 (404)
T KOG0728|consen  216 ELVQKYI---G-E--------GSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEA  283 (404)
T ss_pred             HHHHHHh---h-h--------hHHHHHHHHHHHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhcccccc
Confidence            2222221   1 0        012223332222 346789999998764210                11111121  12


Q ss_pred             CCCcEEEEecCChhHHh--hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHH
Q 042645          277 ASASKVVFTTREFEVCG--LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVA  338 (427)
Q Consensus       277 ~~gs~IivTtR~~~v~~--~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~  338 (427)
                      ....+||..|..-++..  .+.   ....|+.++-+++.-.++++-+...-+....-++..+++++.
T Consensus       284 tknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~  350 (404)
T KOG0728|consen  284 TKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMP  350 (404)
T ss_pred             ccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCC
Confidence            34568888776555422  122   235678888888877788776554333222234444444443

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=96.71  E-value=0.0015  Score=53.67  Aligned_cols=23  Identities=30%  Similarity=0.528  Sum_probs=21.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|.++|++|+||||+|+.+....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~   23 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRL   23 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHS
T ss_pred             CEEEECCCCCCHHHHHHHHHHHC
Confidence            58899999999999999998776

...

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.70  E-value=0.011  Score=52.83  Aligned_cols=53  Identities=17%  Similarity=0.258  Sum_probs=34.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ...++.|.|++|+|||||+.+++..... .+  ..+++++..  .+..++++.+ .+++
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~-~g--~~~~yi~~e--~~~~~~~~~~-~~~g   75 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQ-NG--YSVSYVSTQ--LTTTEFIKQM-MSLG   75 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh-CC--CcEEEEeCC--CCHHHHHHHH-HHhC
Confidence            3468999999999999998776655421 11  345666633  3556666666 3444

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.70  E-value=0.023  Score=52.92  Aligned_cols=145  Identities=20%  Similarity=0.299  Sum_probs=76.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ..+-|.++|++|.|||-||+.++.+.   ...|-.+   .++.-.+  .       .++         ..+.+...+...
T Consensus       126 p~kGiLL~GPpG~GKTmlAKA~Akea---ga~fInv---~~s~lt~--K-------Wfg---------E~eKlv~AvFsl  181 (386)
T KOG0737|consen  126 PPKGILLYGPPGTGKTMLAKAIAKEA---GANFINV---SVSNLTS--K-------WFG---------EAQKLVKAVFSL  181 (386)
T ss_pred             CCccceecCCCCchHHHHHHHHHHHc---CCCccee---eccccch--h-------hHH---------HHHHHHHHHHhh
Confidence            45679999999999999999999887   4444332   2222111  0       000         001122222221


Q ss_pred             h-cCCcEEEEEeccCCcc--------------------cccccccCCCCCCCCcEEEE---ecCChhHHhh--cCCCcce
Q 042645          248 M-RNRKIVLLLDDIWELF--------------------DLAQVGLPVPSRASASKVVF---TTREFEVCGL--MDAHKSF  301 (427)
Q Consensus       248 L-~~k~~LlVlDdv~~~~--------------------~~~~~~~~l~~~~~gs~Iiv---TtR~~~v~~~--~~~~~~~  301 (427)
                      - +=++.+|.+|.+++.-                    .|+.+.     .+.+.+|||   |-|..++-..  -.-.+.+
T Consensus       182 AsKl~P~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~-----s~~~~rVlVlgATNRP~DlDeAiiRR~p~rf  256 (386)
T KOG0737|consen  182 ASKLQPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLS-----SKDSERVLVLGATNRPFDLDEAIIRRLPRRF  256 (386)
T ss_pred             hhhcCcceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhcccc-----CCCCceEEEEeCCCCCccHHHHHHHhCccee
Confidence            1 2368889999886531                    133331     233456776   5555444211  1122345


Q ss_pred             eccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          302 KVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       302 ~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      .++--+.++-.++++-.......+.+-+    ..+|++.|.|.-
T Consensus       257 ~V~lP~~~qR~kILkviLk~e~~e~~vD----~~~iA~~t~GyS  296 (386)
T KOG0737|consen  257 HVGLPDAEQRRKILKVILKKEKLEDDVD----LDEIAQMTEGYS  296 (386)
T ss_pred             eeCCCchhhHHHHHHHHhcccccCcccC----HHHHHHhcCCCc
Confidence            5554445555556655554443333333    567778888865

>PRK08233 hypothetical protein; Provisional

Probab=96.70  E-value=0.0015  Score=56.10  Aligned_cols=25  Identities=28%  Similarity=0.492  Sum_probs=22.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|.+|+||||||..+...+
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhC
Confidence            4689999999999999999999877

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

Probab=96.68  E-value=0.0067  Score=52.63  Aligned_cols=91  Identities=16%  Similarity=0.223  Sum_probs=47.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCC-------CCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC-------------
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPN-------DFDFVIWEVVSRDLQLGKIQESIAKKIGLYN-------------  229 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~-------------  229 (427)
                      .++.|.|++|+||||++..+.........       .-..++|++....  ...+.+.+........             
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~--~~~~~~rl~~~~~~~~~~~~~~~~~~~~~  110 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS--ESQIARRLRALLQDYDDDANLFFVDLSNW  110 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS---HHHHHHHHHHHHTTS-HHHHHHHHHH--E
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC--HHHHHHHHHHHhcccCCccceEEeecccc
Confidence            57999999999999999998887743221       2236778776654  3333333332221100             


Q ss_pred             -------CCCCCCCHHHHHHHHHHHhcC--CcEEEEEeccCC
Q 042645          230 -------ESWDNKSFDEKAQEIFKTMRN--RKIVLLLDDIWE  262 (427)
Q Consensus       230 -------~~~~~~~~~~~~~~l~~~L~~--k~~LlVlDdv~~  262 (427)
                             ............+.+.+.+..  +.-++|+|.+.+
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~l~~  152 (193)
T PF13481_consen  111 GCIRLFEPDSGGPLLDEDLEELEAALKELYGPDLVVIDPLQS  152 (193)
T ss_dssp             -EE---TTS---TTSHHHHHHHHHHHTT----SEEEEE-GGG
T ss_pred             ccceeeecccccccchHHHHHHHHHHhhcCCCcEEEEcCHHH
Confidence                   000111124455566666654  456999998753

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.68  E-value=0.0092  Score=56.81  Aligned_cols=89  Identities=20%  Similarity=0.182  Sum_probs=49.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK  246 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~  246 (427)
                      ..++|+|+|++|+||||++..++..+.   ..-..+..++.... ....+-+......++.+..  ...++..+...+..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~---~~GkkVglI~aDt~RiaAvEQLk~yae~lgipv~--v~~d~~~L~~aL~~  314 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFH---GKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVI--AVRDEAAMTRALTY  314 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHH---HcCCcEEEEecCCcchHHHHHHHHHhhhcCCcEE--ecCCHHHHHHHHHH
Confidence            347999999999999999999988762   11223444544321 1122233344444444321  13355555555544


Q ss_pred             HhcC-CcEEEEEeccC
Q 042645          247 TMRN-RKIVLLLDDIW  261 (427)
Q Consensus       247 ~L~~-k~~LlVlDdv~  261 (427)
                      .-.. +.=+|++|-.-
T Consensus       315 lk~~~~~DvVLIDTaG  330 (436)
T PRK11889        315 FKEEARVDYILIDTAG  330 (436)
T ss_pred             HHhccCCCEEEEeCcc
Confidence            3322 23467778764

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.68  E-value=0.0038  Score=59.80  Aligned_cols=46  Identities=20%  Similarity=0.257  Sum_probs=37.5

Q ss_pred             CccccchhhHHHHHHHhccC--------------CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEE--------------PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~--------------~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.++.++.+.-++...              ..+.|.++|++|+|||++|+.++...
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l   71 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLA   71 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            56889998888887666431              23679999999999999999999887

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.

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=96.67  E-value=0.0024  Score=57.76  Aligned_cols=66  Identities=20%  Similarity=0.266  Sum_probs=48.3

Q ss_pred             HHHHHHHhc--cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          157 LDRVWRCLT--EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       157 ~~~l~~~l~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      -.+|+..+.  .++..+|+|.|.||+|||||...+...+ ...++--.++=|.-|.+++-..++-+=.+
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l-~~~G~rVaVlAVDPSSp~TGGsiLGDRiR  104 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGREL-RERGHRVAVLAVDPSSPFTGGSILGDRIR  104 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHH-HHCCcEEEEEEECCCCCCCCccccccHhh
Confidence            345666654  3577899999999999999999998888 44555556666666777776666655443

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

Probab=96.67  E-value=0.0042  Score=60.30  Aligned_cols=47  Identities=19%  Similarity=0.200  Sum_probs=36.8

Q ss_pred             CCccccchhhHHHHHHHhcc-------C---------CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE-------E---------PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~-------~---------~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|.+..++.+..++..       .         ..+.+.++|++|+|||+||+.++...
T Consensus        70 ~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l  132 (412)
T PRK05342         70 DQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARIL  132 (412)
T ss_pred             hhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHh
Confidence            34589999998888666521       0         23569999999999999999998776

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=96.67  E-value=0.0034  Score=53.66  Aligned_cols=119  Identities=16%  Similarity=0.131  Sum_probs=64.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC---CCCHHHHHHHHH--H--HhCCCCCCCCCCCHHH-
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR---DLQLGKIQESIA--K--KIGLYNESWDNKSFDE-  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~---~~~~~~l~~~i~--~--~l~~~~~~~~~~~~~~-  239 (427)
                      ....|.|+|..|-||||.|.-+.-+..   .+-..+..+.+-+   .......+..+-  .  +.+... .+...+.++ 
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~---g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~-~~~~~~~~e~   96 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAV---GHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGF-TWETQDRERD   96 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHH---HCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCC-cccCCCcHHH
Confidence            346899999999999999988877652   2223344444322   334444443321  0  001100 011111111 


Q ss_pred             ------HHHHHHHHhcC-CcEEEEEeccCCc-----ccccccccCCCCCCCCcEEEEecCChh
Q 042645          240 ------KAQEIFKTMRN-RKIVLLLDDIWEL-----FDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       240 ------~~~~l~~~L~~-k~~LlVlDdv~~~-----~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                            ..+..++.+.. +-=|||||++-..     -+.+++...+.....+..||+|-|+.+
T Consensus        97 ~~~~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p  159 (191)
T PRK05986         97 IAAAREGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAP  159 (191)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCC
Confidence                  22333444544 4459999998543     233445455555556778999999854

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=96.66  E-value=0.0081  Score=55.00  Aligned_cols=96  Identities=13%  Similarity=0.078  Sum_probs=52.2

Q ss_pred             HHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC-----CCCC
Q 042645          160 VWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE-----SWDN  234 (427)
Q Consensus       160 l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~-----~~~~  234 (427)
                      ...++.+.+..++.|.|.+|+|||||+..+.+.+   .......+ + .....+..+  ...+...+.+.-     ....
T Consensus        95 ~r~~~~~~~~~~v~l~G~pGsGKTTLl~~l~~~l---~~~~~~~V-I-~gD~~t~~D--a~rI~~~g~pvvqi~tG~~Ch  167 (290)
T PRK10463         95 NRARFAARKQLVLNLVSSPGSGKTTLLTETLMRL---KDSVPCAV-I-EGDQQTVND--AARIRATGTPAIQVNTGKGCH  167 (290)
T ss_pred             HHHHHHhcCCeEEEEECCCCCCHHHHHHHHHHHh---ccCCCEEE-E-CCCcCcHHH--HHHHHhcCCcEEEecCCCCCc
Confidence            3344445678899999999999999999999887   22222222 2 222222222  222344333211     0112


Q ss_pred             CCHHHHHHHHHHHhcCCcEEEEEeccCC
Q 042645          235 KSFDEKAQEIFKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       235 ~~~~~~~~~l~~~L~~k~~LlVlDdv~~  262 (427)
                      .+...+...+..+.....-+||++++-+
T Consensus       168 l~a~mv~~Al~~L~~~~~d~liIEnvGn  195 (290)
T PRK10463        168 LDAQMIADAAPRLPLDDNGILFIENVGN  195 (290)
T ss_pred             CcHHHHHHHHHHHhhcCCcEEEEECCCC
Confidence            2333344444444334446788999865

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.65  E-value=0.0079  Score=58.32  Aligned_cols=26  Identities=27%  Similarity=0.465  Sum_probs=23.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.++|++|+||||++..++..+
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l  124 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYY  124 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999998766

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.65  E-value=0.013  Score=53.75  Aligned_cols=90  Identities=20%  Similarity=0.197  Sum_probs=49.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH--HHHHHHHHHHhCCCCC-CCCCCCHHHH-HHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL--GKIQESIAKKIGLYNE-SWDNKSFDEK-AQE  243 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~--~~l~~~i~~~l~~~~~-~~~~~~~~~~-~~~  243 (427)
                      +.+++.++|++|+||||++..++..+.   ..-..+..+.... +..  .+-+....+..+.+.. .....++... ...
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~l~---~~g~~V~li~~D~-~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~  146 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANKLK---KQGKSVLLAAGDT-FRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDA  146 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH---hcCCEEEEEeCCC-CCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHH
Confidence            457899999999999999999988772   2223555565442 222  2333344455553311 0112233332 233


Q ss_pred             HHHHhcCCcEEEEEeccC
Q 042645          244 IFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       244 l~~~L~~k~~LlVlDdv~  261 (427)
                      +.....+..=++++|-.-
T Consensus       147 l~~~~~~~~D~ViIDT~G  164 (272)
T TIGR00064       147 IQKAKARNIDVVLIDTAG  164 (272)
T ss_pred             HHHHHHCCCCEEEEeCCC
Confidence            433333444578888764

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.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.64  E-value=0.014  Score=53.87  Aligned_cols=79  Identities=13%  Similarity=0.061  Sum_probs=42.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCC--CCCCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLY--NESWDNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~--~~~~~~~~~~~~~~~l~  245 (427)
                      ...+|+|.|+.|+||||+|+.+..-....... ..+..++...-......+.    ..+..  ..-....+.+.+...+.
T Consensus        61 ~p~IIGIaG~~GSGKSTlar~L~~ll~~~~~~-g~V~vi~~D~f~~~~~~l~----~~g~~~~~g~P~s~D~~~l~~~L~  135 (290)
T TIGR00554        61 IPYIISIAGSVAVGKSTTARILQALLSRWPEH-RKVELITTDGFLHPNQVLK----ERNLMKKKGFPESYDMHRLVKFLS  135 (290)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHhhcCCC-CceEEEecccccccHHHHH----HcCCccccCCChhccHHHHHHHHH
Confidence            45799999999999999998776554111111 1233344333222222222    22211  11124456666766666


Q ss_pred             HHhcCC
Q 042645          246 KTMRNR  251 (427)
Q Consensus       246 ~~L~~k  251 (427)
                      ....++
T Consensus       136 ~Lk~g~  141 (290)
T TIGR00554       136 DLKSGK  141 (290)
T ss_pred             HHHCCC
Confidence            665554

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=96.62  E-value=0.023  Score=57.00  Aligned_cols=135  Identities=17%  Similarity=0.155  Sum_probs=71.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCC-----CCcEEEEEEeCC-C--------------C-C-HHHHHHHHHHHh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPN-----DFDFVIWEVVSR-D--------------L-Q-LGKIQESIAKKI  225 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-----~f~~~~wv~~~~-~--------------~-~-~~~l~~~i~~~l  225 (427)
                      ....|+|+|+.|+|||||.+.+........+     .--.+.|+.-.. .              + + ...-.+..+..+
T Consensus       347 ~g~riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f  426 (530)
T COG0488         347 RGDRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRF  426 (530)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHc
Confidence            4457999999999999999999665521111     111122222111 0              0 0 134444455555


Q ss_pred             CCCCCCC----CCCCHHHHHH-HHHHHhcCCcEEEEEeccCCccccc---ccccCCCCCCCCcEEEEecCChhHHhhcCC
Q 042645          226 GLYNESW----DNKSFDEKAQ-EIFKTMRNRKIVLLLDDIWELFDLA---QVGLPVPSRASASKVVFTTREFEVCGLMDA  297 (427)
Q Consensus       226 ~~~~~~~----~~~~~~~~~~-~l~~~L~~k~~LlVlDdv~~~~~~~---~~~~~l~~~~~gs~IivTtR~~~v~~~~~~  297 (427)
                      +...+..    ...+..+..+ .+...+-.++-+||||+--|.-+.+   .+...+.. -.| .||+.|.+..+..... 
T Consensus       427 ~F~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~-f~G-tvl~VSHDr~Fl~~va-  503 (530)
T COG0488         427 GFTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLD-FEG-TVLLVSHDRYFLDRVA-  503 (530)
T ss_pred             CCChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHh-CCC-eEEEEeCCHHHHHhhc-
Confidence            5443211    1223333333 3344556789999999876643322   22223322 123 4888999988776543 


Q ss_pred             CcceeccC
Q 042645          298 HKSFKVEC  305 (427)
Q Consensus       298 ~~~~~l~~  305 (427)
                      ...+.+.+
T Consensus       504 ~~i~~~~~  511 (530)
T COG0488         504 TRIWLVED  511 (530)
T ss_pred             ceEEEEcC
Confidence            34455543

>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=96.62  E-value=0.0017  Score=45.95  Aligned_cols=23  Identities=26%  Similarity=0.569  Sum_probs=20.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|.+|+||||+++.+.+.+
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998875

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.

>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=96.61  E-value=0.0021  Score=50.88  Aligned_cols=40  Identities=38%  Similarity=0.400  Sum_probs=22.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHH
Q 042645          172 VGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l  217 (427)
                      |.|+|.+|+||||+|+.++...   ...|..   |.+..+..+.++
T Consensus         2 vLleg~PG~GKT~la~~lA~~~---~~~f~R---Iq~tpdllPsDi   41 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSL---GLSFKR---IQFTPDLLPSDI   41 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHT---T--EEE---EE--TT--HHHH
T ss_pred             EeeECCCccHHHHHHHHHHHHc---CCceeE---EEecCCCCcccc
Confidence            6899999999999999999887   455643   333444444443

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.

>PRK05973 replicative DNA helicase; Provisional

Probab=96.61  E-value=0.016  Score=51.73  Aligned_cols=86  Identities=15%  Similarity=0.157  Sum_probs=49.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---------CCCCHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---------DNKSFD  238 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---------~~~~~~  238 (427)
                      ...++.|.|.+|+|||+++.++.....   ..-..+++++....  ..++...+. +++......         .....+
T Consensus        63 ~Gsl~LIaG~PG~GKT~lalqfa~~~a---~~Ge~vlyfSlEes--~~~i~~R~~-s~g~d~~~~~~~~~~d~~d~~~~~  136 (237)
T PRK05973         63 PGDLVLLGARPGHGKTLLGLELAVEAM---KSGRTGVFFTLEYT--EQDVRDRLR-ALGADRAQFADLFEFDTSDAICAD  136 (237)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHH---hcCCeEEEEEEeCC--HHHHHHHHH-HcCCChHHhccceEeecCCCCCHH
Confidence            446899999999999999999876652   22345667766543  455555543 233321110         112233


Q ss_pred             HHHHHHHHHhcCCcEEEEEeccC
Q 042645          239 EKAQEIFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       239 ~~~~~l~~~L~~k~~LlVlDdv~  261 (427)
                      ..+..+..  ..+.-++|+|-+.
T Consensus       137 ~ii~~l~~--~~~~~lVVIDsLq  157 (237)
T PRK05973        137 YIIARLAS--APRGTLVVIDYLQ  157 (237)
T ss_pred             HHHHHHHH--hhCCCEEEEEcHH
Confidence            33333333  1234588899875

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.61  E-value=0.012  Score=52.19  Aligned_cols=23  Identities=30%  Similarity=0.476  Sum_probs=21.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|++|+||||||+.+...+
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l   23 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALL   23 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999877

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.61  E-value=0.07  Score=53.85  Aligned_cols=47  Identities=17%  Similarity=0.220  Sum_probs=39.2

Q ss_pred             CCccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|+...++++.+.+..  .....|.|+|..|+|||++|+.+.+..
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s  234 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAAS  234 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC
Confidence            35789999999888888754  344568999999999999999998765

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

Probab=96.60  E-value=0.0098  Score=51.05  Aligned_cols=120  Identities=19%  Similarity=0.234  Sum_probs=62.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEE---eCCCCCHHHHH------HHHHHHhCCCCC---CCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEV---VSRDLQLGKIQ------ESIAKKIGLYNE---SWDNK  235 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~---~~~~~~~~~l~------~~i~~~l~~~~~---~~~~~  235 (427)
                      ...+++|.|+.|+|||||++.++....    .....+++.   +. ..+.....      .++++.+++...   .....
T Consensus        24 ~G~~~~l~G~nGsGKStLl~~i~G~~~----~~~G~v~~~g~~~~-~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~L   98 (180)
T cd03214          24 AGEIVGILGPNGAGKSTLLKTLAGLLK----PSSGEILLDGKDLA-SLSPKELARKIAYVPQALELLGLAHLADRPFNEL   98 (180)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC----CCCcEEEECCEECC-cCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccC
Confidence            446899999999999999999987651    122233322   11 11222211      124455554321   11122


Q ss_pred             CHHHH-HHHHHHHhcCCcEEEEEeccCCccc---ccccccCCCCC-CC-CcEEEEecCChhHH
Q 042645          236 SFDEK-AQEIFKTMRNRKIVLLLDDIWELFD---LAQVGLPVPSR-AS-ASKVVFTTREFEVC  292 (427)
Q Consensus       236 ~~~~~-~~~l~~~L~~k~~LlVlDdv~~~~~---~~~~~~~l~~~-~~-gs~IivTtR~~~v~  292 (427)
                      +..+. .-.+...+-..+-++++|+.-+.-+   ...+...+... .. +..||++|.+....
T Consensus        99 S~G~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~  161 (180)
T cd03214          99 SGGERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLA  161 (180)
T ss_pred             CHHHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHH
Confidence            22222 2234445566788999999754322   22222222211 12 56788888876653

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

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.59  E-value=0.004  Score=53.17  Aligned_cols=23  Identities=26%  Similarity=0.465  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+|+.+.+.+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999886

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.59  E-value=0.012  Score=53.80  Aligned_cols=91  Identities=14%  Similarity=0.097  Sum_probs=56.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHH---HHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDE---KAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~---~~~~l  244 (427)
                      ..+++=|+|+.|+||||+|.+++-..   +..-..++|+..-..+++..+..-....+..-.- ....+.++   ++..+
T Consensus        59 ~g~ItEiyG~~gsGKT~lal~~~~~a---q~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~v-~~~~~~e~q~~i~~~~  134 (279)
T COG0468          59 RGRITEIYGPESSGKTTLALQLVANA---QKPGGKAAFIDTEHALDPERAKQLGVDLLDNLLV-SQPDTGEQQLEIAEKL  134 (279)
T ss_pred             cceEEEEecCCCcchhhHHHHHHHHh---hcCCCeEEEEeCCCCCCHHHHHHHHHhhhcceeE-ecCCCHHHHHHHHHHH
Confidence            45788999999999999999987666   3334488999998888877654333221211000 02223333   33333


Q ss_pred             HHHhcCCcEEEEEeccCC
Q 042645          245 FKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~~k~~LlVlDdv~~  262 (427)
                      ......+--|+|+|.+-.
T Consensus       135 ~~~~~~~i~LvVVDSvaa  152 (279)
T COG0468         135 ARSGAEKIDLLVVDSVAA  152 (279)
T ss_pred             HHhccCCCCEEEEecCcc
Confidence            334334466999999853

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.59  E-value=0.012  Score=56.57  Aligned_cols=91  Identities=19%  Similarity=0.203  Sum_probs=53.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCC-CCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTP-NDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~  245 (427)
                      ..++|.++|+.|+||||.+..++..+.... ..-..+..++.... .....-+...++.++.+..  ...+.+.+...+.
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~--~~~~~~~l~~~L~  250 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVK--AIESFKDLKEEIT  250 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceE--eeCcHHHHHHHHH
Confidence            346899999999999999999988762111 12234555555432 1222335556666665432  2334444444444


Q ss_pred             HHhcCCcEEEEEeccCC
Q 042645          246 KTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       246 ~~L~~k~~LlVlDdv~~  262 (427)
                      ..  .+.-++++|....
T Consensus       251 ~~--~~~DlVLIDTaGr  265 (388)
T PRK12723        251 QS--KDFDLVLVDTIGK  265 (388)
T ss_pred             Hh--CCCCEEEEcCCCC
Confidence            33  3455888898753

>TIGR01069 mutS2 MutS2 family protein

Probab=96.57  E-value=0.0023  Score=67.21  Aligned_cols=115  Identities=17%  Similarity=0.169  Sum_probs=59.2

Q ss_pred             CCcEEEEEeccCCcccc---c----ccccCCCCCCCCcEEEEecCChhHHhhcCCCcceeccCCChHHHHHHHHHHhCCC
Q 042645          250 NRKIVLLLDDIWELFDL---A----QVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRD  322 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~~---~----~~~~~l~~~~~gs~IivTtR~~~v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~  322 (427)
                      ..+-|++||++-.-.+.   .    .+...+.  ..|+.+|+||....+.........+....+..++-.--|..++...
T Consensus       401 ~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l~--~~g~~viitTH~~eL~~~~~~~~~v~~~~~~~d~~~l~p~Ykl~~G  478 (771)
T TIGR01069       401 TENSLVLFDELGAGTDPDEGSALAISILEYLL--KQNAQVLITTHYKELKALMYNNEGVENASVLFDEETLSPTYKLLKG  478 (771)
T ss_pred             CCCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHHhcCCCCeEEeEEEEcCCCCceEEEECCC
Confidence            47899999998654221   1    1222222  3478899999998775543222222111111111000011111111


Q ss_pred             CCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHhh
Q 042645          323 ILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRS  373 (427)
Q Consensus       323 ~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~~  373 (427)
                      .  +.   ...+-.|++++ |+|-.+.--|..+.. ....+...+++.|..
T Consensus       479 ~--~g---~S~a~~iA~~~-Glp~~ii~~A~~~~~-~~~~~~~~li~~L~~  522 (771)
T TIGR01069       479 I--PG---ESYAFEIAQRY-GIPHFIIEQAKTFYG-EFKEEINVLIEKLSA  522 (771)
T ss_pred             C--CC---CcHHHHHHHHh-CcCHHHHHHHHHHHH-hhHHHHHHHHHHHHH
Confidence            1  11   12377777776 789888887777765 234456666666554

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PRK14974 cell division protein FtsY; Provisional

Probab=96.57  E-value=0.021  Score=53.81  Aligned_cols=91  Identities=19%  Similarity=0.159  Sum_probs=50.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC--CHHHHHHHHHHHhCCCCCC-CCCCCHHHHH-HH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL--QLGKIQESIAKKIGLYNES-WDNKSFDEKA-QE  243 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~--~~~~l~~~i~~~l~~~~~~-~~~~~~~~~~-~~  243 (427)
                      +..+|.++|++|+||||++..++..+. . ..+ .++.+... .+  ...+-+...+..++.+... ....++.... ..
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~-~-~g~-~V~li~~D-t~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~a  214 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLK-K-NGF-SVVIAAGD-TFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDA  214 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-H-cCC-eEEEecCC-cCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHH
Confidence            457999999999999999999887762 2 223 33334322 22  2233455666777654321 1223333332 22


Q ss_pred             HHHHhcCCcEEEEEeccCC
Q 042645          244 IFKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       244 l~~~L~~k~~LlVlDdv~~  262 (427)
                      +........=++++|-...
T Consensus       215 i~~~~~~~~DvVLIDTaGr  233 (336)
T PRK14974        215 IEHAKARGIDVVLIDTAGR  233 (336)
T ss_pred             HHHHHhCCCCEEEEECCCc
Confidence            2222222223889998754

>PRK06762 hypothetical protein; Provisional

Probab=96.57  E-value=0.002  Score=54.51  Aligned_cols=25  Identities=28%  Similarity=0.496  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.|+|++|+||||+|+.+.+.+
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999998876

>TIGR00416 sms DNA repair protein RadA

Probab=96.57  E-value=0.01  Score=58.52  Aligned_cols=96  Identities=21%  Similarity=0.286  Sum_probs=54.6

Q ss_pred             HHHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---
Q 042645          158 DRVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---  232 (427)
Q Consensus       158 ~~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---  232 (427)
                      ..+-+.|..+  ...++.|.|.+|+|||||+.+++.....   .-..++|++..+.  ..++.. -+..++......   
T Consensus        81 ~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~a~---~g~kvlYvs~EEs--~~qi~~-ra~rlg~~~~~l~~~  154 (454)
T TIGR00416        81 GELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAK---NQMKVLYVSGEES--LQQIKM-RAIRLGLPEPNLYVL  154 (454)
T ss_pred             HHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHHHh---cCCcEEEEECcCC--HHHHHH-HHHHcCCChHHeEEc
Confidence            3344444332  5578999999999999999999776622   1235778775443  333332 233444322110   


Q ss_pred             CCCCHHHHHHHHHHHhcCCcEEEEEeccCC
Q 042645          233 DNKSFDEKAQEIFKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       233 ~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~  262 (427)
                      ...+.+.+...+.   +.+.-++|+|.+..
T Consensus       155 ~e~~~~~I~~~i~---~~~~~~vVIDSIq~  181 (454)
T TIGR00416       155 SETNWEQICANIE---EENPQACVIDSIQT  181 (454)
T ss_pred             CCCCHHHHHHHHH---hcCCcEEEEecchh
Confidence            1233344433332   23667899998854

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)).

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=96.57  E-value=0.015  Score=51.15  Aligned_cols=61  Identities=11%  Similarity=0.172  Sum_probs=35.6

Q ss_pred             HHHHHHHhcCCcEEEEEeccCCcc---cccccccCCCC--CCCCcEEEEecCChhHHhhcCCCcceec
Q 042645          241 AQEIFKTMRNRKIVLLLDDIWELF---DLAQVGLPVPS--RASASKVVFTTREFEVCGLMDAHKSFKV  303 (427)
Q Consensus       241 ~~~l~~~L~~k~~LlVlDdv~~~~---~~~~~~~~l~~--~~~gs~IivTtR~~~v~~~~~~~~~~~l  303 (427)
                      .-.+.+.|-..+-+|+.|+--..-   .-..+...+..  ...|..||+.|.+..++..+  .+.|.+
T Consensus       150 RVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~lA~~~--dr~i~l  215 (226)
T COG1136         150 RVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDPELAKYA--DRVIEL  215 (226)
T ss_pred             HHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHhC--CEEEEE
Confidence            334556667788899999853211   11122222221  23477899999999998854  344444

>PTZ00301 uridine kinase; Provisional

Probab=96.56  E-value=0.002  Score=56.54  Aligned_cols=25  Identities=32%  Similarity=0.631  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|.+|+||||||+.+.+.+
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l   27 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSEL   27 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHH
Confidence            4689999999999999999988765

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=96.55  E-value=0.013  Score=54.65  Aligned_cols=88  Identities=17%  Similarity=0.155  Sum_probs=54.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..+++-|+|+.|+||||||..+.....   ..-..++|+.....+++     ..+..++++.+..   .....++.....
T Consensus        52 ~G~ivEi~G~~ssGKttLaL~~ia~~q---~~g~~~a~ID~e~~ld~-----~~a~~lGvdl~rllv~~P~~~E~al~~~  123 (322)
T PF00154_consen   52 RGRIVEIYGPESSGKTTLALHAIAEAQ---KQGGICAFIDAEHALDP-----EYAESLGVDLDRLLVVQPDTGEQALWIA  123 (322)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH---HTT-EEEEEESSS---H-----HHHHHTT--GGGEEEEE-SSHHHHHHHH
T ss_pred             cCceEEEeCCCCCchhhhHHHHHHhhh---cccceeEEecCcccchh-----hHHHhcCccccceEEecCCcHHHHHHHH
Confidence            457999999999999999999887762   23457889988776554     3455566543321   133455666666


Q ss_pred             HHHhcCC-cEEEEEeccCCc
Q 042645          245 FKTMRNR-KIVLLLDDIWEL  263 (427)
Q Consensus       245 ~~~L~~k-~~LlVlDdv~~~  263 (427)
                      ...++.. --++|+|.|-..
T Consensus       124 e~lirsg~~~lVVvDSv~al  143 (322)
T PF00154_consen  124 EQLIRSGAVDLVVVDSVAAL  143 (322)
T ss_dssp             HHHHHTTSESEEEEE-CTT-
T ss_pred             HHHhhcccccEEEEecCccc
Confidence            6666643 458999998653

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.54  E-value=0.0082  Score=62.34  Aligned_cols=86  Identities=16%  Similarity=0.177  Sum_probs=58.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..+++-|+|++|+|||||+.+++....   ..-..++|+.....+++     ..+++++++....   ...+.+.....+
T Consensus        59 ~GsiteI~G~~GsGKTtLal~~~~~a~---~~G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i  130 (790)
T PRK09519         59 RGRVIEIYGPESSGKTTVALHAVANAQ---AAGGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIA  130 (790)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHH
Confidence            467899999999999999988766542   22356788887776663     3667777653211   233445566666


Q ss_pred             HHHhc-CCcEEEEEeccC
Q 042645          245 FKTMR-NRKIVLLLDDIW  261 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~  261 (427)
                      ...++ ++.-|||+|.+-
T Consensus       131 ~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        131 DMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             HHHhhcCCCeEEEEcchh
Confidence            66554 466799999975

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.52  E-value=0.0021  Score=57.25  Aligned_cols=23  Identities=30%  Similarity=0.462  Sum_probs=21.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+|+.+.+.+
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            38899999999999999998876

>PRK05439 pantothenate kinase; Provisional

Probab=96.52  E-value=0.023  Score=52.90  Aligned_cols=83  Identities=12%  Similarity=0.011  Sum_probs=44.6

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK  246 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~  246 (427)
                      +..-+|+|.|.+|+||||+|+.+...+. .......+.-++...-+.....+..  ..+..........+.+.+...|..
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~-~~~~~~~v~vi~~DdFy~~~~~l~~--~~l~~~kg~Pes~D~~~l~~~L~~  160 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLS-RWPEHPKVELVTTDGFLYPNAVLEE--RGLMKRKGFPESYDMRALLRFLSD  160 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH-hhCCCCceEEEeccccccCHHHHhh--hhccccCCCcccccHHHHHHHHHH
Confidence            3567999999999999999999887652 1111122333443332222222211  011000111234566777777776


Q ss_pred             HhcCCc
Q 042645          247 TMRNRK  252 (427)
Q Consensus       247 ~L~~k~  252 (427)
                      ...++.
T Consensus       161 Lk~G~~  166 (311)
T PRK05439        161 VKSGKP  166 (311)
T ss_pred             HHcCCC
Confidence            666665

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.52  E-value=0.0022  Score=55.43  Aligned_cols=26  Identities=27%  Similarity=0.340  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|+|.|++|+||||+++.+.+.+
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998765

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.51  E-value=0.016  Score=54.94  Aligned_cols=90  Identities=21%  Similarity=0.115  Sum_probs=54.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK  246 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~  246 (427)
                      +.++++|+|+.|+||||++..++..+. ..  -..+.+++.... ....+-+...++.++.+..  ...++.++...+..
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~-~~--g~~V~lItaDtyR~gAveQLk~yae~lgvpv~--~~~dp~dL~~al~~  279 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLL-KQ--NRTVGFITTDTFRSGAVEQFQGYADKLDVELI--VATSPAELEEAVQY  279 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-Hc--CCeEEEEeCCccCccHHHHHHHHhhcCCCCEE--ecCCHHHHHHHHHH
Confidence            457999999999999999999987662 22  234566665432 2234455556666655432  23455666554543


Q ss_pred             Hhc-CCcEEEEEeccCC
Q 042645          247 TMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       247 ~L~-~k~~LlVlDdv~~  262 (427)
                      .-. +..=+|++|-.-.
T Consensus       280 l~~~~~~D~VLIDTAGr  296 (407)
T PRK12726        280 MTYVNCVDHILIDTVGR  296 (407)
T ss_pred             HHhcCCCCEEEEECCCC
Confidence            321 3345778887643

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.50  E-value=0.0025  Score=56.19  Aligned_cols=26  Identities=35%  Similarity=0.502  Sum_probs=23.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..+|+|.|++|+|||||++.+...+
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            56799999999999999999999876

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.50  E-value=0.0049  Score=49.61  Aligned_cols=39  Identities=26%  Similarity=0.351  Sum_probs=29.7

Q ss_pred             hhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          155 STLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       155 ~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++..++.+.|..  ....+|.+.|.-|+||||+++.+++.+
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            344555555543  344689999999999999999999987

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.

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

Probab=96.50  E-value=0.0097  Score=53.14  Aligned_cols=90  Identities=20%  Similarity=0.189  Sum_probs=55.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC-------------CCC-
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE-------------SWD-  233 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~-------------~~~-  233 (427)
                      ...++.|.|++|+|||+|+.++......  ..-..++|++...+  +.++.+.+. .++.+..             ... 
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~--~~ge~vlyvs~ee~--~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~   92 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLK--NFGEKVLYVSFEEP--PEELIENMK-SFGWDLEEYEDSGKLKIIDAFPER   92 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH--HHT--EEEEESSS---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGG
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhh--hcCCcEEEEEecCC--HHHHHHHHH-HcCCcHHHHhhcCCEEEEeccccc
Confidence            5679999999999999999987654311  11345778877543  344444433 3332110             001 


Q ss_pred             ----CCCHHHHHHHHHHHhcC-CcEEEEEeccCC
Q 042645          234 ----NKSFDEKAQEIFKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       234 ----~~~~~~~~~~l~~~L~~-k~~LlVlDdv~~  262 (427)
                          ..+.+.+...+.+.++. +...+|+|.+..
T Consensus        93 ~~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls~  126 (226)
T PF06745_consen   93 IGWSPNDLEELLSKIREAIEELKPDRVVIDSLSA  126 (226)
T ss_dssp             ST-TSCCHHHHHHHHHHHHHHHTSSEEEEETHHH
T ss_pred             ccccccCHHHHHHHHHHHHHhcCCCEEEEECHHH
Confidence                35677778888777664 568999999743

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 ....

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=96.49  E-value=0.0089  Score=61.22  Aligned_cols=74  Identities=15%  Similarity=0.179  Sum_probs=51.1

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.++.+..+...+..+.  .+.++|++|+||||+++.+.+.+.  ...|...+++ .....+...++..+...++
T Consensus        18 ~~viG~~~a~~~l~~a~~~~~--~~ll~G~pG~GKT~la~~la~~l~--~~~~~~~~~~-~n~~~~~~~~~~~v~~~~g   91 (608)
T TIGR00764        18 DQVIGQEEAVEIIKKAAKQKR--NVLLIGEPGVGKSMLAKAMAELLP--DEELEDILVY-PNPEDPNMPRIVEVPAGEG   91 (608)
T ss_pred             hhccCHHHHHHHHHHHHHcCC--CEEEECCCCCCHHHHHHHHHHHcC--chhheeEEEE-eCCCCCchHHHHHHHHhhc
Confidence            567899998888887777653  566999999999999999998872  2233333322 2233345566666666554

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

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=96.49  E-value=0.0037  Score=55.67  Aligned_cols=63  Identities=17%  Similarity=0.206  Sum_probs=38.0

Q ss_pred             hHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHH
Q 042645          156 TLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQE  219 (427)
Q Consensus       156 ~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~  219 (427)
                      ...++++.+..  ++..+|+|.|+||+|||||...+...+ ...++--.++=|.-|.+++-..++-
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~-~~~g~~VaVlAVDPSSp~tGGAlLG   78 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIREL-RERGKRVAVLAVDPSSPFTGGALLG   78 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHH-HHTT--EEEEEE-GGGGCC---SS-
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHH-hhcCCceEEEEECCCCCCCCCcccc
Confidence            44555665543  477899999999999999999998888 3334444455555565665544443

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.49  E-value=0.021  Score=52.14  Aligned_cols=40  Identities=15%  Similarity=0.287  Sum_probs=30.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      ...++.|.|++|+|||+++.+++....   ..-..+++++...
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a---~~Ge~vlyis~Ee   74 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQA---SRGNPVLFVTVES   74 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH---hCCCcEEEEEecC
Confidence            467899999999999999999866542   2234677888764

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.48  E-value=0.018  Score=51.67  Aligned_cols=125  Identities=17%  Similarity=0.172  Sum_probs=71.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-----CCCHHHHHHHHHHHhCCCCCCC----CCCCHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-----DLQLGKIQESIAKKIGLYNESW----DNKSFD  238 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-----~~~~~~l~~~i~~~l~~~~~~~----~~~~~~  238 (427)
                      ...+++|+|..|+|||||++.+..-.   ......+.| .-.+     .....+-..+++..+++.....    ..-+..
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~---~pt~G~i~f-~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGG  113 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLE---EPTSGEILF-EGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGG  113 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCc---CCCCceEEE-cCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCch
Confidence            45689999999999999999998765   222222332 2111     1223345566677766543210    122223


Q ss_pred             HHHH-HHHHHhcCCcEEEEEeccCCcccc---cccccCCCC--CCCCcEEEEecCChhHHhhcC
Q 042645          239 EKAQ-EIFKTMRNRKIVLLLDDIWELFDL---AQVGLPVPS--RASASKVVFTTREFEVCGLMD  296 (427)
Q Consensus       239 ~~~~-~l~~~L~~k~~LlVlDdv~~~~~~---~~~~~~l~~--~~~gs~IivTtR~~~v~~~~~  296 (427)
                      +.++ .|...|.-++-++|.|+.-+..+.   .++...+.+  ...|-..+..|.+-.+...+.
T Consensus       114 QrQRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~is  177 (268)
T COG4608         114 QRQRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYIS  177 (268)
T ss_pred             hhhhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhhhc
Confidence            3333 345567789999999997654332   222222211  123566788888877766654

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=96.47  E-value=0.0053  Score=62.78  Aligned_cols=74  Identities=12%  Similarity=0.180  Sum_probs=56.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.++.++.|...+..+  +.+.++|++|+||||+|+.+.+.+.  ..+++..+|..- ...+...+++.++..++
T Consensus        31 ~~vigq~~a~~~L~~~~~~~--~~~l~~G~~G~GKttla~~l~~~l~--~~~~~~~~~~~n-p~~~~~~~~~~v~~~~G  104 (637)
T PRK13765         31 DQVIGQEHAVEVIKKAAKQR--RHVMMIGSPGTGKSMLAKAMAELLP--KEELQDILVYPN-PEDPNNPKIRTVPAGKG  104 (637)
T ss_pred             HHcCChHHHHHHHHHHHHhC--CeEEEECCCCCcHHHHHHHHHHHcC--hHhHHHheEeeC-CCcchHHHHHHHHHhcC
Confidence            56899999998888877665  4689999999999999999998762  344577777554 44467777777776554

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.47  E-value=0.016  Score=57.97  Aligned_cols=99  Identities=14%  Similarity=0.131  Sum_probs=63.0

Q ss_pred             HHHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----
Q 042645          158 DRVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES----  231 (427)
Q Consensus       158 ~~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~----  231 (427)
                      ..|-+.|..+  ...++.|.|++|+|||||+.+++....   ..-..+++++..+  +..++...+ +.++.+...    
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~---~~ge~~~y~s~eE--s~~~i~~~~-~~lg~~~~~~~~~  323 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENAC---ANKERAILFAYEE--SRAQLLRNA-YSWGIDFEEMEQQ  323 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHH---HCCCeEEEEEeeC--CHHHHHHHH-HHcCCChHHHhhC
Confidence            3444444442  567999999999999999999987762   2334567776554  455555554 455543211    


Q ss_pred             ---------CCCCCHHHHHHHHHHHhcC-CcEEEEEeccCC
Q 042645          232 ---------WDNKSFDEKAQEIFKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       232 ---------~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~~  262 (427)
                               ....+.++....+.+.+.. +.-++|+|.+..
T Consensus       324 g~l~~~~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi~~  364 (484)
T TIGR02655       324 GLLKIICAYPESAGLEDHLQIIKSEIADFKPARIAIDSLSA  364 (484)
T ss_pred             CcEEEEEcccccCChHHHHHHHHHHHHHcCCCEEEEcCHHH
Confidence                     1223446677777776654 566899999853

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=96.47  E-value=0.079  Score=46.82  Aligned_cols=44  Identities=27%  Similarity=0.389  Sum_probs=33.7

Q ss_pred             cccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          150 VVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +=|-+-.++++.+...-             +..+-|.++|++|.|||.||+.++++-
T Consensus       157 iggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t  213 (408)
T KOG0727|consen  157 IGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  213 (408)
T ss_pred             cccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhcc
Confidence            44566666666665531             356789999999999999999999886

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.45  E-value=0.036  Score=55.69  Aligned_cols=173  Identities=17%  Similarity=0.176  Sum_probs=89.2

Q ss_pred             Cccccchhh---HHHHHHHhccCC---------CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQST---LDRVWRCLTEEP---------VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~---~~~l~~~l~~~~---------~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .++.|.++.   +.++++.|.++.         ++-|.++|++|.|||.||+.++... .+ ..|      +.|.+    
T Consensus       150 ~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA-~V-PFf------~iSGS----  217 (596)
T COG0465         150 ADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-GV-PFF------SISGS----  217 (596)
T ss_pred             hhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhccc-CC-Cce------eccch----
Confidence            456787765   555566666542         4568899999999999999999876 22 112      12211    


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc------------c----cccccCCCCCC--
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD------------L----AQVGLPVPSRA--  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~------------~----~~~~~~l~~~~--  277 (427)
                          +..+.+       ...........+.+..+.-++++++|.++....            +    .++........  
T Consensus       218 ----~FVemf-------VGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~  286 (596)
T COG0465         218 ----DFVEMF-------VGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGN  286 (596)
T ss_pred             ----hhhhhh-------cCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCC
Confidence                011111       111222333444555566789999999875411            1    22211111112  


Q ss_pred             CCcEEEEecCChhHH--hhcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          278 SASKVVFTTREFEVC--GLMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       278 ~gs~IivTtR~~~v~--~~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      .|-.|+..|...+|.  ..+.   -...+.++..+-..-.++++-++........-++    ..|++.+-|.-.|
T Consensus       287 ~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl----~~iAr~tpGfsGA  357 (596)
T COG0465         287 EGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDL----KKIARGTPGFSGA  357 (596)
T ss_pred             CceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCH----HHHhhhCCCcccc
Confidence            233333333333332  1222   2345566666656666666655533332222232    3377777776554

>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=96.45  E-value=0.0079  Score=54.97  Aligned_cols=25  Identities=24%  Similarity=0.308  Sum_probs=20.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      +.|.|+|.||+||||+|+.+...+.
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~   26 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLE   26 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHH
Confidence            5789999999999999999998873

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.43  E-value=0.002  Score=50.13  Aligned_cols=22  Identities=32%  Similarity=0.700  Sum_probs=19.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|++|+|||+||..++.++
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l   22 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDL   22 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            5799999999999999988776

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

>TIGR00235 udk uridine kinase

Probab=96.42  E-value=0.0028  Score=55.80  Aligned_cols=26  Identities=35%  Similarity=0.457  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|++|+|||||++.+...+
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~~l   30 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYEQL   30 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998876

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

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

Probab=96.41  E-value=0.0086  Score=56.82  Aligned_cols=67  Identities=24%  Similarity=0.205  Sum_probs=50.6

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..++|++..+..+..++..++  .+.+.|++|+|||+||+.++...   .   ....++.+.....+.++.....
T Consensus        24 ~~~~g~~~~~~~~l~a~~~~~--~vll~G~PG~gKT~la~~lA~~l---~---~~~~~i~~t~~l~p~d~~G~~~   90 (329)
T COG0714          24 KVVVGDEEVIELALLALLAGG--HVLLEGPPGVGKTLLARALARAL---G---LPFVRIQCTPDLLPSDLLGTYA   90 (329)
T ss_pred             CeeeccHHHHHHHHHHHHcCC--CEEEECCCCccHHHHHHHHHHHh---C---CCeEEEecCCCCCHHHhcCchh
Confidence            347898888888877777654  38899999999999999999887   2   2345667777777776654443

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

Probab=96.41  E-value=0.022  Score=51.02  Aligned_cols=123  Identities=16%  Similarity=0.218  Sum_probs=68.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCC----------CC---cEEEEEEe----CCCC--CH--------------
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPN----------DF---DFVIWEVV----SRDL--QL--------------  214 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----------~f---~~~~wv~~----~~~~--~~--------------  214 (427)
                      ....++|+|+.|.|||||.+.+..-.....+          ..   ..+.||.=    ...+  ++              
T Consensus        29 ~G~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~  108 (254)
T COG1121          29 KGEITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGW  108 (254)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCcccccc
Confidence            3468999999999999999999874421111          01   23445431    1111  11              


Q ss_pred             --------HHHHHHHHHHhCCCC---CCCCCCCHHHHHHH-HHHHhcCCcEEEEEeccCCc------ccccccccCCCCC
Q 042645          215 --------GKIQESIAKKIGLYN---ESWDNKSFDEKAQE-IFKTMRNRKIVLLLDDIWEL------FDLAQVGLPVPSR  276 (427)
Q Consensus       215 --------~~l~~~i~~~l~~~~---~~~~~~~~~~~~~~-l~~~L~~k~~LlVlDdv~~~------~~~~~~~~~l~~~  276 (427)
                              .+...+.++.+++..   ......+-.+..+. |-+.|..++=||+||+--.-      ...-++...+.. 
T Consensus       109 ~~~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~-  187 (254)
T COG1121         109 FRRLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQ-  187 (254)
T ss_pred             cccccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHH-
Confidence                    134444555554432   12233344444443 44567888999999986432      112223233332 


Q ss_pred             CCCcEEEEecCChhHH
Q 042645          277 ASASKVVFTTREFEVC  292 (427)
Q Consensus       277 ~~gs~IivTtR~~~v~  292 (427)
                       .|+.||++|.+-+..
T Consensus       188 -eg~tIl~vtHDL~~v  202 (254)
T COG1121         188 -EGKTVLMVTHDLGLV  202 (254)
T ss_pred             -CCCEEEEEeCCcHHh
Confidence             288899999986643

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

Probab=96.41  E-value=0.028  Score=53.50  Aligned_cols=101  Identities=24%  Similarity=0.201  Sum_probs=56.1

Q ss_pred             hHHHHHHHhccC----CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCC
Q 042645          156 TLDRVWRCLTEE----PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNE  230 (427)
Q Consensus       156 ~~~~l~~~l~~~----~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~  230 (427)
                      ....+..++.++    +.++|.++|+.|+||||...+++..+ .....-..+..++...- ....+-++..++-++++..
T Consensus       186 ~l~~~~~~~~~~~~~~~~~vi~LVGPTGVGKTTTlAKLAar~-~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~  264 (407)
T COG1419         186 KLRKLLLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARY-VMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLE  264 (407)
T ss_pred             HHHHHHHhhccccccccCcEEEEECCCCCcHHHHHHHHHHHH-HhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceE
Confidence            344444444443    47899999999999998776666665 21233445666665431 2334445556666666542


Q ss_pred             CCCCCCHHHHHHHHHHHhcCCcEEEEEeccC
Q 042645          231 SWDNKSFDEKAQEIFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       231 ~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~  261 (427)
                        ...++.++...+... ++. =+|.+|-+.
T Consensus       265 --vv~~~~el~~ai~~l-~~~-d~ILVDTaG  291 (407)
T COG1419         265 --VVYSPKELAEAIEAL-RDC-DVILVDTAG  291 (407)
T ss_pred             --EecCHHHHHHHHHHh-hcC-CEEEEeCCC
Confidence              234445555444433 333 345556553

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

Probab=96.39  E-value=0.0076  Score=57.85  Aligned_cols=47  Identities=21%  Similarity=0.258  Sum_probs=38.5

Q ss_pred             CCccccchhhHHHHHHHhcc---------C-----CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLTE---------E-----PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~---------~-----~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|.+..++.+..++..         +     ..+.|.++|++|+|||+||+.+....
T Consensus        14 d~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l   74 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            35689999999988877743         0     14679999999999999999999887

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.39  E-value=0.0038  Score=51.71  Aligned_cols=25  Identities=32%  Similarity=0.457  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.|+|.+|+||||||+.+.+.+
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L   26 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRL   26 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Confidence            3589999999999999999999988

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>PRK03839 putative kinase; Provisional

Probab=96.39  E-value=0.0027  Score=54.53  Aligned_cols=23  Identities=35%  Similarity=0.601  Sum_probs=21.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+++.+++.+
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999987

>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=96.38  E-value=0.016  Score=47.76  Aligned_cols=26  Identities=42%  Similarity=0.682  Sum_probs=22.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|.|||||++.+....
T Consensus        25 ~Ge~~~i~G~nGsGKStLl~~l~G~~   50 (144)
T cd03221          25 PGDRIGLVGRNGAGKSTLLKLIAGEL   50 (144)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCC
Confidence            44689999999999999999998765

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.

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

Probab=96.37  E-value=0.014  Score=53.43  Aligned_cols=104  Identities=19%  Similarity=0.214  Sum_probs=57.3

Q ss_pred             ccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC
Q 042645          151 VGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE  230 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~  230 (427)
                      .|-..+..+.+..+......+|.|.|+.|+||||++..+.+...   ..-..++.+.-........     ..++...  
T Consensus        62 lg~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l~all~~i~---~~~~~iitiEdp~E~~~~~-----~~q~~v~--  131 (264)
T cd01129          62 LGLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSELN---TPEKNIITVEDPVEYQIPG-----INQVQVN--  131 (264)
T ss_pred             cCCCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHHHHHHhhhC---CCCCeEEEECCCceecCCC-----ceEEEeC--
Confidence            34444444444444444556899999999999999998877652   1111222222111111110     0111111  


Q ss_pred             CCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccccc
Q 042645          231 SWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLA  267 (427)
Q Consensus       231 ~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~  267 (427)
                         ..........+...|+..+=.|+++++.+.+...
T Consensus       132 ---~~~~~~~~~~l~~~lR~~PD~i~vgEiR~~e~a~  165 (264)
T cd01129         132 ---EKAGLTFARGLRAILRQDPDIIMVGEIRDAETAE  165 (264)
T ss_pred             ---CcCCcCHHHHHHHHhccCCCEEEeccCCCHHHHH
Confidence               1111234556677788889999999998776543

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.

>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=96.35  E-value=0.023  Score=48.43  Aligned_cols=26  Identities=42%  Similarity=0.529  Sum_probs=22.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|.|||||++.++...
T Consensus        25 ~Ge~~~i~G~nGsGKStLl~~l~G~~   50 (173)
T cd03230          25 KGEIYGLLGPNGAGKTTLIKIILGLL   50 (173)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            44689999999999999999998765

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.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.35  E-value=0.0016  Score=55.44  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.+.|.+|+||||+|+++++.+
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L   25 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKEL   25 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHH
Confidence            568899999999999999998877

>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=96.35  E-value=0.014  Score=49.77  Aligned_cols=26  Identities=31%  Similarity=0.416  Sum_probs=22.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.++...
T Consensus        27 ~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          27 PGESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            44689999999999999999998765

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

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=96.34  E-value=0.024  Score=49.84  Aligned_cols=87  Identities=22%  Similarity=0.378  Sum_probs=52.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCC----CCCCCCHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNE----SWDNKSFDE---  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~----~~~~~~~~~---  239 (427)
                      ....++|.|.+|+|||+|+..+.+..     .-+.++++.+++. ....++.+++...-.....    .....+...   
T Consensus        14 ~Gqr~~I~g~~g~GKt~Ll~~i~~~~-----~~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~   88 (215)
T PF00006_consen   14 RGQRIGIFGGAGVGKTVLLQEIANNQ-----DADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYR   88 (215)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHC-----TTTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHH
T ss_pred             cCCEEEEEcCcccccchhhHHHHhcc-----cccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhh
Confidence            34579999999999999999999886     1334477777654 3455666666433111100    001111111   


Q ss_pred             -------HHHHHHHHhcCCcEEEEEeccC
Q 042645          240 -------KAQEIFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       240 -------~~~~l~~~L~~k~~LlVlDdv~  261 (427)
                             ..+.++.  +++++|+++||+-
T Consensus        89 ~~~~a~t~AEyfrd--~G~dVlli~Dslt  115 (215)
T PF00006_consen   89 APYTALTIAEYFRD--QGKDVLLIIDSLT  115 (215)
T ss_dssp             HHHHHHHHHHHHHH--TTSEEEEEEETHH
T ss_pred             hhccchhhhHHHhh--cCCceeehhhhhH
Confidence                   1222222  6899999999984

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=96.33  E-value=0.0085  Score=51.34  Aligned_cols=23  Identities=39%  Similarity=0.736  Sum_probs=21.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|.+|+||||||..+...+
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l   23 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQL   23 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999887

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK06217 hypothetical protein; Validated

Probab=96.32  E-value=0.007  Score=52.12  Aligned_cols=23  Identities=26%  Similarity=0.421  Sum_probs=21.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|.+|+||||+|+.+.+.+
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999887

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

Probab=96.32  E-value=0.012  Score=56.87  Aligned_cols=47  Identities=19%  Similarity=0.186  Sum_probs=37.0

Q ss_pred             CCccccchhhHHHHHHHhc-------c----C-------CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDRVWRCLT-------E----E-------PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~-------~----~-------~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|.++.++.+...+.       .    .       ....+.++|++|+|||++|+.++..+
T Consensus        76 ~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l  140 (413)
T TIGR00382        76 DEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARIL  140 (413)
T ss_pred             cceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhc
Confidence            4568999999988876651       1    1       12579999999999999999998776

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.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.31  E-value=0.0097  Score=50.15  Aligned_cols=114  Identities=18%  Similarity=0.192  Sum_probs=58.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC--CCCHHHHHHHHHHHhCCCCCCCCCCCHHH-HHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR--DLQLGKIQESIAKKIGLYNESWDNKSFDE-KAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~--~~~~~~l~~~i~~~l~~~~~~~~~~~~~~-~~~~l  244 (427)
                      ...+++|.|+.|+|||||.+.++....    .....+++.-..  ..+..+..   ....+...   . .+..+ ..-.+
T Consensus        25 ~Ge~~~l~G~nGsGKSTLl~~i~G~~~----~~~G~v~~~g~~~~~~~~~~~~---~~~i~~~~---q-LS~G~~qrl~l   93 (163)
T cd03216          25 RGEVHALLGENGAGKSTLMKILSGLYK----PDSGEILVDGKEVSFASPRDAR---RAGIAMVY---Q-LSVGERQMVEI   93 (163)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC----CCCeEEEECCEECCcCCHHHHH---hcCeEEEE---e-cCHHHHHHHHH
Confidence            446899999999999999999987651    223333332111  11111111   11111110   0 22222 22233


Q ss_pred             HHHhcCCcEEEEEeccCCccc---ccccccCCCC-CCCCcEEEEecCChhHH
Q 042645          245 FKTMRNRKIVLLLDDIWELFD---LAQVGLPVPS-RASASKVVFTTREFEVC  292 (427)
Q Consensus       245 ~~~L~~k~~LlVlDdv~~~~~---~~~~~~~l~~-~~~gs~IivTtR~~~v~  292 (427)
                      ...+-.++-++++|+.-+.-+   ...+...+.. ...+..||++|.+....
T Consensus        94 aral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~  145 (163)
T cd03216          94 ARALARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEV  145 (163)
T ss_pred             HHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHH
Confidence            445556778999999754322   2222222211 12356788888886643

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.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=96.31  E-value=0.03  Score=50.46  Aligned_cols=23  Identities=30%  Similarity=0.537  Sum_probs=20.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..|+|++|+|||+|+..++-..
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~v   25 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAM   25 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHH
Confidence            56789999999999999998765

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.31  E-value=0.0058  Score=54.12  Aligned_cols=23  Identities=30%  Similarity=0.348  Sum_probs=21.0

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+|+.++..+
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998876

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.30  E-value=0.0034  Score=55.46  Aligned_cols=23  Identities=26%  Similarity=0.345  Sum_probs=20.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      .+.+.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            37899999999999999999873

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

>PRK04040 adenylate kinase; Provisional

Probab=96.30  E-value=0.0037  Score=53.99  Aligned_cols=46  Identities=33%  Similarity=0.549  Sum_probs=32.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      .+|+|+|++|+||||+++.+.+.+.   ..+..   +      +..+++..++...+.
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~---~~~~~---~------~~g~~~~~~a~~~g~   48 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLK---EDYKI---V------NFGDVMLEVAKEEGL   48 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhc---cCCeE---E------ecchHHHHHHHHcCC
Confidence            5799999999999999999998872   12222   2      234566666666664

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.29  E-value=0.0064  Score=57.92  Aligned_cols=112  Identities=14%  Similarity=0.173  Sum_probs=61.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ....|.|.|+.|+||||++..+.+..   .......++. +.++...  ..... ..+ ..... .+.+.......+...
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i---~~~~~~~i~t-iEdp~E~--~~~~~-~~~-i~q~e-vg~~~~~~~~~l~~~  191 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYI---NKNAAGHIIT-IEDPIEY--VHRNK-RSL-INQRE-VGLDTLSFANALRAA  191 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhh---CcCCCCEEEE-EcCChhh--hccCc-cce-EEccc-cCCCCcCHHHHHHHh
Confidence            45789999999999999999988766   2223333332 2221110  00000 000 00000 111123345567778


Q ss_pred             hcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhH
Q 042645          248 MRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEV  291 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v  291 (427)
                      |+..+=+|++|++.+.+.+......   ...|..++.|....+.
T Consensus       192 lr~~pd~i~vgEird~~~~~~~l~a---a~tGh~v~~T~Ha~~~  232 (343)
T TIGR01420       192 LREDPDVILIGEMRDLETVELALTA---AETGHLVFGTLHTNSA  232 (343)
T ss_pred             hccCCCEEEEeCCCCHHHHHHHHHH---HHcCCcEEEEEcCCCH
Confidence            8889999999999876555432222   2345556666665444

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.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.28  E-value=0.0038  Score=53.13  Aligned_cols=25  Identities=24%  Similarity=0.299  Sum_probs=22.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|+|++|+||||+|+.+++.+
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999999887

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.28  E-value=0.023  Score=59.66  Aligned_cols=101  Identities=22%  Similarity=0.300  Sum_probs=65.6

Q ss_pred             ccccchhhHHHHHHHhcc------C--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHH
Q 042645          149 TVVGMQSTLDRVWRCLTE------E--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  220 (427)
                      .++|.++.+..|.+++..      .  +.-...+.|+.|+|||-||+.++.-+   .+..+..+-+..+.      ... 
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~---Fgse~~~IriDmse------~~e-  632 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYV---FGSEENFIRLDMSE------FQE-  632 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHH---cCCccceEEechhh------hhh-
Confidence            467888888888888753      1  34567789999999999999999887   45555555554443      222 


Q ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcE-EEEEeccCCc
Q 042645          221 IAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKI-VLLLDDIWEL  263 (427)
Q Consensus       221 i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~-LlVlDdv~~~  263 (427)
                      +.+..+. .+   ..-..+....|.+.++.++| +|+|||++..
T Consensus       633 vskligs-p~---gyvG~e~gg~LteavrrrP~sVVLfdeIEkA  672 (898)
T KOG1051|consen  633 VSKLIGS-PP---GYVGKEEGGQLTEAVKRRPYSVVLFEEIEKA  672 (898)
T ss_pred             hhhccCC-Cc---ccccchhHHHHHHHHhcCCceEEEEechhhc
Confidence            2222232 21   12223344467778888776 7789999754

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.28  E-value=0.01  Score=54.31  Aligned_cols=89  Identities=18%  Similarity=0.152  Sum_probs=59.1

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------------
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE----------------  230 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~----------------  230 (427)
                      +..+++.|+|.+|+|||+++.++....   ......++||+....  ..++.....+ ++....                
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~---~~~ge~vlyvs~~e~--~~~l~~~~~~-~g~d~~~~~~~g~l~i~d~~~~   94 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEG---AREGEPVLYVSTEES--PEELLENARS-FGWDLEVYIEKGKLAILDAFLS   94 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHH---HhcCCcEEEEEecCC--HHHHHHHHHH-cCCCHHHHhhcCCEEEEEcccc
Confidence            356899999999999999999998877   344788999988764  4445444432 322110                


Q ss_pred             --C------CCCCCHHHHHHHHHHHhcC-CcEEEEEeccC
Q 042645          231 --S------WDNKSFDEKAQEIFKTMRN-RKIVLLLDDIW  261 (427)
Q Consensus       231 --~------~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~  261 (427)
                        .      ....+.+.+...+.+.... +...+|+|.+-
T Consensus        95 ~~~~~~~~~~~~~~~~~l~~~I~~~~~~~~~~~~ViDsi~  134 (260)
T COG0467          95 EKGLVSIVVGDPLDLEELLDRIREIVEKEGADRVVIDSIT  134 (260)
T ss_pred             ccccccccccCCccHHHHHHHHHHHHHHhCCCEEEEeCCc
Confidence              0      0123445566666665543 47788999885

>PRK12678 transcription termination factor Rho; Provisional

Probab=96.27  E-value=0.0069  Score=60.05  Aligned_cols=98  Identities=22%  Similarity=0.215  Sum_probs=51.7

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEE-EEEEeCCCCC-HHHHHHHHHHHhCCCCCCCCCCC
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFV-IWEVVSRDLQ-LGKIQESIAKKIGLYNESWDNKS  236 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~-~wv~~~~~~~-~~~l~~~i~~~l~~~~~~~~~~~  236 (427)
                      ++++|.- +.....+|+|++|+|||||++.+++....  .+-++. +.+-+.+... +.++.+.+-..+-..  .++...
T Consensus       406 vIDll~PIGkGQR~LIvgpp~aGKTtLL~~IAn~i~~--n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVas--T~D~p~  481 (672)
T PRK12678        406 VIDLIMPIGKGQRGLIVSPPKAGKTTILQNIANAITT--NNPECHLMVVLVDERPEEVTDMQRSVKGEVIAS--TFDRPP  481 (672)
T ss_pred             eeeeecccccCCEeEEeCCCCCCHHHHHHHHHHHHhh--cCCCeEEEEEEEeCchhhHHHHHHhccceEEEE--CCCCCH
Confidence            3444432 34567899999999999999999987632  233333 3444554432 333322221111111  111111


Q ss_pred             H-----HHHHHHHHHHh--cCCcEEEEEeccC
Q 042645          237 F-----DEKAQEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       237 ~-----~~~~~~l~~~L--~~k~~LlVlDdv~  261 (427)
                      .     ..+.-.+-+++  .++.+||++|++-
T Consensus       482 ~~~~~~a~~ai~~Ae~fre~G~dVlillDSlT  513 (672)
T PRK12678        482 SDHTTVAELAIERAKRLVELGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEEEeCch
Confidence            1     11122233344  5799999999985

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.25  E-value=0.017  Score=55.61  Aligned_cols=25  Identities=28%  Similarity=0.438  Sum_probs=22.1

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++++|++|+||||++.+++...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998754

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.24  E-value=0.031  Score=54.28  Aligned_cols=25  Identities=36%  Similarity=0.484  Sum_probs=21.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++++|+.|+||||++..++...
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~  215 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARA  215 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999887654

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=96.23  E-value=0.33  Score=45.16  Aligned_cols=160  Identities=13%  Similarity=0.061  Sum_probs=88.2

Q ss_pred             HHHHHHHhccC-CCeEEEEEecCCCcHHHHHHHHHhhccC-------CCCCCcEEEEEEe-CCCCCHHHHHHHHHHHhCC
Q 042645          157 LDRVWRCLTEE-PVGIVGLYGMGGVGKTTLLTQINNSFLH-------TPNDFDFVIWEVV-SRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       157 ~~~l~~~l~~~-~~~vi~I~G~gGiGKTtLa~~v~~~~~~-------~~~~f~~~~wv~~-~~~~~~~~l~~~i~~~l~~  227 (427)
                      +..+.+.+..+ -.++..++|..|.||+++|..+.+....       ...+.+...++.. +......++. ++.+.+..
T Consensus         5 ~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir-~l~~~~~~   83 (299)
T PRK07132          5 IKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFL-SAINKLYF   83 (299)
T ss_pred             HHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHH-HHHHHhcc
Confidence            44556666554 3567779999999999999999877511       1112222223221 1112222222 22222221


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCC-hhHHh-hcCCCcceec
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTRE-FEVCG-LMDAHKSFKV  303 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~-~~v~~-~~~~~~~~~l  303 (427)
                      ..                 .-.+.+=++|+|+++....  ...+...+......+.+|++|.+ ..+.. .......+++
T Consensus        84 ~~-----------------~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f  146 (299)
T PRK07132         84 SS-----------------FVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNV  146 (299)
T ss_pred             CC-----------------cccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEEC
Confidence            10                 0014677899999876532  33444444444556667765544 33332 2334567899


Q ss_pred             cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCC
Q 042645          304 ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGG  343 (427)
Q Consensus       304 ~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G  343 (427)
                      .++++++..+.+... +     .+   .+.+..++...+|
T Consensus       147 ~~l~~~~l~~~l~~~-~-----~~---~~~a~~~a~~~~~  177 (299)
T PRK07132        147 KEPDQQKILAKLLSK-N-----KE---KEYNWFYAYIFSN  177 (299)
T ss_pred             CCCCHHHHHHHHHHc-C-----CC---hhHHHHHHHHcCC
Confidence            999999999887764 1     11   1225556666665

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=96.22  E-value=0.0057  Score=57.81  Aligned_cols=46  Identities=20%  Similarity=0.296  Sum_probs=41.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.+||.++.+..|+..+.++...-|.|.|..|+||||+|+.+++-.
T Consensus        17 ~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l   62 (350)
T CHL00081         17 TAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLL   62 (350)
T ss_pred             HHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999988888888899999999999999997765

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.22  E-value=0.022  Score=47.13  Aligned_cols=23  Identities=26%  Similarity=0.600  Sum_probs=21.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|.|+|.+|+||||+|+.+....
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l   23 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKL   23 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            47899999999999999998876

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK00625 shikimate kinase; Provisional

Probab=96.20  E-value=0.0038  Score=53.10  Aligned_cols=23  Identities=26%  Similarity=0.340  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|+|++|+||||+++.+.+.+
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l   24 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL   24 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998886

>PRK15453 phosphoribulokinase; Provisional

Probab=96.18  E-value=0.043  Score=49.96  Aligned_cols=80  Identities=19%  Similarity=0.133  Sum_probs=45.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC--CCCHHHHHHHHH--HHhCCCCCC--CCCCCHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR--DLQLGKIQESIA--KKIGLYNES--WDNKSFDEKA  241 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~--~~~~~~l~~~i~--~~l~~~~~~--~~~~~~~~~~  241 (427)
                      ...+|+|.|.+|+||||+++.+.+.+. ..+  .....++...  .++-.++-..+.  ..-+...+.  ....+.+.+.
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~if~-~~~--~~~~vi~~D~yh~ydr~~~~~~~~~~~r~g~nfdhf~PdAnd~dlL~   80 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEKIFR-REN--INAAVVEGDSFHRYTRPEMKAAIAKARAAGRHFSHFGPEANLFDELE   80 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHh-hcC--CCeEEEecccccccChhhHhhhhHHHHhcCCCCCCCCCCcccHHHHH
Confidence            457999999999999999999987662 111  1233333222  223333322221  122222211  3566777788


Q ss_pred             HHHHHHhcC
Q 042645          242 QEIFKTMRN  250 (427)
Q Consensus       242 ~~l~~~L~~  250 (427)
                      +.++.+.++
T Consensus        81 ~~l~~l~~~   89 (290)
T PRK15453         81 QLFREYGET   89 (290)
T ss_pred             HHHHHHhcC
Confidence            888877654

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.17  E-value=0.025  Score=49.36  Aligned_cols=60  Identities=15%  Similarity=0.160  Sum_probs=38.8

Q ss_pred             HHHHHHHHhcCCcEEEEEeccCCcccccccc------cCCCCCCCCcEEEEecCChhHHhhcCCCcce
Q 042645          240 KAQEIFKTMRNRKIVLLLDDIWELFDLAQVG------LPVPSRASASKVVFTTREFEVCGLMDAHKSF  301 (427)
Q Consensus       240 ~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~------~~l~~~~~gs~IivTtR~~~v~~~~~~~~~~  301 (427)
                      ....+.+.+--++-+.|||+.++--+.+.+.      ..+.  ..++-+++.|..+.+.....+...+
T Consensus       151 KR~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr--~~~~~~liITHy~rll~~i~pD~vh  216 (251)
T COG0396         151 KRNEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINALR--EEGRGVLIITHYQRLLDYIKPDKVH  216 (251)
T ss_pred             HHHHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHh--cCCCeEEEEecHHHHHhhcCCCEEE
Confidence            3445555556678899999998754433321      2222  3467788888888888877655444

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=96.17  E-value=0.0076  Score=56.91  Aligned_cols=46  Identities=20%  Similarity=0.281  Sum_probs=39.9

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+||.++.+..|+-.+.++...-+.|.|.+|+|||||++.+..-+
T Consensus         4 ~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             cccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            3579999999998888878777778899999999999999998665

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.

>TIGR01351 adk adenylate kinases

Probab=96.16  E-value=0.0069  Score=53.42  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=20.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|.|++|+||||+|+.+...+
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999998776

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.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=96.14  E-value=0.0085  Score=51.59  Aligned_cols=38  Identities=29%  Similarity=0.448  Sum_probs=30.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      .+++.|+|+.|+|||||+..+....   ...|...+..+-.
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~---~~~~~~~v~~TTR   39 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEF---PDKFGRVVSHTTR   39 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHS---TTTEEEEEEEESS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc---ccccccceeeccc
Confidence            4689999999999999999999987   5677655555433

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.13  E-value=0.027  Score=55.63  Aligned_cols=59  Identities=20%  Similarity=0.207  Sum_probs=35.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLY  228 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~  228 (427)
                      ..+++++|+.|+||||++.+++..+. .......+..+.... .....+-+....+.+++.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~-~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVp  315 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCV-MRHGASKVALLTTDSYRIGGHEQLRIYGKILGVP  315 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHH-HhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCC
Confidence            36999999999999999999987762 111112344454432 122334445555555543

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=96.12  E-value=0.059  Score=47.34  Aligned_cols=26  Identities=27%  Similarity=0.441  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.+..-.
T Consensus        33 ~G~~~~i~G~nGsGKSTLl~~l~Gl~   58 (207)
T cd03369          33 AGEKIGIVGRTGAGKSTLILALFRFL   58 (207)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccc
Confidence            44689999999999999999997654

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.10  E-value=0.021  Score=55.81  Aligned_cols=88  Identities=25%  Similarity=0.207  Sum_probs=48.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      .+++.++|++|+||||++..++..+. .......+..++....- ...+-+....+.++++..  ...+..++...+.. 
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~-~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~--~~~~~~~l~~~l~~-  296 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYA-LLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVE--VVYDPKELAKALEQ-  296 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH-HhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceE--ccCCHHhHHHHHHH-
Confidence            35899999999999999998877662 01222355666653311 112233334444554432  22334444444443 


Q ss_pred             hcCCcEEEEEeccC
Q 042645          248 MRNRKIVLLLDDIW  261 (427)
Q Consensus       248 L~~k~~LlVlDdv~  261 (427)
                      +. ..=+|++|..-
T Consensus       297 ~~-~~DlVlIDt~G  309 (424)
T PRK05703        297 LR-DCDVILIDTAG  309 (424)
T ss_pred             hC-CCCEEEEeCCC
Confidence            22 34578889763

>PF13245 AAA_19: Part of AAA domain

Probab=96.10  E-value=0.0079  Score=43.35  Aligned_cols=26  Identities=27%  Similarity=0.249  Sum_probs=18.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.+++.|.|++|.|||+++......+
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l   34 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAEL   34 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            34678889999999996655544444

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=96.08  E-value=0.007  Score=57.02  Aligned_cols=46  Identities=20%  Similarity=0.321  Sum_probs=37.8

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|.+..+..+.-.+.+.+..-+.+.|.+|+||||+|+.+.+-+
T Consensus         8 ~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          8 SAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             HHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            4679999999988766654445569999999999999999997765

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.08  E-value=0.0054  Score=52.39  Aligned_cols=24  Identities=21%  Similarity=0.385  Sum_probs=22.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|.+.|++|+||||+|+.+.+..
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            589999999999999999998875

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=96.07  E-value=0.021  Score=53.83  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=20.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +++.|++|+||||+++.+.+.+
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l   23 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATL   23 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHH
Confidence            6789999999999999999887

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=96.07  E-value=0.036  Score=54.36  Aligned_cols=92  Identities=18%  Similarity=0.261  Sum_probs=56.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDE---  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~---  239 (427)
                      ....++|.|.+|+|||||+..+.+...  ..+-+.++++-+++.. ...++...+...-.....    .....+...   
T Consensus       142 kGQR~gIfa~~G~GKt~Ll~~~~~~~~--~~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~  219 (461)
T PRK12597        142 KGGKTGLFGGAGVGKTVLMMELIFNIS--KQHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMR  219 (461)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHH--hhCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHH
Confidence            456799999999999999999888762  2256777787776543 455666666543221110    001111111   


Q ss_pred             ---HHHHHHHHh---cCCcEEEEEeccC
Q 042645          240 ---KAQEIFKTM---RNRKIVLLLDDIW  261 (427)
Q Consensus       240 ---~~~~l~~~L---~~k~~LlVlDdv~  261 (427)
                         ..-.+-+++   +++++||++||+-
T Consensus       220 a~~~a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        220 VVLTGLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEeccch
Confidence               112233444   3799999999984

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=96.07  E-value=0.02  Score=55.81  Aligned_cols=90  Identities=22%  Similarity=0.279  Sum_probs=48.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh-----CCCCCCCCCCCHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI-----GLYNESWDNKSFDE---  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l-----~~~~~~~~~~~~~~---  239 (427)
                      ....++|+|..|+|||||++.+....    .....+++..-....++.++....+...     ..-... +......   
T Consensus       164 ~Gqri~I~G~SGsGKTTLL~~Ia~l~----~pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qs-d~~~~~r~~~  238 (450)
T PRK06002        164 AGQRIGIFAGSGVGKSTLLAMLARAD----AFDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATS-DESPMMRRLA  238 (450)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCC----CCCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcC-CCCHHHHHHH
Confidence            44679999999999999999887654    1222344443223344555444443332     111111 1111111   


Q ss_pred             --HHHHHHHHh--cCCcEEEEEeccCC
Q 042645          240 --KAQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 --~~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                        ..-.+-+++  +++.+||++||+-.
T Consensus       239 ~~~a~~iAEyfrd~G~~Vll~~DslTr  265 (450)
T PRK06002        239 PLTATAIAEYFRDRGENVLLIVDSVTR  265 (450)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchHH
Confidence              111223333  47999999999843

>PRK14528 adenylate kinase; Provisional

Probab=96.07  E-value=0.0092  Score=51.50  Aligned_cols=24  Identities=21%  Similarity=0.225  Sum_probs=21.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.|.|++|+||||+++.+.+.+
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            458899999999999999998776

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.06  E-value=0.047  Score=56.72  Aligned_cols=25  Identities=36%  Similarity=0.537  Sum_probs=22.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++++|+.|+||||++.+++..+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~  209 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARC  209 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhH
Confidence            4699999999999999999988766

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.06  E-value=0.0047  Score=51.24  Aligned_cols=23  Identities=26%  Similarity=0.521  Sum_probs=20.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++.|.|++|+||||+|+.+.+..
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            47899999999999999998765

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=96.05  E-value=0.021  Score=49.69  Aligned_cols=125  Identities=17%  Similarity=0.097  Sum_probs=66.0

Q ss_pred             HHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEE--EEEEeCCCCCHHHH-----HHHHHHHhCCCCCCC
Q 042645          160 VWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFV--IWEVVSRDLQLGKI-----QESIAKKIGLYNESW  232 (427)
Q Consensus       160 l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~--~wv~~~~~~~~~~l-----~~~i~~~l~~~~~~~  232 (427)
                      ++..|-+.+..-..|.|++|+|||||.+.++.-.......|-..  .-+.-+..  +..-     ...+........   
T Consensus       128 li~~ly~~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersE--Iag~~~gvpq~~~g~R~dVld---  202 (308)
T COG3854         128 LIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSE--IAGCLNGVPQHGRGRRMDVLD---  202 (308)
T ss_pred             HHHHHHhcCceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccch--hhccccCCchhhhhhhhhhcc---
Confidence            55556565666688999999999999999988764333344322  22221111  0000     000011111000   


Q ss_pred             CCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhhc
Q 042645          233 DNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLM  295 (427)
Q Consensus       233 ~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~~  295 (427)
                      .....+.+...++   .--+=++|+|++-...+-..+...+   ..|-+++.|..-..+...+
T Consensus       203 ~cpk~~gmmmaIr---sm~PEViIvDEIGt~~d~~A~~ta~---~~GVkli~TaHG~~iedl~  259 (308)
T COG3854         203 PCPKAEGMMMAIR---SMSPEVIIVDEIGTEEDALAILTAL---HAGVKLITTAHGNGIEDLI  259 (308)
T ss_pred             cchHHHHHHHHHH---hcCCcEEEEeccccHHHHHHHHHHH---hcCcEEEEeeccccHHHhh
Confidence            0011111222222   2357799999998776655554444   4577888777665554443

>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=96.05  E-value=0.012  Score=49.86  Aligned_cols=44  Identities=23%  Similarity=0.265  Sum_probs=32.6

Q ss_pred             cccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          150 VVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|....+.++++.+..  ....-|.|+|..|+||+.+|+.+.+.-
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s   46 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNS   46 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            46778888888777653  333567799999999999999998865

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 ....

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

Probab=96.05  E-value=0.031  Score=44.19  Aligned_cols=45  Identities=16%  Similarity=0.282  Sum_probs=33.8

Q ss_pred             ccccchhhHHHHHHHhc----c---CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLT----E---EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~----~---~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|..-..+.+++++.    .   ..+-|++.+|.+|+|||.+++.+++.+
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            45676666666666554    2   245588999999999999999998885

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

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.03  E-value=0.0047  Score=53.07  Aligned_cols=23  Identities=39%  Similarity=0.602  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|.+|+||||+|+.+...+
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999876

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.03  E-value=0.014  Score=56.56  Aligned_cols=90  Identities=21%  Similarity=0.266  Sum_probs=53.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHHH--
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDEK--  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~~--  240 (427)
                      ....++|.|..|+|||||++.+.+..     ..+.+++.-+++.. ...++...++..-+....    .....+....  
T Consensus       161 ~GqrigI~G~sG~GKSTLL~~I~~~~-----~~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (444)
T PRK08972        161 KGQRMGLFAGSGVGKSVLLGMMTRGT-----TADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLK  235 (444)
T ss_pred             CCCEEEEECCCCCChhHHHHHhccCC-----CCCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHH
Confidence            45679999999999999999998654     22455556666554 345566665443222110    0011111111  


Q ss_pred             ----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          241 ----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       241 ----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                          .-.+-+++  +++++||++||+-.
T Consensus       236 a~~~A~tiAEyfrd~G~~VLl~~DslTR  263 (444)
T PRK08972        236 GCETATTIAEYFRDQGLNVLLLMDSLTR  263 (444)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEEcChHH
Confidence                11233344  58999999999843

>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=96.02  E-value=0.005  Score=52.05  Aligned_cols=22  Identities=41%  Similarity=0.594  Sum_probs=19.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|.|.+|+|||||++.+++.+
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            7899999999999999999887

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.01  E-value=0.0057  Score=52.42  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=21.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+++|.|++|+|||||++.+...+
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~   25 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARL   25 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            478999999999999999998876

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.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=96.01  E-value=0.051  Score=57.45  Aligned_cols=178  Identities=17%  Similarity=0.206  Sum_probs=88.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhcc--C-----------CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFL--H-----------TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN  234 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~--~-----------~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~  234 (427)
                      +.+++.|+|+.+.||||+.+.+.-...  .           .-..|+. ++..++...++..-+..              
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~~-i~~~ig~~~si~~~lSt--------------  390 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFKE-IFADIGDEQSIEQSLST--------------  390 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccce-EEEecCCccchhhchhH--------------
Confidence            457899999999999999988753310  0           0011222 22333332222211111              


Q ss_pred             CCHHHHHHHHHHHhc--CCcEEEEEeccCCcccc---ccc----ccCCCCCCCCcEEEEecCChhHHhhcCCCcceeccC
Q 042645          235 KSFDEKAQEIFKTMR--NRKIVLLLDDIWELFDL---AQV----GLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVEC  305 (427)
Q Consensus       235 ~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~~---~~~----~~~l~~~~~gs~IivTtR~~~v~~~~~~~~~~~l~~  305 (427)
                        .......+...+.  ..+-|++||++-.-.+.   ..+    ...+.  ..|+.+|+||...++.........+.-..
T Consensus       391 --fS~~m~~~~~Il~~~~~~sLvLlDE~~~GtDp~eg~ala~aile~l~--~~~~~vIitTH~~el~~~~~~~~~v~~~~  466 (782)
T PRK00409        391 --FSGHMTNIVRILEKADKNSLVLFDELGAGTDPDEGAALAISILEYLR--KRGAKIIATTHYKELKALMYNREGVENAS  466 (782)
T ss_pred             --HHHHHHHHHHHHHhCCcCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--HCCCEEEEECChHHHHHHHhcCCCeEEEE
Confidence              1111122222222  47789999998653221   112    22222  24788999999988765543322221111


Q ss_pred             --CChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHhh
Q 042645          306 --LGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRS  373 (427)
Q Consensus       306 --L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~~  373 (427)
                        ++.+...-.++-..|..    .   ...+-.|++++ |+|-.+.--|.-+... .....+.++..|..
T Consensus       467 ~~~d~~~l~~~Ykl~~G~~----g---~S~a~~iA~~~-Glp~~ii~~A~~~~~~-~~~~~~~li~~l~~  527 (782)
T PRK00409        467 VEFDEETLRPTYRLLIGIP----G---KSNAFEIAKRL-GLPENIIEEAKKLIGE-DKEKLNELIASLEE  527 (782)
T ss_pred             EEEecCcCcEEEEEeeCCC----C---CcHHHHHHHHh-CcCHHHHHHHHHHHhh-hhhHHHHHHHHHHH
Confidence              11111000011111111    1   12377788777 7888888877777653 44466666666544

>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=96.00  E-value=0.053  Score=46.25  Aligned_cols=26  Identities=27%  Similarity=0.511  Sum_probs=22.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.+..-.
T Consensus        24 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   49 (177)
T cd03222          24 EGEVIGIVGPNGTGKTTAVKILAGQL   49 (177)
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            45689999999999999999998765

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.

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

Probab=96.00  E-value=0.014  Score=52.03  Aligned_cols=64  Identities=27%  Similarity=0.312  Sum_probs=32.5

Q ss_pred             HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCC----CCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          158 DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHT----PNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       158 ~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      +.+...+....  +..|+|++|.||||++..+.......    .......+-++...+..+..++..+.+
T Consensus         8 ~Ai~~~~~~~~--~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    8 EAIQSALSSNG--ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             HHHHHHCTSSE---EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCC--CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            34444443332  68999999999998777766655110    122333333444444444555554444

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.00  E-value=0.0048  Score=53.85  Aligned_cols=23  Identities=39%  Similarity=0.648  Sum_probs=20.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|++|+|||||++.+...+
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998765

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=95.99  E-value=0.0066  Score=49.66  Aligned_cols=39  Identities=21%  Similarity=0.343  Sum_probs=27.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      ++|.|+|..|+|||||++.+.+.+.  ...+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~--~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELK--RRGYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHH--HTT--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHh--HcCCceEEEEEccC
Confidence            5799999999999999999999983  23344444555544

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

Probab=95.98  E-value=0.067  Score=49.17  Aligned_cols=53  Identities=17%  Similarity=0.095  Sum_probs=36.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ...++.|.|.+|+||||++.+++....  ..+-..++|++...  +..++...+...
T Consensus        29 ~g~~~~i~g~~G~GKT~l~~~~~~~~~--~~~g~~vl~iS~E~--~~~~~~~r~~~~   81 (271)
T cd01122          29 KGELIILTAGTGVGKTTFLREYALDLI--TQHGVRVGTISLEE--PVVRTARRLLGQ   81 (271)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH--HhcCceEEEEEccc--CHHHHHHHHHHH
Confidence            345889999999999999999887652  12235678887655  345555555443

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

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.98  E-value=0.0054  Score=50.96  Aligned_cols=20  Identities=35%  Similarity=0.640  Sum_probs=18.8

Q ss_pred             EEEEEecCCCcHHHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~  190 (427)
                      .|+|.|.||+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999987

>PRK14530 adenylate kinase; Provisional

Probab=95.96  E-value=0.0058  Score=54.12  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=21.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.|.|++|+||||+++.++..+
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999998876

>PRK05922 type III secretion system ATPase; Validated

Probab=95.96  E-value=0.023  Score=55.16  Aligned_cols=91  Identities=13%  Similarity=0.242  Sum_probs=50.1

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----CCCCCCH-HH-
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNE----SWDNKSF-DE-  239 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~-~~-  239 (427)
                      .....++|.|..|+|||||++.+.+..     ..+...++.++. .....+.+.+..........    .....+. .. 
T Consensus       155 ~~GqrigI~G~nG~GKSTLL~~Ia~~~-----~~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~  229 (434)
T PRK05922        155 GKGQRIGVFSEPGSGKSSLLSTIAKGS-----KSTINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKV  229 (434)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHhccC-----CCCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHH
Confidence            345679999999999999999998764     123333333333 22334555554433322110    0011111 11 


Q ss_pred             ----HHHHHHHHh--cCCcEEEEEeccCC
Q 042645          240 ----KAQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ----~~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                          ..-.+-+++  +++++||++||+-.
T Consensus       230 ~a~~~a~tiAEyfrd~G~~VLl~~DslTR  258 (434)
T PRK05922        230 IAGRAAMTIAEYFRDQGHRVLFIMDSLSR  258 (434)
T ss_pred             HHHHHHHHHHHHHHHcCCCEEEeccchhH
Confidence                112233444  47999999999853

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=95.95  E-value=0.043  Score=53.26  Aligned_cols=90  Identities=22%  Similarity=0.369  Sum_probs=49.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCC-----CCCCCCHHHH-
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNE-----SWDNKSFDEK-  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~-  240 (427)
                      ....++|.|..|+|||||++.+.... .   . +......+.. .-...++....+..-++...     ..+....... 
T Consensus       139 ~Gq~i~I~G~sG~GKTtLl~~I~~~~-~---~-~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~  213 (418)
T TIGR03498       139 RGQRLGIFAGSGVGKSTLLSMLARNT-D---A-DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQ  213 (418)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhCCC-C---C-CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHH
Confidence            44689999999999999999888765 1   1 2222233332 33455555555443222110     0011111111 


Q ss_pred             ----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          241 ----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       241 ----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                          .-.+-+++  +++++||++||+-.
T Consensus       214 a~~~a~~iAEyfrd~G~~Vll~~DslTr  241 (418)
T TIGR03498       214 AAYTATAIAEYFRDQGKDVLLLMDSVTR  241 (418)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhH
Confidence                11233444  47999999999853

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.95  E-value=0.014  Score=50.18  Aligned_cols=48  Identities=27%  Similarity=0.355  Sum_probs=33.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..+|+|-||-|+||||||+.+.+++.     | .+.+-.+.+++-+..++.++-
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~-----~-~~~~E~vednp~L~~FY~d~~   51 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLG-----F-KVFYELVEDNPFLDLFYEDPE   51 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhC-----C-ceeeecccCChHHHHHHHhHH
Confidence            46899999999999999999999982     2 223334445544555555443

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=95.95  E-value=0.046  Score=49.67  Aligned_cols=95  Identities=11%  Similarity=0.146  Sum_probs=57.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC-CCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCH-HH-
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH-TPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSF-DE-  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~-~~-  239 (427)
                      ....++|.|..|+|||+|+..+.++..- ...+-+.++++-+++.. ...+++..+...=.+...    .....+. .. 
T Consensus        68 ~GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~  147 (276)
T cd01135          68 RGQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERI  147 (276)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHH
Confidence            4567899999999999999998877520 12335677888887654 456666666553222110    0011111 11 


Q ss_pred             ----HHHHHHHHh---cCCcEEEEEeccCC
Q 042645          240 ----KAQEIFKTM---RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ----~~~~l~~~L---~~k~~LlVlDdv~~  262 (427)
                          ..-.+-+++   +++++|+++||+-.
T Consensus       148 ~a~~~a~aiAEyfrd~~g~~VLl~~D~ltr  177 (276)
T cd01135         148 ITPRMALTTAEYLAYEKGKHVLVILTDMTN  177 (276)
T ss_pred             HHHHHHHHHHHHHHhccCCeEEEEEcChhH
Confidence                111233444   36899999999854

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.95  E-value=0.0074  Score=51.50  Aligned_cols=26  Identities=27%  Similarity=0.378  Sum_probs=23.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|.+|+||||+|+.+...+
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l   28 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKL   28 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999999887

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=95.95  E-value=0.0027  Score=54.78  Aligned_cols=20  Identities=35%  Similarity=0.409  Sum_probs=18.2

Q ss_pred             EEEEEecCCCcHHHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~  190 (427)
                      ++.|+|+.|.||||+.+.+.
T Consensus         1 ~~~ltG~N~~GKst~l~~i~   20 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVG   20 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHH
Confidence            47899999999999999987

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=95.94  E-value=0.0055  Score=50.47  Aligned_cols=23  Identities=26%  Similarity=0.525  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|.|.|++|+||||+|+.+...+
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~   23 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999876

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=95.93  E-value=0.025  Score=52.78  Aligned_cols=63  Identities=16%  Similarity=0.155  Sum_probs=42.0

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~  218 (427)
                      +.++=.......++.++..+  +.|.|.|++|+||||+|+.++..+   ...   .+.|+++...+..++.
T Consensus        45 ~~y~f~~~~~~~vl~~l~~~--~~ilL~G~pGtGKTtla~~lA~~l---~~~---~~rV~~~~~l~~~Dli  107 (327)
T TIGR01650        45 PAYLFDKATTKAICAGFAYD--RRVMVQGYHGTGKSTHIEQIAARL---NWP---CVRVNLDSHVSRIDLV  107 (327)
T ss_pred             CCccCCHHHHHHHHHHHhcC--CcEEEEeCCCChHHHHHHHHHHHH---CCC---eEEEEecCCCChhhcC
Confidence            44554555566677777543  459999999999999999999987   222   2345555555444433

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.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=95.93  E-value=0.014  Score=51.01  Aligned_cols=41  Identities=27%  Similarity=0.332  Sum_probs=27.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCC
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ  213 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~  213 (427)
                      .|+|+|-||+||||+|..++..+.....  ..+.=|...++++
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~~--~~VLvVDaDpd~n   42 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKGG--YNVLVVDADPDSN   42 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhcCC--ceEEEEeCCCCCC
Confidence            5899999999999999997766632222  2344455554444

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

Probab=95.90  E-value=0.0074  Score=52.12  Aligned_cols=102  Identities=17%  Similarity=0.060  Sum_probs=52.3

Q ss_pred             HHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC--CCCCCCC
Q 042645          157 LDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL--YNESWDN  234 (427)
Q Consensus       157 ~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~--~~~~~~~  234 (427)
                      ..+++...... ...++|.|+.|+|||||++.+.....   ... ..+.+  ...   .++...-......  .......
T Consensus        14 ~~~~l~~~v~~-g~~i~I~G~tGSGKTTll~aL~~~i~---~~~-~~i~i--ed~---~E~~~~~~~~~~~~~~~~~~~~   83 (186)
T cd01130          14 QAAYLWLAVEA-RKNILISGGTGSGKTTLLNALLAFIP---PDE-RIITI--EDT---AELQLPHPNWVRLVTRPGNVEG   83 (186)
T ss_pred             HHHHHHHHHhC-CCEEEEECCCCCCHHHHHHHHHhhcC---CCC-CEEEE--CCc---cccCCCCCCEEEEEEecCCCCC
Confidence            34444444333 46899999999999999999887652   111 12211  111   0000000000000  0000011


Q ss_pred             CCHHHHHHHHHHHhcCCcEEEEEeccCCcccccc
Q 042645          235 KSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQ  268 (427)
Q Consensus       235 ~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~  268 (427)
                      .......+.+...++..+=.++++++.+.+.+..
T Consensus        84 ~~~~~~~~~l~~~lR~~pd~i~igEir~~ea~~~  117 (186)
T cd01130          84 SGEVTMADLLRSALRMRPDRIIVGEVRGGEALDL  117 (186)
T ss_pred             CCccCHHHHHHHHhccCCCEEEEEccCcHHHHHH
Confidence            1223344556667777788899999987665543

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.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=95.90  E-value=0.065  Score=52.23  Aligned_cols=90  Identities=16%  Similarity=0.254  Sum_probs=52.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHHH--
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDEK--  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~~--  240 (427)
                      ....++|+|..|+|||||++.+++..     ..+.++++-+++.. ...++..+.+..-++...    .....+....  
T Consensus       157 ~Gqri~I~G~sG~GKTtLL~~I~~~~-----~~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~  231 (442)
T PRK08927        157 RGQRMGIFAGSGVGKSVLLSMLARNA-----DADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQ  231 (442)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc-----CCCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHH
Confidence            55789999999999999999998765     12345556665544 344555544443222110    0011111111  


Q ss_pred             ----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          241 ----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       241 ----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                          .-.+-+++  +++.+||++||+-.
T Consensus       232 a~~~a~tiAEyfrd~G~~Vll~~DslTr  259 (442)
T PRK08927        232 AAYLTLAIAEYFRDQGKDVLCLMDSVTR  259 (442)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCcHH
Confidence                11233444  48999999999843

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.89  E-value=0.061  Score=50.49  Aligned_cols=26  Identities=27%  Similarity=0.502  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++++|++|+||||++..++..+
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l  138 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKY  138 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            45799999999999999999998887

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=95.89  E-value=0.01  Score=53.30  Aligned_cols=34  Identities=21%  Similarity=0.174  Sum_probs=23.3

Q ss_pred             EEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          174 LYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       174 I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      |+|++|+||||+++.+.+...   .....++-|+..+
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~---~~~~~~~~vNLDP   34 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLE---SNGRDVYIVNLDP   34 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHT---TT-S-EEEEE--T
T ss_pred             CCCCCCCCHHHHHHHHHHHHH---hccCCceEEEcch
Confidence            689999999999999999882   3334456666544

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=95.88  E-value=0.013  Score=50.65  Aligned_cols=44  Identities=20%  Similarity=0.231  Sum_probs=33.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++++|.+..+..+.-+....  .-+.++|++|+|||++|+.+..-+
T Consensus         3 ~dI~GQe~aKrAL~iAAaG~--h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAAGG--HHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHHCC----EEEES-CCCTHHHHHHHHHHCS
T ss_pred             hhhcCcHHHHHHHHHHHcCC--CCeEEECCCCCCHHHHHHHHHHhC
Confidence            45789888888887666654  579999999999999999987644

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.

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

Probab=95.88  E-value=0.024  Score=55.51  Aligned_cols=40  Identities=23%  Similarity=0.335  Sum_probs=32.3

Q ss_pred             hhhHHHHHHHhc-----cC--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          154 QSTLDRVWRCLT-----EE--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       154 ~~~~~~l~~~l~-----~~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+.++..||.     .+  +.++..|+|++|+||||.++.++..+
T Consensus        88 kkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskel  134 (634)
T KOG1970|consen   88 KKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKEL  134 (634)
T ss_pred             HHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhh
Confidence            345677778876     33  55699999999999999999998776

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.88  E-value=0.089  Score=49.35  Aligned_cols=90  Identities=21%  Similarity=0.279  Sum_probs=50.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----CCCCCCHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNE----SWDNKSFDE---  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~---  239 (427)
                      ....++|.|..|+|||||++.+.... .    .+......+.. ..+..++.......-++...    .....+...   
T Consensus        68 ~Gqri~I~G~sG~GKTtLl~~Ia~~~-~----~~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~  142 (326)
T cd01136          68 KGQRLGIFAGSGVGKSTLLGMIARGT-T----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVK  142 (326)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhCCC-C----CCEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHH
Confidence            45679999999999999999888765 1    22333444442 33555555555544322110    001111111   


Q ss_pred             ---HHHHHHHHh--cCCcEEEEEeccCC
Q 042645          240 ---KAQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ---~~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                         ..-.+-+++  +++.+||++||+-.
T Consensus       143 ~~~~a~~~AEyfr~~g~~Vll~~Dsltr  170 (326)
T cd01136         143 AAYTATAIAEYFRDQGKDVLLLMDSLTR  170 (326)
T ss_pred             HHHHHHHHHHHHHHcCCCeEEEeccchH
Confidence               111222333  48999999999743

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=95.86  E-value=0.043  Score=49.55  Aligned_cols=79  Identities=14%  Similarity=0.101  Sum_probs=44.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC--CCHHHHHHHHHHHh--CCCCCC--CCCCCHHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD--LQLGKIQESIAKKI--GLYNES--WDNKSFDEKAQEI  244 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~--~~~~~l~~~i~~~l--~~~~~~--~~~~~~~~~~~~l  244 (427)
                      +|+|.|.+|+||||++..+.+.+. ..+  ..+..++...-  ++-...-..+....  +...+.  ....+.+.+.+.+
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~-~~g--~~v~vI~~D~yyr~~r~~~~~~~~~a~~~~~nfdHf~PeAnd~dlL~~~l   77 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFA-REG--IHPAVVEGDSFHRYERMEMKMAIAEALDAGRNFSHFGPEANLFDLLEELF   77 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH-hcC--CceEEEeccccccCCchhHHHHHHHHhhcCCCCCCCCcccccHHHHHHHH
Confidence            589999999999999999988772 111  12333432221  22222222222221  112111  3556777788888


Q ss_pred             HHHhcCCc
Q 042645          245 FKTMRNRK  252 (427)
Q Consensus       245 ~~~L~~k~  252 (427)
                      +.+.+++.
T Consensus        78 ~~L~~g~~   85 (277)
T cd02029          78 RTYGETGR   85 (277)
T ss_pred             HHHHcCCC
Confidence            88777654

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK14529 adenylate kinase; Provisional

Probab=95.85  E-value=0.035  Score=49.15  Aligned_cols=82  Identities=21%  Similarity=0.234  Sum_probs=44.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhccCCCCCCcEE--EEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSFLHTPNDFDFV--IWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~--~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      |.|.|++|+||||+++.+...+ . ..+.+..  +.-.+..........++++.+-       ...+.+-....+.+.+.
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~-~-~~~is~gdllr~~i~~~t~lg~~i~~~i~~G-------~lvpdei~~~lv~~~l~   73 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKY-D-LAHIESGAIFREHIGGGTELGKKAKEYIDRG-------DLVPDDITIPMILETLK   73 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-C-CCCcccchhhhhhccCCChHHHHHHHHHhcc-------CcchHHHHHHHHHHHHh
Confidence            7889999999999999999887 2 1222211  1111222223333333443321       12233444555566664


Q ss_pred             CC-cEEEEEeccCC
Q 042645          250 NR-KIVLLLDDIWE  262 (427)
Q Consensus       250 ~k-~~LlVlDdv~~  262 (427)
                      +. .-=+|||.+-.
T Consensus        74 ~~~~~g~iLDGfPR   87 (223)
T PRK14529         74 QDGKNGWLLDGFPR   87 (223)
T ss_pred             ccCCCcEEEeCCCC
Confidence            31 34589999864

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=95.85  E-value=0.025  Score=51.68  Aligned_cols=59  Identities=27%  Similarity=0.326  Sum_probs=37.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCC-------CCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCC
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPN-------DFDFVIWEVVSRD-LQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~  229 (427)
                      ++.|+|.+|+|||||+...+=.+....+       ....+++|++... .++-.=++.+..+++++.
T Consensus        91 ~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~L~Rl~~v~a~mgLsP  157 (402)
T COG3598          91 VSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILERLEPVRARMGLSP  157 (402)
T ss_pred             eEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccChHHHHHHHHHHHHHcCCCh
Confidence            5667799999999998776544432222       3346677776532 344455566777777654

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=95.84  E-value=0.061  Score=52.67  Aligned_cols=92  Identities=18%  Similarity=0.335  Sum_probs=55.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHHH--
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDEK--  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~~--  240 (427)
                      ....++|.|.+|+|||||+..+..... . ++-+.++++-+++.. ...+++.++...-.....    .....++...  
T Consensus       143 kGQR~gIfa~~GvGKt~Ll~~i~~~~~-~-~~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~  220 (463)
T PRK09280        143 KGGKIGLFGGAGVGKTVLIQELINNIA-K-EHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLR  220 (463)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHH-h-cCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            456799999999999999999876652 1 222456777776543 456666666653222110    0011112111  


Q ss_pred             ----HHHHHHHh---cCCcEEEEEeccC
Q 042645          241 ----AQEIFKTM---RNRKIVLLLDDIW  261 (427)
Q Consensus       241 ----~~~l~~~L---~~k~~LlVlDdv~  261 (427)
                          .-.+-+++   +++++||++|++-
T Consensus       221 a~~~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        221 VALTGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEecchH
Confidence                12234454   6799999999984

>PRK08149 ATP synthase SpaL; Validated

Probab=95.84  E-value=0.038  Score=53.64  Aligned_cols=90  Identities=18%  Similarity=0.293  Sum_probs=51.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCC-----CCCCCCCHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYN-----ESWDNKSFD---  238 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~-----~~~~~~~~~---  238 (427)
                      ....++|.|..|+|||||+..++...     ..+.++...+.. ..+..++..+.........     ...+.....   
T Consensus       150 ~Gq~i~I~G~sG~GKTTLl~~i~~~~-----~~dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~  224 (428)
T PRK08149        150 VGQRMGIFASAGCGKTSLMNMLIEHS-----EADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCN  224 (428)
T ss_pred             cCCEEEEECCCCCChhHHHHHHhcCC-----CCCeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHh
Confidence            45679999999999999999988754     123333444433 2345566666665432211     010111111   


Q ss_pred             --HHHHHHHHHh--cCCcEEEEEeccCC
Q 042645          239 --EKAQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       239 --~~~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                        ...-.+-+++  +++++||++||+-.
T Consensus       225 a~~~a~tiAE~fr~~G~~Vll~~DslTr  252 (428)
T PRK08149        225 AALVATTVAEYFRDQGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEccchHH
Confidence              1122233333  48999999999853

>PRK13949 shikimate kinase; Provisional

Probab=95.83  E-value=0.0071  Score=51.28  Aligned_cols=23  Identities=35%  Similarity=0.397  Sum_probs=21.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|+|++|+||||+++.+++.+
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l   25 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAREL   25 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999887

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=95.83  E-value=0.01  Score=63.31  Aligned_cols=196  Identities=14%  Similarity=0.079  Sum_probs=99.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCC-CCcEEEEEEeCCCC----CHH--HHHHHHHHHhCCCCCCCCCCCHHHHHH
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPN-DFDFVIWEVVSRDL----QLG--KIQESIAKKIGLYNESWDNKSFDEKAQ  242 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~f~~~~wv~~~~~~----~~~--~l~~~i~~~l~~~~~~~~~~~~~~~~~  242 (427)
                      .-+.|+|.+|+||||+...++-....... .-+..+++.+....    ...  .+..-+...+....      ...+...
T Consensus       223 ~~~~Ilg~pGsGKTtfl~~lA~~~~~~~~~~~~vpi~~~l~~~~~~~~~~~q~~~~~~l~~~~~~~~------~~~~~~~  296 (824)
T COG5635         223 AKLLILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLIDYLAEELFSQG------IAKQLIE  296 (824)
T ss_pred             hheeeecCCCCCceehHHHHHHHhccCcCCcccCceeeechhHHHhhhhHhhccHHHHHHHHHhccC------CcchhhH
Confidence            47999999999999999998766632221 11223444433110    111  22222222222211      1122333


Q ss_pred             HHHHHhcCCcEEEEEeccCCccc------ccccccCCCCCCCCcEEEEecCChhHHhhcCCCcceeccCCChHHHHHHHH
Q 042645          243 EIFKTMRNRKIVLLLDDIWELFD------LAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKSFKVECLGYEDAWRLFE  316 (427)
Q Consensus       243 ~l~~~L~~k~~LlVlDdv~~~~~------~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~~~~~~~l~~L~~~e~~~lf~  316 (427)
                      ...++++..++++++|.++....      ...+ ..+...-+.+.+|+|+|....-........+++..+.++.......
T Consensus       297 ~~~e~l~~g~~llLlDGlDe~~~~~~~~~~~~i-~~f~~~~~~~~~iltcR~~~~~~~~~~f~~~ei~~~~~~~i~~~~~  375 (824)
T COG5635         297 AHQELLKTGKLLLLLDGLDELEPKNQRALIREI-NKFLQEYPDAQVLLTCRPDTYKEEFKGFAVFEIYKFLDLQINQFIL  375 (824)
T ss_pred             HHHHHHhccchhhHhhccchhhhhhHHHHHHHH-HHHhhhccCCeEEEEeccchhhhhhhhhhhccchhhhHHHHHHHHH
Confidence            33678889999999999876421      1111 1122233578899999986654443334455666666655554433


Q ss_pred             HHh-----CC-CCCCCCC---CHHHH---HHHHHHHcCCCchHHHHHHHHHcCC-----CChHHHHHHHHHHh
Q 042645          317 EKV-----GR-DILDSHP---DIPEL---AETVARECGGLPLALITVGRAMASK-----KAPREWAHAIEVLR  372 (427)
Q Consensus       317 ~~~-----~~-~~~~~~~---~~~~~---~~~i~~~~~G~Plai~~~~~~L~~~-----~~~~~w~~~l~~l~  372 (427)
                      ...     .. ......+   ....+   ...-.+.....|+.+.+.+..-...     ....-++.+++.+-
T Consensus       376 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ik~l~~~p~~L~l~c~~~~~~~~lP~~~~~ly~~~~~~~~  448 (824)
T COG5635         376 YQWLDAFIEDWFGDSRLLAKKLLERLKLPENRRIKELALTPLLLALECLIWQAQGDLPESRAELYEQAVDALL  448 (824)
T ss_pred             HHHHHHHHHhhhcccchhhHHHHHHhcchhhHHHHHhccCHHHHHHHHHhhhHHhhCCCCcHHHHHHHHHHHH
Confidence            211     10 0000111   00111   1122233477899998888555421     34455555555443

>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=95.82  E-value=0.013  Score=54.69  Aligned_cols=46  Identities=26%  Similarity=0.398  Sum_probs=41.2

Q ss_pred             CccccchhhHHHHHHHhcc------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|.++.++++++.+..      ...+++.+.|+.|.|||||+..+-+-+
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~l  112 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGL  112 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHh
Confidence            4799999999999999863      367899999999999999999998877

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

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

Probab=95.82  E-value=0.048  Score=57.31  Aligned_cols=144  Identities=16%  Similarity=0.130  Sum_probs=80.5

Q ss_pred             hhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-
Q 042645          154 QSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW-  232 (427)
Q Consensus       154 ~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~-  232 (427)
                      ...+.+|++.+.+.  .++.|.|..|+||||-.-+++-+..   ......+-+.=........+-..+++.++...... 
T Consensus        52 ~~~~~~i~~ai~~~--~vvii~getGsGKTTqlP~~lle~g---~~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~V  126 (845)
T COG1643          52 TAVRDEILKAIEQN--QVVIIVGETGSGKTTQLPQFLLEEG---LGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETV  126 (845)
T ss_pred             HHHHHHHHHHHHhC--CEEEEeCCCCCChHHHHHHHHHhhh---cccCCeEEecCchHHHHHHHHHHHHHHhCCCcCcee
Confidence            45677777777654  5799999999999999988887652   11222232222222345667777777776542110 


Q ss_pred             ----------------CCCCHHHHHHHHH-HHhcCCcEEEEEeccCCccccccc-----ccCCCCCCCCcEEEEecCChh
Q 042645          233 ----------------DNKSFDEKAQEIF-KTMRNRKIVLLLDDIWELFDLAQV-----GLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       233 ----------------~~~~~~~~~~~l~-~~L~~k~~LlVlDdv~~~~~~~~~-----~~~l~~~~~gs~IivTtR~~~  290 (427)
                                      .-.+...+.+.+. +.+-.+--.||+|++++..--.++     ...+......-||||+|-.-+
T Consensus       127 GY~iRfe~~~s~~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld  206 (845)
T COG1643         127 GYSIRFESKVSPRTRIKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLD  206 (845)
T ss_pred             eEEEEeeccCCCCceeEEeccHHHHHHHhhCcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccC
Confidence                            1123344444444 233345558999999875322111     111222223478999887644


Q ss_pred             ---HHhhcCCCccee
Q 042645          291 ---VCGLMDAHKSFK  302 (427)
Q Consensus       291 ---v~~~~~~~~~~~  302 (427)
                         ++..++....++
T Consensus       207 ~~rfs~~f~~apvi~  221 (845)
T COG1643         207 AERFSAYFGNAPVIE  221 (845)
T ss_pred             HHHHHHHcCCCCEEE
Confidence               344444333333

>CHL00206 ycf2 Ycf2; Provisional

Probab=95.82  E-value=0.074  Score=59.92  Aligned_cols=26  Identities=19%  Similarity=0.289  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+-|.++|++|+|||.||+.++.+.
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~es 1654 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATNS 1654 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHhc
Confidence            35678999999999999999999876

>PLN02165 adenylate isopentenyltransferase

Probab=95.81  E-value=0.01  Score=55.41  Aligned_cols=29  Identities=24%  Similarity=0.383  Sum_probs=25.0

Q ss_pred             ccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          165 TEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       165 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ......+++|+|+.|+||||||..++..+
T Consensus        39 ~~~~g~iivIiGPTGSGKStLA~~LA~~l   67 (334)
T PLN02165         39 QNCKDKVVVIMGATGSGKSRLSVDLATRF   67 (334)
T ss_pred             cCCCCCEEEEECCCCCcHHHHHHHHHHHc
Confidence            34456699999999999999999998886

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.81  E-value=0.056  Score=54.60  Aligned_cols=89  Identities=12%  Similarity=0.153  Sum_probs=56.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC-------------CCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE-------------SWDN  234 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~-------------~~~~  234 (427)
                      ...++.|.|.+|+|||+|+.+++....   ..-..++|++....  +.++...+ ..++.+..             ....
T Consensus       272 ~g~~~li~G~~G~GKT~l~~~~~~~~~---~~g~~~~yis~e~~--~~~i~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~  345 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLASKFAEAAC---RRGERCLLFAFEES--RAQLIRNA-RSWGIDLEKMEEKGLLKIICARPES  345 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH---hCCCcEEEEEecCC--HHHHHHHH-HHcCCChHHHhhcCCceeecCCccc
Confidence            456899999999999999999987652   23457788877653  45554443 34443211             0112


Q ss_pred             CCHHHHHHHHHHHhcC-CcEEEEEeccCC
Q 042645          235 KSFDEKAQEIFKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       235 ~~~~~~~~~l~~~L~~-k~~LlVlDdv~~  262 (427)
                      .+.++....+.+.+.. +.-++|+|.+-.
T Consensus       346 ~~~~~~~~~i~~~i~~~~~~~vVIDslt~  374 (509)
T PRK09302        346 YGLEDHLIIIKREIEEFKPSRVAIDPLSA  374 (509)
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEEcCHHH
Confidence            2345556666665543 556899999853

>PRK13947 shikimate kinase; Provisional

Probab=95.80  E-value=0.0078  Score=51.11  Aligned_cols=23  Identities=30%  Similarity=0.468  Sum_probs=21.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|+|++|+||||+++.+.+.+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l   25 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL   25 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999887

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

Probab=95.80  E-value=0.011  Score=48.30  Aligned_cols=43  Identities=26%  Similarity=0.340  Sum_probs=31.7

Q ss_pred             ccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          151 VGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ||+...++++.+.+..  .....|.|+|..|+||+++|+.+++..
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~   45 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYS   45 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhc
Confidence            4666777777777653  344568999999999999999988765

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.79  E-value=0.0077  Score=51.63  Aligned_cols=24  Identities=29%  Similarity=0.412  Sum_probs=21.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++++|+|+.|+|||||++.+++..
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            579999999999999999998865

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=95.79  E-value=0.0083  Score=47.36  Aligned_cols=22  Identities=32%  Similarity=0.537  Sum_probs=20.2

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|..|+|||||.+.+....
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            7899999999999999998765

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.79  E-value=0.009  Score=50.50  Aligned_cols=26  Identities=27%  Similarity=0.487  Sum_probs=23.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++++|+|..|+|||||++.+...+
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l   30 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPAL   30 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHH
Confidence            45799999999999999999999887

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=95.78  E-value=0.37  Score=42.92  Aligned_cols=46  Identities=20%  Similarity=0.311  Sum_probs=36.7

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +++=|-+..+++|++++.-             ..++-+..||++|.|||-+|+..+.+-
T Consensus       171 sDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT  229 (424)
T KOG0652|consen  171 SDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQT  229 (424)
T ss_pred             cccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhc
Confidence            3566889999999998742             245678999999999999999887654

>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=95.78  E-value=0.011  Score=56.48  Aligned_cols=76  Identities=13%  Similarity=0.203  Sum_probs=43.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      .+-+=|||..|.|||.|+-.+|+... ....  .++        -...+..++-+.+.....  ....    +..+.+.+
T Consensus        62 ~~GlYl~G~vG~GKT~Lmd~f~~~lp-~~~k--~R~--------HFh~Fm~~vh~~l~~~~~--~~~~----l~~va~~l  124 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTMLMDLFYDSLP-IKRK--RRV--------HFHEFMLDVHSRLHQLRG--QDDP----LPQVADEL  124 (362)
T ss_pred             CceEEEECCCCCchhHHHHHHHHhCC-cccc--ccc--------cccHHHHHHHHHHHHHhC--CCcc----HHHHHHHH
Confidence            45688999999999999999999883 2110  111        112233333333321110  1112    33344555


Q ss_pred             cCCcEEEEEeccC
Q 042645          249 RNRKIVLLLDDIW  261 (427)
Q Consensus       249 ~~k~~LlVlDdv~  261 (427)
                      .++..||.||++.
T Consensus       125 ~~~~~lLcfDEF~  137 (362)
T PF03969_consen  125 AKESRLLCFDEFQ  137 (362)
T ss_pred             HhcCCEEEEeeee
Confidence            6677799999975

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

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.77  E-value=0.06  Score=47.90  Aligned_cols=89  Identities=21%  Similarity=0.287  Sum_probs=53.0

Q ss_pred             cccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHH
Q 042645          150 VVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGK  216 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~  216 (427)
                      +=|=.+.+++|.+.+.-             +..+-|.++|++|.|||-+|+.|+|+-   ..-     |+.+-       
T Consensus       179 vggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrt---dac-----firvi-------  243 (435)
T KOG0729|consen  179 VGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRT---DAC-----FIRVI-------  243 (435)
T ss_pred             ccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhccc---Cce-----EEeeh-------
Confidence            33455566666554421             245678999999999999999999875   222     22221       


Q ss_pred             HHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcC-CcEEEEEeccCC
Q 042645          217 IQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       217 l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~~  262 (427)
                       -.++.+..-.        .-......+.+.-+. |-++|.+|+++.
T Consensus       244 -gselvqkyvg--------egarmvrelf~martkkaciiffdeida  281 (435)
T KOG0729|consen  244 -GSELVQKYVG--------EGARMVRELFEMARTKKACIIFFDEIDA  281 (435)
T ss_pred             -hHHHHHHHhh--------hhHHHHHHHHHHhcccceEEEEeecccc
Confidence             1122222111        113445556665554 668999999864

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.77  E-value=0.0095  Score=51.79  Aligned_cols=25  Identities=32%  Similarity=0.312  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.|.|.+|+||||+|+.+++..
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998875

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.76  E-value=0.011  Score=52.10  Aligned_cols=30  Identities=23%  Similarity=0.453  Sum_probs=26.3

Q ss_pred             hccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          164 LTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       164 l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+.++|+++|+.|+|||||..++.+..
T Consensus        17 ~~~~~~~~i~~~G~~gsGKTTli~~l~~~~   46 (207)
T TIGR00073        17 LDKHGLVVLNFMSSPGSGKTTLIEKLIDNL   46 (207)
T ss_pred             hhhcCcEEEEEECCCCCCHHHHHHHHHHHH
Confidence            344578999999999999999999998875

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=95.75  E-value=0.018  Score=58.87  Aligned_cols=54  Identities=19%  Similarity=0.222  Sum_probs=32.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      .++..|.|.+|.||||++..+...+.+....-...+.+.....--...+...+.
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~  220 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLG  220 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHH
Confidence            468999999999999999888776522111112344444443333344444443

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

Probab=95.75  E-value=0.025  Score=54.42  Aligned_cols=38  Identities=24%  Similarity=0.270  Sum_probs=31.4

Q ss_pred             hHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          156 TLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       156 ~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+.+++.+.......+.|.|+||.|||+|.+.+.+.+
T Consensus         9 ~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~   46 (364)
T PF05970_consen    9 VFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYL   46 (364)
T ss_pred             HHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHh
Confidence            44556666666667789999999999999999999887

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

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=95.75  E-value=0.0051  Score=54.55  Aligned_cols=111  Identities=11%  Similarity=0.048  Sum_probs=58.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh-ccCCCCCCcE----------EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS-FLHTPNDFDF----------VIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKS  236 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~-~~~~~~~f~~----------~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~  236 (427)
                      ..+++.|.|+.|.||||+.+.+... .....+.|..          .++..+....++..                ....
T Consensus        30 ~g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~----------------~~St   93 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQH----------------GMST   93 (222)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCcccccc----------------ccch
Confidence            3468899999999999999888762 2111111110          11222222111111                1122


Q ss_pred             HHHHHHHHHHHhc--CCcEEEEEeccCCccc-------ccccccCCCCCCCCcEEEEecCChhHHhhc
Q 042645          237 FDEKAQEIFKTMR--NRKIVLLLDDIWELFD-------LAQVGLPVPSRASASKVVFTTREFEVCGLM  295 (427)
Q Consensus       237 ~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~-------~~~~~~~l~~~~~gs~IivTtR~~~v~~~~  295 (427)
                      ...-...+...++  .++-|++||++..-.+       ...+...+... .++.+|++|....++...
T Consensus        94 F~~e~~~~~~il~~~~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~~-~~~~~i~~TH~~~l~~~~  160 (222)
T cd03287          94 FMVELSETSHILSNCTSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYPSLGEIL  160 (222)
T ss_pred             HHHHHHHHHHHHHhCCCCeEEEEccCCCCCChhhHHHHHHHHHHHHHhc-cCCeEEEEcccHHHHHHH
Confidence            2233333444443  4789999999743211       11122223222 478899999998886554

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

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.73  E-value=0.054  Score=49.23  Aligned_cols=90  Identities=10%  Similarity=0.115  Sum_probs=49.9

Q ss_pred             CCeEEEEEecCCCcHHHHH-HHHHhhccCCCCCCcEE-EEEEeCCCC-CHHHHHHHHHHHhCCCC-----CCCCCCCHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLL-TQINNSFLHTPNDFDFV-IWEVVSRDL-QLGKIQESIAKKIGLYN-----ESWDNKSFDE  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~~f~~~-~wv~~~~~~-~~~~l~~~i~~~l~~~~-----~~~~~~~~~~  239 (427)
                      ....++|.|.+|+|||+|+ ..+.+..     .-+.+ +++-+.+.. ...++...+...-....     ...+......
T Consensus        68 rGQr~~Ifg~~g~GKt~L~l~~i~~~~-----~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r  142 (274)
T cd01132          68 RGQRELIIGDRQTGKTAIAIDTIINQK-----GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQ  142 (274)
T ss_pred             cCCEEEeeCCCCCCccHHHHHHHHHhc-----CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHH
Confidence            4467999999999999995 5555543     22333 666666553 45566666654321110     0001111111


Q ss_pred             H-----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          240 K-----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ~-----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                      .     .-.+-+++  +++.+||++||+-.
T Consensus       143 ~~a~~~a~aiAE~fr~~G~~Vlvl~DslTr  172 (274)
T cd01132         143 YLAPYTGCAMGEYFMDNGKHALIIYDDLSK  172 (274)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEcChHH
Confidence            0     11222232  47999999999854

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

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.73  E-value=0.0093  Score=48.62  Aligned_cols=23  Identities=43%  Similarity=0.733  Sum_probs=20.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|+|+.|+|||||++.+.+.+
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~   23 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEF   23 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcC
Confidence            37899999999999999998875

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=95.73  E-value=0.023  Score=49.34  Aligned_cols=24  Identities=25%  Similarity=0.397  Sum_probs=22.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|.|..|+||||+++.+.+.+
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l   27 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLL   27 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            579999999999999999999887

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>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=95.72  E-value=0.03  Score=46.79  Aligned_cols=118  Identities=21%  Similarity=0.192  Sum_probs=59.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      +..+++|.|..|.|||||++.+.....    .....+++.-......  ........++....  -........ .+...
T Consensus        24 ~g~~~~i~G~nGsGKStll~~l~g~~~----~~~G~i~~~~~~~~~~--~~~~~~~~i~~~~q--lS~G~~~r~-~l~~~   94 (157)
T cd00267          24 AGEIVALVGPNGSGKSTLLRAIAGLLK----PTSGEILIDGKDIAKL--PLEELRRRIGYVPQ--LSGGQRQRV-ALARA   94 (157)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC----CCccEEEECCEEcccC--CHHHHHhceEEEee--CCHHHHHHH-HHHHH
Confidence            346899999999999999999987651    2233344332111100  00111111221110  011122222 34444


Q ss_pred             hcCCcEEEEEeccCCccc---ccccccCCCC-CCCCcEEEEecCChhHHhh
Q 042645          248 MRNRKIVLLLDDIWELFD---LAQVGLPVPS-RASASKVVFTTREFEVCGL  294 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~~~---~~~~~~~l~~-~~~gs~IivTtR~~~v~~~  294 (427)
                      +...+-++++|+.-...+   ...+...+.. ...+..++++|.+......
T Consensus        95 l~~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~  145 (157)
T cd00267          95 LLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAEL  145 (157)
T ss_pred             HhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            555678999999864322   1222222211 1124678888888766544

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=95.71  E-value=0.026  Score=45.39  Aligned_cols=36  Identities=22%  Similarity=-0.047  Sum_probs=25.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEE
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEV  207 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~  207 (427)
                      .+.|.|+.|+|||+.+..+...... ......+++++
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~-~~~~~~~lv~~   37 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLD-SLKGGQVLVLA   37 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHh-cccCCCEEEEc
Confidence            4789999999999998888777622 22345566664

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

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=95.70  E-value=0.012  Score=54.91  Aligned_cols=46  Identities=22%  Similarity=0.271  Sum_probs=30.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHH
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~  218 (427)
                      +++.+.|-||+||||+|...+-...+ .+  ..++-++..+..++.+++
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~-~G--~rtLlvS~Dpa~~L~d~l   47 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALAR-RG--KRTLLVSTDPAHSLSDVL   47 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHH-TT--S-EEEEESSTTTHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhh-CC--CCeeEeecCCCccHHHHh
Confidence            67899999999999999887776632 22  335555555444444433

...

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.69  E-value=0.068  Score=48.17  Aligned_cols=51  Identities=12%  Similarity=0.165  Sum_probs=34.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ...++.|.|.+|+|||+++.+++.+..  ..+-..++|++...  +..++...+.
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~--~~~g~~vly~s~E~--~~~~~~~r~~   62 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIA--KKQGKPVLFFSLEM--SKEQLLQRLL   62 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH--HhCCCceEEEeCCC--CHHHHHHHHH
Confidence            346899999999999999999877662  12234567776554  3455555554

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.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.69  E-value=0.0072  Score=50.89  Aligned_cols=22  Identities=27%  Similarity=0.563  Sum_probs=19.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|++|+||||+|+.+.+..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999998876

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.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=95.69  E-value=0.35  Score=44.55  Aligned_cols=38  Identities=5%  Similarity=0.040  Sum_probs=30.0

Q ss_pred             hHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          156 TLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       156 ~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .-++|.+.+..+. .....++|+.|+||+++|..++...
T Consensus         5 ~~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~l   43 (290)
T PRK05917          5 AWEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLI   43 (290)
T ss_pred             HHHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHH
Confidence            3456777776654 4577899999999999999988776

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.68  E-value=0.01  Score=52.05  Aligned_cols=26  Identities=27%  Similarity=0.295  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|+|++|+|||||++.++...
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34689999999999999999998875

>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=95.68  E-value=0.023  Score=49.31  Aligned_cols=23  Identities=30%  Similarity=0.596  Sum_probs=21.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|+.|+||||+++.+.+.+
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l   24 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERL   24 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999887

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.67  E-value=0.067  Score=52.27  Aligned_cols=92  Identities=22%  Similarity=0.281  Sum_probs=50.8

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC-----CCCCCCHHH--
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE-----SWDNKSFDE--  239 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~--  239 (427)
                      .....++|.|..|+|||||++.++... ..   -..++...-.......++...+...-++...     ..+......  
T Consensus       161 ~~Gq~~~I~G~sG~GKTtLl~~ia~~~-~~---d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~  236 (441)
T PRK09099        161 GEGQRMGIFAPAGVGKSTLMGMFARGT-QC---DVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAK  236 (441)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC-CC---CeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHH
Confidence            355689999999999999999998765 11   1233333323333455555555443222110     001111111  


Q ss_pred             ---HHHHHHHHh--cCCcEEEEEeccCC
Q 042645          240 ---KAQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ---~~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                         ..-.+-+++  +++++||++||+-.
T Consensus       237 a~~~a~tiAEyfrd~G~~VLl~~DslTr  264 (441)
T PRK09099        237 AAYVATAIAEYFRDRGLRVLLMMDSLTR  264 (441)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhH
Confidence               111233344  47999999999843

>PTZ00185 ATPase alpha subunit; Provisional

Probab=95.67  E-value=0.066  Score=52.73  Aligned_cols=95  Identities=14%  Similarity=0.076  Sum_probs=53.2

Q ss_pred             CCeEEEEEecCCCcHHHHH-HHHHhhccC----CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC-CCCC-----CCCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLL-TQINNSFLH----TPNDFDFVIWEVVSRDLQLGKIQESIAKKIG-LYNE-----SWDNKS  236 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa-~~v~~~~~~----~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~-~~~~-----~~~~~~  236 (427)
                      ....++|.|..|+|||+|| ..+.++...    ...+-..++++.+++......-+...++.-+ +...     ..+...
T Consensus       188 RGQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~  267 (574)
T PTZ00185        188 RGQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPA  267 (574)
T ss_pred             CCCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCH
Confidence            4567999999999999996 556665310    1124456788888876543333444444433 2110     001111


Q ss_pred             HHHH-----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          237 FDEK-----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       237 ~~~~-----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                      ..+.     .-.+-+++  +++.+|+|+||+-.
T Consensus       268 ~~r~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr  300 (574)
T PTZ00185        268 GLQYLAPYSGVTMGEYFMNRGRHCLCVYDDLSK  300 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEEEcCchH
Confidence            1111     11222333  47999999999854

>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=95.67  E-value=0.0089  Score=49.69  Aligned_cols=22  Identities=36%  Similarity=0.516  Sum_probs=20.5

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|++|+||||+|+.+...+
T Consensus         2 i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            7899999999999999998876

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.

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=95.66  E-value=0.018  Score=48.11  Aligned_cols=30  Identities=20%  Similarity=0.464  Sum_probs=26.1

Q ss_pred             hccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          164 LTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       164 l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+..+|.+.|.+|+||||+|..+...+
T Consensus        18 ~~~~~~~viW~TGLSGsGKSTiA~ale~~L   47 (197)
T COG0529          18 LKGQKGAVIWFTGLSGSGKSTIANALEEKL   47 (197)
T ss_pred             HhCCCCeEEEeecCCCCCHHHHHHHHHHHH
Confidence            344566799999999999999999999988

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=95.64  E-value=0.042  Score=47.75  Aligned_cols=26  Identities=31%  Similarity=0.543  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|.|||||.+.++.-.
T Consensus        34 ~Ge~~~l~G~nGsGKStLl~~i~Gl~   59 (194)
T cd03213          34 PGELTAIMGPSGAGKSTLLNALAGRR   59 (194)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            44689999999999999999998754

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=95.64  E-value=0.16  Score=52.88  Aligned_cols=46  Identities=24%  Similarity=0.195  Sum_probs=36.1

Q ss_pred             CccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|....+.++.+.+..  .....|.|+|..|+||+++|+.+.+..
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s  372 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNES  372 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhC
Confidence            4578998888888777653  233348899999999999999998765

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

Probab=95.64  E-value=0.013  Score=52.29  Aligned_cols=60  Identities=18%  Similarity=0.217  Sum_probs=37.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC---------CCCCHHH--HHHHHHHHhCCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS---------RDLQLGK--IQESIAKKIGLYNE  230 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~---------~~~~~~~--l~~~i~~~l~~~~~  230 (427)
                      ....|.++||+|+||||..+.++.+.. .+  +..-+-+++.         .+.++++  -+++..++.++..+
T Consensus        18 ~p~~ilVvGMAGSGKTTF~QrL~~hl~-~~--~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPN   88 (366)
T KOG1532|consen   18 RPVIILVVGMAGSGKTTFMQRLNSHLH-AK--KTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPN   88 (366)
T ss_pred             CCcEEEEEecCCCCchhHHHHHHHHHh-hc--cCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCC
Confidence            456788899999999999999998872 22  2222223322         2234443  35577777776543

>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=95.62  E-value=0.019  Score=47.75  Aligned_cols=36  Identities=22%  Similarity=0.337  Sum_probs=29.8

Q ss_pred             hhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          155 STLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       155 ~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++|.+.+..   +++++.|..|+|||||+..+....
T Consensus        24 ~g~~~l~~~l~~---k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   24 EGIEELKELLKG---KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTHHHHHHHHTT---SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             cCHHHHHHHhcC---CEEEEECCCCCCHHHHHHHHHhhc
Confidence            456677777755   689999999999999999998764

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.

>PLN02200 adenylate kinase family protein

Probab=95.62  E-value=0.011  Score=52.93  Aligned_cols=25  Identities=32%  Similarity=0.287  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.|.|++|+||||+|+.+.+.+
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998876

>PRK13975 thymidylate kinase; Provisional

Probab=95.61  E-value=0.01  Score=51.61  Aligned_cols=24  Identities=25%  Similarity=0.415  Sum_probs=22.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|.|+.|+||||+++.+.+.+
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l   26 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKL   26 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999999999988

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=95.59  E-value=0.021  Score=53.41  Aligned_cols=47  Identities=28%  Similarity=0.341  Sum_probs=31.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~  218 (427)
                      .+++...|.||+||||+|...+-.... .+  ..++-|+..+..++.+++
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~-~g--~kvLlvStDPAhsL~d~f   48 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAE-SG--KKVLLVSTDPAHSLGDVF   48 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHH-cC--CcEEEEEeCCCCchHhhh
Confidence            478999999999999999887665522 22  335556555444444433

>PRK06761 hypothetical protein; Provisional

Probab=95.58  E-value=0.025  Score=51.84  Aligned_cols=24  Identities=25%  Similarity=0.477  Sum_probs=22.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|.|.|++|+||||+++.+++.+
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L   27 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDIL   27 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            579999999999999999999987

>COG4240 Predicted kinase [General function prediction only]

Probab=95.58  E-value=0.066  Score=46.61  Aligned_cols=85  Identities=14%  Similarity=0.005  Sum_probs=53.2

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC---CCCCCCCCCHHHHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL---YNESWDNKSFDEKAQE  243 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~---~~~~~~~~~~~~~~~~  243 (427)
                      ++.-+++|.|+-|+||||++..+++.+. .++. ..+...++.+-+-...-...++++...   ........++.-..+.
T Consensus        48 grPli~gisGpQGSGKStls~~i~~~L~-~kg~-ert~~lSLDDlYlthadrl~La~q~npllq~RGlpGTHD~tlglnV  125 (300)
T COG4240          48 GRPLIVGISGPQGSGKSTLSALIVRLLA-AKGL-ERTATLSLDDLYLTHADRLRLARQVNPLLQTRGLPGTHDPTLGLNV  125 (300)
T ss_pred             CCceEEEeecCCCCchhhHHHHHHHHHH-Hhcc-cceEEeehhhhhcchHHHHHHHHhcCchhcccCCCCCCchHHHHHH
Confidence            4566899999999999999999999883 2222 356666655544444444455555321   1111134566666777


Q ss_pred             HHHHhcCCcE
Q 042645          244 IFKTMRNRKI  253 (427)
Q Consensus       244 l~~~L~~k~~  253 (427)
                      +....+++.-
T Consensus       126 Lnai~~g~~~  135 (300)
T COG4240         126 LNAIARGGPT  135 (300)
T ss_pred             HHHHhcCCCC
Confidence            7777777643

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.57  E-value=0.1  Score=50.90  Aligned_cols=90  Identities=21%  Similarity=0.350  Sum_probs=53.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHHH--
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDEK--  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~~--  240 (427)
                      ....++|.|..|+|||||+..+++..     ..+.++++-+++.. ...++....+..-+....    .....+....  
T Consensus       161 ~Gq~~~I~G~sG~GKStLl~~Ia~~~-----~~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (439)
T PRK06936        161 EGQRMGIFAAAGGGKSTLLASLIRSA-----EVDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAK  235 (439)
T ss_pred             CCCEEEEECCCCCChHHHHHHHhcCC-----CCCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHH
Confidence            45689999999999999999998775     22456777776553 344555443332221110    0011111111  


Q ss_pred             ----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          241 ----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       241 ----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                          .-.+-+++  +++++||++||+-.
T Consensus       236 a~~~a~tiAEyfrd~G~~Vll~~DslTR  263 (439)
T PRK06936        236 AGFVATSIAEYFRDQGKRVLLLMDSVTR  263 (439)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhH
Confidence                11233333  58999999999853

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.56  E-value=0.05  Score=54.96  Aligned_cols=90  Identities=14%  Similarity=0.051  Sum_probs=55.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------------
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES----------------  231 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~----------------  231 (427)
                      ..+++.|.|.+|+|||+|+.++.....  ..+-..++|++...  +..++...+.. ++.....                
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~--~~~ge~~lyis~ee--~~~~i~~~~~~-~g~d~~~~~~~g~l~~~~~~~~~  104 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGI--KRFDEPGVFVTFEE--SPEDIIRNVAS-FGWDLQKLIDEGKLFILDASPDP  104 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHH--HhcCCCEEEEEccC--CHHHHHHHHHH-cCCCHHHHhhCCeEEEEecCccc
Confidence            567999999999999999999876542  12235678887765  34455554432 3322100                


Q ss_pred             -----CCCCCHHHHHHHHHHHhcC-CcEEEEEeccCC
Q 042645          232 -----WDNKSFDEKAQEIFKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       232 -----~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~~  262 (427)
                           ....+.+.+...+.+.+.. +.-.+|+|.+..
T Consensus       105 ~~~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls~  141 (509)
T PRK09302        105 SEQEEAGEYDLEALFIRIEYAIDKIGAKRVVLDSIEA  141 (509)
T ss_pred             ccccccccccHHHHHHHHHHHHHhhCCCEEEECCHHH
Confidence                 0112344555566655543 556799999854

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.56  E-value=0.013  Score=50.57  Aligned_cols=26  Identities=15%  Similarity=0.291  Sum_probs=23.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|+|++|+|||||++.+....
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            35789999999999999999998765

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=95.54  E-value=0.057  Score=48.75  Aligned_cols=45  Identities=29%  Similarity=0.417  Sum_probs=36.3

Q ss_pred             ccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++=|-+..+++|.+.+.-             ...+-|.+||.+|.|||-||+.|+|+-
T Consensus       186 diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqT  243 (440)
T KOG0726|consen  186 DIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQT  243 (440)
T ss_pred             ccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhccc
Confidence            455788888888888642             135568899999999999999999976

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.53  E-value=0.032  Score=52.46  Aligned_cols=36  Identities=22%  Similarity=0.419  Sum_probs=28.7

Q ss_pred             HHHHHHhc--cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          158 DRVWRCLT--EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       158 ~~l~~~l~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|++.+.  .++..+|+|.|.+|+|||||+..+...+
T Consensus        43 ~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l   80 (332)
T PRK09435         43 QELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHL   80 (332)
T ss_pred             HHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHH
Confidence            34555543  3567899999999999999999988877

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.53  E-value=0.09  Score=51.35  Aligned_cols=93  Identities=23%  Similarity=0.325  Sum_probs=56.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDE---  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~---  239 (427)
                      ....++|.|.+|+|||+|+..+.....  ..+-+.++++-+++.. ...+++.++...-.+...    .....+...   
T Consensus       137 kGQr~~Ifg~~G~GKt~l~~~~~~~~~--~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~  214 (449)
T TIGR03305       137 RGGKAGLFGGAGVGKTVLLTEMIHNMV--GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFR  214 (449)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHH--hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHH
Confidence            456799999999999999999887752  2234677888887654 455666666543221110    001111211   


Q ss_pred             ---HHHHHHHHh---cCCcEEEEEeccCC
Q 042645          240 ---KAQEIFKTM---RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ---~~~~l~~~L---~~k~~LlVlDdv~~  262 (427)
                         ..-.+-+++   +++++||++||+-.
T Consensus       215 ~~~~a~tiAEyfrd~~G~~VLl~~DslTR  243 (449)
T TIGR03305       215 VGHTALTMAEYFRDDEKQDVLLLIDNIFR  243 (449)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEecChHH
Confidence               112233454   46899999999853

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PHA02244 ATPase-like protein

Probab=95.52  E-value=0.032  Score=52.84  Aligned_cols=44  Identities=23%  Similarity=0.292  Sum_probs=29.9

Q ss_pred             CccccchhhH----HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTL----DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~----~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.....    ..+..++..+.  -|.|+|++|+|||+||+.+++..
T Consensus        96 ~~~ig~sp~~~~~~~ri~r~l~~~~--PVLL~GppGtGKTtLA~aLA~~l  143 (383)
T PHA02244         96 TTKIASNPTFHYETADIAKIVNANI--PVFLKGGAGSGKNHIAEQIAEAL  143 (383)
T ss_pred             CcccCCCHHHHHHHHHHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHh
Confidence            3455654433    34444444332  47889999999999999999876

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.51  E-value=0.061  Score=47.07  Aligned_cols=120  Identities=15%  Similarity=0.104  Sum_probs=58.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC-CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH-TPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW-DNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~-~~~~~~~~~~~l~  245 (427)
                      ..+++.|.|+.|.||||+.+.+..-..- .-+.|     +.... .. -.+...|...++...... .......-...+.
T Consensus        28 ~~~~~~l~G~n~~GKstll~~i~~~~~la~~G~~-----vpa~~-~~-l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~  100 (204)
T cd03282          28 SSRFHIITGPNMSGKSTYLKQIALLAIMAQIGCF-----VPAEY-AT-LPIFNRLLSRLSNDDSMERNLSTFASEMSETA  100 (204)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHHHcCCC-----cchhh-cC-ccChhheeEecCCccccchhhhHHHHHHHHHH
Confidence            3478999999999999998887533210 00111     11100 00 012222222222211100 0011111111222


Q ss_pred             HHh--cCCcEEEEEeccCCcc---c----ccccccCCCCCCCCcEEEEecCChhHHhhcC
Q 042645          246 KTM--RNRKIVLLLDDIWELF---D----LAQVGLPVPSRASASKVVFTTREFEVCGLMD  296 (427)
Q Consensus       246 ~~L--~~k~~LlVlDdv~~~~---~----~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~  296 (427)
                      ..+  ..++-|+++|+...-.   +    ...+...+.  ..++.+|++|.+..++....
T Consensus       101 ~il~~~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~--~~~~~~i~~TH~~~l~~~~~  158 (204)
T cd03282         101 YILDYADGDSLVLIDELGRGTSSADGFAISLAILECLI--KKESTVFFATHFRDIAAILG  158 (204)
T ss_pred             HHHHhcCCCcEEEeccccCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHHhh
Confidence            222  3578899999984321   1    112222232  23788999999988876654

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

>PRK14532 adenylate kinase; Provisional

Probab=95.51  E-value=0.011  Score=51.16  Aligned_cols=22  Identities=23%  Similarity=0.276  Sum_probs=20.4

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|.|++|+||||+|+.+++.+
T Consensus         3 i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7889999999999999998876

>PHA02774 E1; Provisional

Probab=95.51  E-value=0.033  Score=55.59  Aligned_cols=48  Identities=13%  Similarity=0.117  Sum_probs=34.0

Q ss_pred             hHHHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEe
Q 042645          156 TLDRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVV  208 (427)
Q Consensus       156 ~~~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~  208 (427)
                      -+..|..++.. ++...+.|+|++|.|||.+|..+.+-+ .    ...+.|++.
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L-~----G~vi~fvN~  468 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFL-K----GKVISFVNS  468 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHh-C----CCEEEEEEC
Confidence            44555555544 345689999999999999999998876 1    233556664

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.50  E-value=0.011  Score=49.91  Aligned_cols=21  Identities=29%  Similarity=0.412  Sum_probs=17.5

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+|.|.+|+|||||+..+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999865

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=95.49  E-value=0.098  Score=50.94  Aligned_cols=93  Identities=20%  Similarity=0.221  Sum_probs=52.4

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC----CCCCCCHHH---
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE----SWDNKSFDE---  239 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~---  239 (427)
                      +....++|.|..|+|||||+..++... .  . ...++...-.......+++...+..-++...    .....+...   
T Consensus       154 ~~Gqri~I~G~sG~GKTtLl~~Ia~~~-~--~-~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~r  229 (432)
T PRK06793        154 GIGQKIGIFAGSGVGKSTLLGMIAKNA-K--A-DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLR  229 (432)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHhccC-C--C-CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHH
Confidence            345689999999999999999998765 1  1 1123322222335666676666554332210    001111111   


Q ss_pred             ---HHHHHHHHh--cCCcEEEEEeccCCc
Q 042645          240 ---KAQEIFKTM--RNRKIVLLLDDIWEL  263 (427)
Q Consensus       240 ---~~~~l~~~L--~~k~~LlVlDdv~~~  263 (427)
                         ....+-+++  ++++.||++||+-..
T Consensus       230 a~~~a~~iAEyfr~~G~~VLlilDslTr~  258 (432)
T PRK06793        230 AAKLATSIAEYFRDQGNNVLLMMDSVTRF  258 (432)
T ss_pred             HHHHHHHHHHHHHHcCCcEEEEecchHHH
Confidence               112233333  479999999998543

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.47  E-value=0.013  Score=49.76  Aligned_cols=24  Identities=29%  Similarity=0.342  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|.|+|+.|+||||+++.+.+.+
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~l   28 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHHc
Confidence            469999999999999999999876

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

Probab=95.47  E-value=0.023  Score=49.46  Aligned_cols=36  Identities=28%  Similarity=0.376  Sum_probs=27.6

Q ss_pred             HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          158 DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       158 ~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.+..+...+.+++.|.|++|+||||++..+...+
T Consensus         7 ~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~   42 (196)
T PF13604_consen    7 REAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEAL   42 (196)
T ss_dssp             HHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHH
Confidence            334444444455789999999999999999988777

>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=95.46  E-value=0.011  Score=51.20  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=20.5

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|.|++|+||||+|+.+++.+
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999998875

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=95.46  E-value=0.052  Score=52.98  Aligned_cols=93  Identities=17%  Similarity=0.321  Sum_probs=56.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHH---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDE---  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~---  239 (427)
                      ....++|.|.+|+|||||+..+.....  .++-..++++-+++.. ...+++..+...-.....    .....+...   
T Consensus       142 ~GQr~~If~~~G~GKt~L~~~~~~~~~--~~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~  219 (461)
T TIGR01039       142 KGGKIGLFGGAGVGKTVLIQELINNIA--KEHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMR  219 (461)
T ss_pred             cCCEEEeecCCCCChHHHHHHHHHHHH--hcCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            456799999999999999999887652  2223466777776543 456666666543221110    001112111   


Q ss_pred             ---HHHHHHHHh---cCCcEEEEEeccCC
Q 042645          240 ---KAQEIFKTM---RNRKIVLLLDDIWE  262 (427)
Q Consensus       240 ---~~~~l~~~L---~~k~~LlVlDdv~~  262 (427)
                         ..-.+-+++   +++++||++||+-.
T Consensus       220 a~~~a~tiAEyfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       220 VALTGLTMAEYFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHHHHhcCCeeEEEecchhH
Confidence               112334455   46899999999853

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.46  E-value=0.015  Score=50.84  Aligned_cols=27  Identities=19%  Similarity=0.377  Sum_probs=24.2

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+|+|+|.+|+||||||+.+...+
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l   48 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEAL   48 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            456799999999999999999998876

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=95.45  E-value=0.063  Score=51.43  Aligned_cols=41  Identities=17%  Similarity=0.283  Sum_probs=31.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD  211 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~  211 (427)
                      .++.|.|.+|.|||.||..++..+ ..........+++.+..
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l-~~~~~~~~~~~l~~n~~   42 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL-QNSEEGKKVLYLCGNHP   42 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh-hccccCCceEEEEecch
Confidence            579999999999999999999887 22344555666666654

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK14531 adenylate kinase; Provisional

Probab=95.45  E-value=0.012  Score=50.54  Aligned_cols=24  Identities=21%  Similarity=0.245  Sum_probs=21.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|.|+|++|+||||+++.+.+.+
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358899999999999999998876

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=95.45  E-value=0.033  Score=50.52  Aligned_cols=100  Identities=15%  Similarity=0.195  Sum_probs=57.2

Q ss_pred             ccccchhhHHHHHHHhcc----C---CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          149 TVVGMQSTLDRVWRCLTE----E---PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~----~---~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      .++|..-..+.++..+.+    +   ++=+++.+|.+|+||...++.+++.......+-+.+               ...
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V---------------~~f  147 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFV---------------HHF  147 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhH---------------HHh
Confidence            456766666666666653    2   455899999999999999999998873322222221               111


Q ss_pred             HHHhCCCCCCCCCCCHHHHHHHHHHHhc-CCcEEEEEeccCCc
Q 042645          222 AKKIGLYNESWDNKSFDEKAQEIFKTMR-NRKIVLLLDDIWEL  263 (427)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~~~~l~~~L~-~k~~LlVlDdv~~~  263 (427)
                      ...+.-+.+.....--+++...++..++ -++-|+|+|+++..
T Consensus       148 vat~hFP~~~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKm  190 (344)
T KOG2170|consen  148 VATLHFPHASKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKL  190 (344)
T ss_pred             hhhccCCChHHHHHHHHHHHHHHHHHHHhcCCceEEechhhhc
Confidence            1111111110000111233444444443 48999999999875

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.45  E-value=0.012  Score=50.72  Aligned_cols=24  Identities=29%  Similarity=0.476  Sum_probs=21.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|+|+.|+|||||++.+....
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQRE   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccC
Confidence            478999999999999999997765

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=95.43  E-value=0.014  Score=48.11  Aligned_cols=48  Identities=33%  Similarity=0.461  Sum_probs=34.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  229 (427)
                      ..++.|+|.+|+||||+.+.+....  +.  +..         .+-.++.-+++...++..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l--~~--~~i---------vNyG~~Mle~A~k~glve   51 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL--VK--HKI---------VNYGDLMLEIAKKKGLVE   51 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH--hh--cee---------eeHhHHHHHHHHHhCCcc
Confidence            4789999999999999998887654  11  111         244667778887777643

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.42  E-value=0.088  Score=53.52  Aligned_cols=27  Identities=33%  Similarity=0.503  Sum_probs=23.6

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +....++|+|+.|+|||||++.+..-+
T Consensus       359 ~~G~~vaIvG~SGsGKSTLl~lL~g~~  385 (529)
T TIGR02868       359 PPGERVAILGPSGSGKSTLLMLLTGLL  385 (529)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            356789999999999999999998665

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=95.40  E-value=0.062  Score=52.34  Aligned_cols=27  Identities=37%  Similarity=0.384  Sum_probs=23.1

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .....++|.|..|+|||||+..+....
T Consensus       153 ~~GQ~igI~G~sGaGKSTLl~~I~g~~  179 (434)
T PRK07196        153 GKGQRVGLMAGSGVGKSVLLGMITRYT  179 (434)
T ss_pred             ecceEEEEECCCCCCccHHHHHHhccc
Confidence            355789999999999999999887754

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=95.39  E-value=0.1  Score=51.04  Aligned_cols=90  Identities=20%  Similarity=0.336  Sum_probs=51.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCC-----CCCCCCHHHH-
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNE-----SWDNKSFDEK-  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~-  240 (427)
                      ....++|+|..|+|||||++.+....     ..+.++...+... .....+...+...-++...     ..+....... 
T Consensus       167 ~GqrigI~G~sG~GKSTLl~~I~g~~-----~~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~  241 (451)
T PRK05688        167 RGQRLGLFAGTGVGKSVLLGMMTRFT-----EADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLR  241 (451)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCC-----CCCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHH
Confidence            45679999999999999999887653     1234444444433 2455555555544322210     0011111111 


Q ss_pred             ----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          241 ----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       241 ----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                          .-.+-+++  +++++||++||+-.
T Consensus       242 a~~~a~aiAEyfrd~G~~VLl~~DslTR  269 (451)
T PRK05688        242 AAMYCTRIAEYFRDKGKNVLLLMDSLTR  269 (451)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEecchhH
Confidence                11233343  58999999999853

>COG1158 Rho Transcription termination factor [Transcription]

Probab=95.38  E-value=0.17  Score=46.73  Aligned_cols=104  Identities=18%  Similarity=0.149  Sum_probs=61.9

Q ss_pred             hHHHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC-C-CCCHHHHHHHHHHHhCCCCCCC
Q 042645          156 TLDRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS-R-DLQLGKIQESIAKKIGLYNESW  232 (427)
Q Consensus       156 ~~~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~-~-~~~~~~l~~~i~~~l~~~~~~~  232 (427)
                      .-.++++++.- +....-.|+.++-.|||+|.+.+++...  ..|.++..||-+- . +-.+.++.+++-...-.+.-+.
T Consensus       159 ls~RviDL~~PIGkGQR~LIVAPPkaGKT~lLq~IA~aIt--~N~Pe~~LiVLLIDERPEEVTdmqrsV~geViaSTFDe  236 (422)
T COG1158         159 LSTRVIDLISPIGKGQRGLIVAPPKAGKTTLLQNIANAIT--TNHPECELIVLLIDERPEEVTDMQRSVKGEVVASTFDE  236 (422)
T ss_pred             chhHHHhhhcccCCCceeeEecCCCCCchHHHHHHHHHHh--cCCCceEEEEEEecCCchHHHHHHHhhcceEEeecCCC
Confidence            34456666643 3445678999999999999999999973  6788888888753 2 2234555555543222111111


Q ss_pred             CCCCHHHHH----HHHHHHhc-CCcEEEEEeccC
Q 042645          233 DNKSFDEKA----QEIFKTMR-NRKIVLLLDDIW  261 (427)
Q Consensus       233 ~~~~~~~~~----~~l~~~L~-~k~~LlVlDdv~  261 (427)
                      .....-+..    ++-+.... ++.++|+||.+-
T Consensus       237 pp~~HvqVAE~viEkAKRlVE~~kDVVILLDSIT  270 (422)
T COG1158         237 PPSRHVQVAEMVIEKAKRLVEHGKDVVILLDSIT  270 (422)
T ss_pred             cchhhHHHHHHHHHHHHHHHHcCCcEEEEehhHH
Confidence            112222222    22333333 678899999864

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=95.37  E-value=0.016  Score=44.70  Aligned_cols=22  Identities=32%  Similarity=0.297  Sum_probs=19.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~  190 (427)
                      ...++|.|+.|+|||||+..+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4689999999999999999975

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PRK13948 shikimate kinase; Provisional

Probab=95.36  E-value=0.018  Score=49.33  Aligned_cols=26  Identities=31%  Similarity=0.512  Sum_probs=23.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|.++|+.|+||||+++.+.+.+
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~l   34 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRAL   34 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            45689999999999999999999887

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=95.34  E-value=0.011  Score=53.59  Aligned_cols=23  Identities=30%  Similarity=0.612  Sum_probs=21.0

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.++|++|+||||+|+.+...+
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l   23 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKL   23 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999877

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.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.34  E-value=0.024  Score=49.94  Aligned_cols=26  Identities=27%  Similarity=0.345  Sum_probs=22.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|..|+|||||++.+..-.
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~Gl~   57 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAGLE   57 (252)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhccc
Confidence            44689999999999999999987543

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.33  E-value=0.017  Score=50.83  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=21.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ....|.|+|++|+|||||+..+.+.
T Consensus        12 ~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         12 KPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhc
Confidence            4578999999999999999998754

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=95.33  E-value=0.16  Score=49.61  Aligned_cols=90  Identities=19%  Similarity=0.276  Sum_probs=49.8

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----CCCCCCHH---
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNE----SWDNKSFD---  238 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~---  238 (427)
                      .....++|.|..|+|||||++.+....     ..+......+.. ......+..+..........    .....+..   
T Consensus       143 ~~Gq~~~I~G~sG~GKStLl~~I~~~~-----~~~~~vi~~iG~~~~ev~~~~~~~~~~~~~~~tvvv~~~s~~p~~~r~  217 (422)
T TIGR02546       143 GEGQRIGIFAGAGVGKSTLLGMIARGA-----SADVNVIALIGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPSLERL  217 (422)
T ss_pred             cCCCEEEEECCCCCChHHHHHHHhCCC-----CCCEEEEEEEccCCcCHHHHHHHHhccccccceEEEeccccCCHHHHH
Confidence            345678999999999999999998765     123344444443 33444555444432211100    00111111   


Q ss_pred             ---HHHHHHHHHh--cCCcEEEEEeccC
Q 042645          239 ---EKAQEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       239 ---~~~~~l~~~L--~~k~~LlVlDdv~  261 (427)
                         ...-.+.+++  +++++|+++|++-
T Consensus       218 ~~~~~a~~~AE~f~~~g~~Vl~~~Dslt  245 (422)
T TIGR02546       218 KAAYTATAIAEYFRDQGKRVLLMMDSLT  245 (422)
T ss_pred             HHHHHHHHHHHHHHHCCCcEEEEEeCch
Confidence               1112233333  4789999999985

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=95.33  E-value=0.08  Score=49.26  Aligned_cols=56  Identities=18%  Similarity=0.204  Sum_probs=40.0

Q ss_pred             CCCCccccchhhHH---HHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCc
Q 042645          145 PLPPTVVGMQSTLD---RVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFD  201 (427)
Q Consensus       145 ~~~~~~vGR~~~~~---~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~  201 (427)
                      +....+||..+..+   -+++.+.++  ..+.|.|.|++|.|||+||-.+.+.+ -..-.|.
T Consensus        36 ~~~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eL-G~dvPF~   96 (450)
T COG1224          36 FIGDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIAREL-GEDVPFV   96 (450)
T ss_pred             EcCCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHh-CCCCCce
Confidence            34567899876443   345555554  45789999999999999999999998 3334443

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=95.31  E-value=0.15  Score=46.42  Aligned_cols=105  Identities=13%  Similarity=0.173  Sum_probs=66.4

Q ss_pred             CCccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      .+.|+|-... +++..++..  ...+.+.++|..|+|||+-++.+++...       ..+.+..++.++...+...+...
T Consensus        71 ~~~~l~tkt~-r~~~~~~~~A~k~g~l~~vyg~~g~gKt~a~~~y~~s~p-------~~~l~~~~p~~~a~~~i~~i~~~  142 (297)
T COG2842          71 APDFLETKTV-RRIFFRTRPASKTGSLVVVYGYAGLGKTQAAKNYAPSNP-------NALLIEADPSYTALVLILIICAA  142 (297)
T ss_pred             cccccccchh-HhHhhhhhhhhhcCceEEEeccccchhHHHHHhhcccCc-------cceeecCChhhHHHHHHHHHHHH
Confidence            4566665432 222333221  2334899999999999999999987651       23444566666666666666655


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL  263 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~  263 (427)
                      .....    ..........+...+++..-+++.|+.+..
T Consensus       143 ~~~~~----~~~~~d~~~~~~~~l~~~~~~iivDEA~~L  177 (297)
T COG2842         143 AFGAT----DGTINDLTERLMIRLRDTVRLIIVDEADRL  177 (297)
T ss_pred             Hhccc----chhHHHHHHHHHHHHccCcceeeeehhhcc
Confidence            44332    223445555666677888889999998764

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.30  E-value=0.057  Score=53.02  Aligned_cols=94  Identities=11%  Similarity=0.129  Sum_probs=54.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCC--cEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC-----CCCCCCHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDF--DFVIWEVVSRDL-QLGKIQESIAKKIGLYNE-----SWDNKSFDE  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f--~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~-----~~~~~~~~~  239 (427)
                      ....++|.|..|+|||||+..+.++. .....+  ..++++.+++.. ...+++..+...-.+...     ..+......
T Consensus       140 ~GQR~gIfgg~G~GKs~L~~~ia~~~-~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R  218 (458)
T TIGR01041       140 RGQKLPIFSGSGLPHNELAAQIARQA-TVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVER  218 (458)
T ss_pred             cCCEEEeeCCCCCCHHHHHHHHHHhh-cccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHH
Confidence            44679999999999999999998865 221111  145666666543 456666666543222110     001111111


Q ss_pred             -----HHHHHHHHhc---CCcEEEEEeccCC
Q 042645          240 -----KAQEIFKTMR---NRKIVLLLDDIWE  262 (427)
Q Consensus       240 -----~~~~l~~~L~---~k~~LlVlDdv~~  262 (427)
                           ..-.+-++++   ++++||++||+-.
T Consensus       219 ~~a~~~a~tiAEyfr~d~G~~VLli~DslTR  249 (458)
T TIGR01041       219 IVTPRMALTAAEYLAFEKDMHVLVILTDMTN  249 (458)
T ss_pred             HHHHHHHHHHHHHHHHccCCcEEEEEcChhH
Confidence                 1122444544   7899999999843

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=95.30  E-value=0.037  Score=50.44  Aligned_cols=26  Identities=35%  Similarity=0.483  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+..++|||++|.|||-+|+.|+...
T Consensus       165 ~Pkg~ll~GppGtGKTlla~~Vaa~m  190 (388)
T KOG0651|consen  165 PPKGLLLYGPPGTGKTLLARAVAATM  190 (388)
T ss_pred             CCceeEEeCCCCCchhHHHHHHHHhc
Confidence            35689999999999999999999887

>PRK13946 shikimate kinase; Provisional

Probab=95.29  E-value=0.016  Score=49.91  Aligned_cols=25  Identities=28%  Similarity=0.380  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|.+.|++|+||||+++.+.+.+
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~L   34 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATML   34 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc
Confidence            3579999999999999999999987

>PRK04182 cytidylate kinase; Provisional

Probab=95.27  E-value=0.016  Score=49.56  Aligned_cols=23  Identities=30%  Similarity=0.496  Sum_probs=21.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|.|.|+.|+||||+++.+++.+
T Consensus         2 ~I~i~G~~GsGKstia~~la~~l   24 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68999999999999999999876

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=95.27  E-value=0.08  Score=53.17  Aligned_cols=25  Identities=36%  Similarity=0.577  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|..|.|||||.+.+....
T Consensus        29 G~riGLvG~NGaGKSTLLkilaG~~   53 (530)
T COG0488          29 GERIGLVGRNGAGKSTLLKILAGEL   53 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCC
Confidence            4579999999999999999998776

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.26  E-value=0.088  Score=51.28  Aligned_cols=91  Identities=21%  Similarity=0.286  Sum_probs=50.9

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCC-----CCCCCCCHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYN-----ESWDNKSFDEK  240 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~-----~~~~~~~~~~~  240 (427)
                      .....++|.|..|+|||||++.+.+..     +.+..++..+++. ....+++.+....-....     ...+.......
T Consensus       153 ~~GqrigI~G~sG~GKSTLL~~I~~~~-----~~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~  227 (433)
T PRK07594        153 GEGQRVGIFSAPGVGKSTLLAMLCNAP-----DADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERV  227 (433)
T ss_pred             CCCCEEEEECCCCCCccHHHHHhcCCC-----CCCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHH
Confidence            355689999999999999999887654     2334455555543 344455555432110000     00011111111


Q ss_pred             -----HHHHHHHh--cCCcEEEEEeccCC
Q 042645          241 -----AQEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       241 -----~~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                           .-.+-+++  +++++||++||+-.
T Consensus       228 ~a~~~a~tiAEyfrd~G~~VLl~~Dsltr  256 (433)
T PRK07594        228 RALFVATTIAEFFRDNGKRVVLLADSLTR  256 (433)
T ss_pred             HHHHHHHHHHHHHHHCCCcEEEEEeCHHH
Confidence                 11233444  47999999999853

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=95.24  E-value=0.93  Score=41.87  Aligned_cols=67  Identities=12%  Similarity=0.109  Sum_probs=38.9

Q ss_pred             CCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCCh-hHHhh-cCCCcceeccCCChHHHHHHHHH
Q 042645          250 NRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREF-EVCGL-MDAHKSFKVECLGYEDAWRLFEE  317 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~-~v~~~-~~~~~~~~l~~L~~~e~~~lf~~  317 (427)
                      +++-++|+||++...  ....+...+-....++.+|++|.+. .+... .+-...+.+.+ +.++..+++..
T Consensus       103 ~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~~  173 (290)
T PRK07276        103 GKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLEQ  173 (290)
T ss_pred             CCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHHH
Confidence            566799999998653  3444444444434556677666554 33322 22235567766 66666666653

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=95.24  E-value=0.017  Score=48.99  Aligned_cols=23  Identities=30%  Similarity=0.496  Sum_probs=21.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|.|.|+.|+||||+|+.+.+.+
T Consensus         2 iI~i~G~~GSGKstia~~la~~l   24 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKL   24 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68999999999999999998875

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.

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=95.23  E-value=0.017  Score=54.65  Aligned_cols=151  Identities=21%  Similarity=0.305  Sum_probs=78.3

Q ss_pred             ccchhhHHHHHHHhcc-----------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCC-CC---cEEEEE---
Q 042645          151 VGMQSTLDRVWRCLTE-----------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPN-DF---DFVIWE---  206 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~-----------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~f---~~~~wv---  206 (427)
                      .|-..+...|.+.+..                 ....++.|+|.+|+||||+.+.+......... .+   ...+-+   
T Consensus       374 ~~lp~e~~~IleSFGv~~r~ieryvlr~vNL~ikpGdvvaVvGqSGaGKttllRmi~G~~~~~~ee~y~p~sg~v~vp~n  453 (593)
T COG2401         374 KGLPNEFQDILESFGVRQRVIERYVLRNLNLEIKPGDVVAVVGQSGAGKTTLLRMILGAQKGRGEEKYRPDSGKVEVPKN  453 (593)
T ss_pred             ccCChHHHHHHHHhcchheeeeeeeeeceeeEecCCCeEEEEecCCCCcchHHHHHHHHhhcccccccCCCCCceecccc
Confidence            4555677777777642                 13468999999999999999998765521111 00   011111   


Q ss_pred             ----EeC----CCCCHHHHHHH-------------HHHHhCCCCCC-----CCCCCH-HHHHHHHHHHhcCCcEEEEEec
Q 042645          207 ----VVS----RDLQLGKIQES-------------IAKKIGLYNES-----WDNKSF-DEKAQEIFKTMRNRKIVLLLDD  259 (427)
Q Consensus       207 ----~~~----~~~~~~~l~~~-------------i~~~l~~~~~~-----~~~~~~-~~~~~~l~~~L~~k~~LlVlDd  259 (427)
                          .+.    ..++-..++..             |++..++....     +...+. ..-..+|...+..++-+++.|.
T Consensus       454 t~~a~iPge~Ep~f~~~tilehl~s~tGD~~~AveILnraGlsDAvlyRr~f~ELStGQKeR~KLAkllaerpn~~~iDE  533 (593)
T COG2401         454 TVSALIPGEYEPEFGEVTILEHLRSKTGDLNAAVEILNRAGLSDAVLYRRKFSELSTGQKERAKLAKLLAERPNVLLIDE  533 (593)
T ss_pred             chhhccCcccccccCchhHHHHHhhccCchhHHHHHHHhhccchhhhhhccHhhcCcchHHHHHHHHHHhcCCCcEEhhh
Confidence                011    11121233333             33333332211     111122 2233567778888989999999


Q ss_pred             cCCccc-ccc--cccCCCC--CCCCcEEEEecCChhHHhhcCCCcce
Q 042645          260 IWELFD-LAQ--VGLPVPS--RASASKVVFTTREFEVCGLMDAHKSF  301 (427)
Q Consensus       260 v~~~~~-~~~--~~~~l~~--~~~gs~IivTtR~~~v~~~~~~~~~~  301 (427)
                      +...-+ ...  +...+..  ...|+.+++.|+..++...+.++..+
T Consensus       534 F~AhLD~~TA~rVArkiselaRe~giTlivvThrpEv~~AL~PD~li  580 (593)
T COG2401         534 FAAHLDELTAVRVARKISELAREAGITLIVVTHRPEVGNALRPDTLI  580 (593)
T ss_pred             hhhhcCHHHHHHHHHHHHHHHHHhCCeEEEEecCHHHHhccCCceeE
Confidence            865322 111  1111111  12466777777777777666555433

>TIGR01287 nifH nitrogenase iron protein

Probab=95.21  E-value=0.02  Score=52.79  Aligned_cols=25  Identities=32%  Similarity=0.667  Sum_probs=21.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      +.|+|+|-||+||||++..++..+.
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~La   25 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAALA   25 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHHHH
Confidence            4689999999999999999887773

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=95.18  E-value=0.14  Score=49.80  Aligned_cols=89  Identities=22%  Similarity=0.303  Sum_probs=49.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHH-H--
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFD-E--  239 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~-~--  239 (427)
                      ....++|.|..|+|||||+..+.+.. .    .+..+...+.... ...++.......-.+...    .....+.. .  
T Consensus       136 ~Gq~~~I~G~sG~GKTtLl~~I~~~~-~----~~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~  210 (411)
T TIGR03496       136 RGQRMGIFAGSGVGKSTLLGMMARYT-E----ADVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLR  210 (411)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhcCC-C----CCEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHH
Confidence            45679999999999999999888654 1    2334445555432 344455544433111110    00111111 1  


Q ss_pred             ---HHHHHHHHh--cCCcEEEEEeccC
Q 042645          240 ---KAQEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       240 ---~~~~l~~~L--~~k~~LlVlDdv~  261 (427)
                         ..-.+-+++  +++++||++||+-
T Consensus       211 a~~~a~tiAEyfr~~G~~Vll~~Dslt  237 (411)
T TIGR03496       211 AAFYATAIAEYFRDQGKDVLLLMDSLT  237 (411)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEeChH
Confidence               111223333  5899999999984

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=95.17  E-value=0.11  Score=52.18  Aligned_cols=134  Identities=18%  Similarity=0.210  Sum_probs=68.0

Q ss_pred             hHHHHHHHhccCCCeEEEEEecCCCcHHHHHHH-HHhhccCCCCCCcEEEEEEeCCCCC--HHHHHHHHHHHhCCCCCCC
Q 042645          156 TLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQ-INNSFLHTPNDFDFVIWEVVSRDLQ--LGKIQESIAKKIGLYNESW  232 (427)
Q Consensus       156 ~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~-v~~~~~~~~~~f~~~~wv~~~~~~~--~~~l~~~i~~~l~~~~~~~  232 (427)
                      ..++|++.+.++  .||.|+|..|+||||-..+ +|.+-     +-+.. -|.+.++-.  .-.+.+.+...++......
T Consensus       360 ~R~~ll~~ir~n--~vvvivgETGSGKTTQl~QyL~edG-----Y~~~G-mIGcTQPRRvAAiSVAkrVa~EM~~~lG~~  431 (1042)
T KOG0924|consen  360 CRDQLLSVIREN--QVVVIVGETGSGKTTQLAQYLYEDG-----YADNG-MIGCTQPRRVAAISVAKRVAEEMGVTLGDT  431 (1042)
T ss_pred             HHHHHHHHHhhC--cEEEEEecCCCCchhhhHHHHHhcc-----cccCC-eeeecCchHHHHHHHHHHHHHHhCCccccc
Confidence            344555555443  6899999999999986554 44432     11111 233444332  3345556666665432110


Q ss_pred             --------CCCCHHHH------HHHHHHHhc----CCcEEEEEeccCCccccccc-----ccCCCCCCCCcEEEEecCCh
Q 042645          233 --------DNKSFDEK------AQEIFKTMR----NRKIVLLLDDIWELFDLAQV-----GLPVPSRASASKVVFTTREF  289 (427)
Q Consensus       233 --------~~~~~~~~------~~~l~~~L~----~k~~LlVlDdv~~~~~~~~~-----~~~l~~~~~gs~IivTtR~~  289 (427)
                              +..+.+..      --.|++.|.    +|--.||+|+.++..--.++     ...+ .....-|+||||-..
T Consensus       432 VGYsIRFEdvT~~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~l-arRrdlKliVtSATm  510 (1042)
T KOG0924|consen  432 VGYSIRFEDVTSEDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVL-ARRRDLKLIVTSATM  510 (1042)
T ss_pred             cceEEEeeecCCCceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHH-HhhccceEEEeeccc
Confidence                    00011111      012344444    45669999999865321111     1112 223467899999764


Q ss_pred             h---HHhhcCCC
Q 042645          290 E---VCGLMDAH  298 (427)
Q Consensus       290 ~---v~~~~~~~  298 (427)
                      +   ++...+..
T Consensus       511 ~a~kf~nfFgn~  522 (1042)
T KOG0924|consen  511 DAQKFSNFFGNC  522 (1042)
T ss_pred             cHHHHHHHhCCC
Confidence            4   45555533

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=95.17  E-value=0.088  Score=51.32  Aligned_cols=94  Identities=9%  Similarity=0.151  Sum_probs=56.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC----------CCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC-CCCC-----C
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH----------TPNDFDFVIWEVVSRDLQLGKIQESIAKKIG-LYNE-----S  231 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~----------~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~-~~~~-----~  231 (427)
                      ...-++|.|.+|+|||||+..+.++...          ..+.-..+++..+++.....+.+...+..-+ +...     .
T Consensus       140 ~GQRigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~at  219 (466)
T TIGR01040       140 RGQKIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNL  219 (466)
T ss_pred             cCCeeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEEC
Confidence            4567999999999999999999877520          0011115567777777666666666666554 2210     0


Q ss_pred             CCCCCHHHH-----HHHHHHHhc---CCcEEEEEeccC
Q 042645          232 WDNKSFDEK-----AQEIFKTMR---NRKIVLLLDDIW  261 (427)
Q Consensus       232 ~~~~~~~~~-----~~~l~~~L~---~k~~LlVlDdv~  261 (427)
                      .+.......     .-.+-++++   ++++||++||+-
T Consensus       220 sd~p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslT  257 (466)
T TIGR01040       220 ANDPTIERIITPRLALTTAEYLAYQCEKHVLVILTDMS  257 (466)
T ss_pred             CCCCHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChH
Confidence            011111111     112344444   699999999984

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.15  E-value=0.13  Score=47.08  Aligned_cols=90  Identities=20%  Similarity=0.162  Sum_probs=48.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK  246 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~  246 (427)
                      +...++++|.+|+||||++..+...+.   ..-..+.+++..... ....-+......++.+..  ...+...+...+..
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~---~~~~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~--~~~~~~~l~~~l~~  148 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFH---GKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVI--AVRDEAAMTRALTY  148 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHH---HcCCeEEEEecCCCCHHHHHHHHHHhhhcCceEE--ecCCHHHHHHHHHH
Confidence            346899999999999999999877662   112345555554221 112222233333333221  22344455444433


Q ss_pred             Hhc-CCcEEEEEeccCC
Q 042645          247 TMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       247 ~L~-~k~~LlVlDdv~~  262 (427)
                      .-+ .+.=++++|..-.
T Consensus       149 l~~~~~~D~ViIDt~Gr  165 (270)
T PRK06731        149 FKEEARVDYILIDTAGK  165 (270)
T ss_pred             HHhcCCCCEEEEECCCC
Confidence            222 2445788888743

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.15  E-value=0.039  Score=51.54  Aligned_cols=27  Identities=33%  Similarity=0.511  Sum_probs=24.3

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+|+|.|++|+|||||+..+...+
T Consensus        32 ~~~~~i~i~G~~G~GKttl~~~l~~~~   58 (300)
T TIGR00750        32 GNAHRVGITGTPGAGKSTLLEALGMEL   58 (300)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            467899999999999999999998876

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

>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=95.15  E-value=0.034  Score=52.28  Aligned_cols=47  Identities=21%  Similarity=0.299  Sum_probs=34.6

Q ss_pred             CCccccchhhHHH---HHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          147 PPTVVGMQSTLDR---VWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       147 ~~~~vGR~~~~~~---l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+||..+..+.   +++.+.++  ..+.|.|.|++|.|||+||..+.+.+
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eL   74 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKEL   74 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHC
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHh
Confidence            3578998765443   45666655  36889999999999999999999988

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.

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

Probab=95.14  E-value=0.04  Score=43.66  Aligned_cols=26  Identities=31%  Similarity=0.482  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.+.|.=|+||||+++.++..+
T Consensus        14 ~g~vi~L~GdLGaGKTtf~r~l~~~l   39 (123)
T PF02367_consen   14 PGDVILLSGDLGAGKTTFVRGLARAL   39 (123)
T ss_dssp             S-EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            44789999999999999999999877

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=95.14  E-value=0.022  Score=48.08  Aligned_cols=25  Identities=32%  Similarity=0.372  Sum_probs=22.1

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++.|.|++|+|||||++.++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3578999999999999999998764

>smart00072 GuKc Guanylate kinase homologues

Probab=95.12  E-value=0.025  Score=48.68  Aligned_cols=25  Identities=36%  Similarity=0.458  Sum_probs=22.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|.|+|++|+|||||+..+.+..
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcC
Confidence            3679999999999999999998875

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.

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=95.12  E-value=0.02  Score=46.53  Aligned_cols=25  Identities=36%  Similarity=0.537  Sum_probs=22.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++|+|..|+|||||.+.++...
T Consensus        11 g~~~~i~G~nGsGKStLl~~l~g~~   35 (137)
T PF00005_consen   11 GEIVAIVGPNGSGKSTLLKALAGLL   35 (137)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEEccCCCccccceeeecccc
Confidence            4589999999999999999987765

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	427
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-50
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	6e-46
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-37
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	5e-17

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score =  177 bits (451), Expect = 2e-50
 Identities = 55/415 (13%), Positives = 121/415 (29%), Gaps = 39/415 (9%)

Query: 31  HLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQMRRLQQVQGWLSRVQDVEEEVRRREQ 90
             +D L  L  +     +    +    T        RL+++  +L   +    E+     
Sbjct: 22  EPRDALTYLEGKNIFTEDHSELISKMST--------RLERIANFLRIYRRQASELGPLID 73

Query: 91  EVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGLRKEGDFKDVAQTVPENPVDERPLPPTV 150
                +       ++ Y         L     +  +   + + + +    V   P   T 
Sbjct: 74  FFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNV---PKQMTC 130

Query: 151 VGMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQI-NNSFLHTPNDFDFVIWE 206
              +  +DRV + L E        + L+G  G GK+ + +Q  + S      ++D ++W 
Sbjct: 131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWL 190

Query: 207 VVSRDL--QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR------NRKIVLLLD 258
             S         +   I   +   ++  +  S +     + K M           + + D
Sbjct: 191 KDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFD 250

Query: 259 DIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMDAHKS-FKVECLGYEDAWRLFEE 317
           D+ +   +        ++    + + TTR+ E+           +V  L  ++ +   E 
Sbjct: 251 DVVQEETIR------WAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEA 304

Query: 318 KVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASK 377
                         ++         G P  L+   ++   K    + A     L S    
Sbjct: 305 YGMPM--PVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTF-EKMAQLNNKLESRGLV 361

Query: 378 -----FSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI 427
                     K     L+   + L   + R  L +    P    I ++       
Sbjct: 362 GVECITPYSYKSLAMALQRCVEVLSDED-RSALAFAVVMPPGVDIPVKLWSCVIP 415

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  166 bits (421), Expect = 6e-46
 Identities = 61/382 (15%), Positives = 134/382 (35%), Gaps = 48/382 (12%)

Query: 78  VQDVEEEVRRREQEVICLDGLRYRSSIKSYKYGKRVVKS--------LKNVQGLRKEGDF 129
            + V  E  ++++  + +  +  + +     +   ++          L +   +      
Sbjct: 40  EEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSG 99

Query: 130 KD--------VAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLT--EEPVGIVGLYGMGG 179
           KD        V   + E  V +   P   V  +  ++ + + L+  +   G V ++GM G
Sbjct: 100 KDSVSGITSYVRTVLCEGGVPQ--RPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAG 157

Query: 180 VGKTTLLTQINNSFLHTPNDF-DFVIWEVVSRDLQLGKI--QESIAKKIGLYNESWDNKS 236
            GK+ L  +           F   V W  V +  + G +   +++  ++           
Sbjct: 158 CGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLP 217

Query: 237 FD-EKAQEI---FKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVC 292
            + E+A++        ++ + +L+LDD+W+ + L           S  +++ TTR+  V 
Sbjct: 218 LNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVT 270

Query: 293 GLMDAHKS--FKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT 350
             +   K        LG E    +    V         D+PE A ++ +EC G PL +  
Sbjct: 271 DSVMGPKYVVPVESSLGKEKGLEILSLFVNMK----KADLPEQAHSIIKECKGSPLVVSL 326

Query: 351 VGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKA-----LSRLKFSYDFLPSNETRFCL 405
           +G  +     P  W + ++ L++   K                +  S + L  +  +   
Sbjct: 327 IGALLRDF--PNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDI-KDYY 383

Query: 406 LYCGFFPEDYSISIEDLIDCWI 427
                  +D  +  + L   W 
Sbjct: 384 TDLSILQKDVKVPTKVLCILWD 405

>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 =  144 bits (363), Expect = 2e-37
 Identities = 69/449 (15%), Positives = 139/449 (30%), Gaps = 99/449 (22%)

Query: 9   LSCDDTISRCLDCIVSQTGYICHLKDNLDALR-----TEFQKLIEARNDVLIRVTVAEQR 63
               D +S   D  V    + C  KD  D  +      E   +I +++ V          
Sbjct: 16  YQYKDILSVFEDAFVDN--FDC--KDVQDMPKSILSKEEIDHIIMSKDAVS--------- 62

Query: 64  QMRRLQQVQGWLSRVQDVEEEVRRREQEVICLDGLRYRSSIKSYKYGKRVVKSLKNVQGL 123
              RL     W    +  EE V++  +EV+ ++          YK+   ++  +K  +  
Sbjct: 63  GTLRLF----WTLLSKQ-EEMVQKFVEEVLRIN----------YKF---LMSPIKT-EQR 103

Query: 124 RKEGDFKDVAQTVPENPVDERPLPPTVVGMQSTLDRVWRCLTE-EPVGIVGLYGMGGVGK 182
           +     +   +       D +      V       ++ + L E  P   V + G+ G GK
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK 163

Query: 183 TTLLTQINNSF-LHTPNDFDFVIW----EVVSRDLQLGKIQESIAKKI---------GLY 228
           T +   +  S+ +    DF  + W       S +  L ++ + +  +I            
Sbjct: 164 TWVALDVCLSYKVQCKMDFK-IFWLNLKNCNSPETVL-EMLQKLLYQIDPNWTSRSDHSS 221

Query: 229 NESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIW-----ELFDLAQVGLPVPSRASASKVV 283
           N      S   + + + K+      +L+L ++        F+L            + K++
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL------------SCKIL 269

Query: 284 FTTREFEVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDIL-----DSHPDIPELAETVA 338
            TTR  +V   + A  +  +     +           + +L         D+P       
Sbjct: 270 LTTRFKQVTDFLSAATTTHIS---LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREV---- 322

Query: 339 RECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSASKFSGMEKKALSR-LKFSYDFLP 397
                 P  L  +  ++      R+     +  +        +    L+  ++ S + L 
Sbjct: 323 --LTTNPRRLSIIAESI------RDGLATWDNWKH-------VNCDKLTTIIESSLNVLE 367

Query: 398 SNETRFCLLYCGFFPEDYSISIEDLIDCW 426
             E R        FP    I    L   W
Sbjct: 368 PAEYRKMFDRLSVFPPSAHIPTILLSLIW 396

>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 = 45.2 bits (106), Expect = 3e-05
 Identities = 46/379 (12%), Positives = 104/379 (27%), Gaps = 77/379 (20%)

Query: 5   CSTSLSCDDTISRCLDCIVSQTGYICHL-------KDNLDALRTEFQKLIEARNDVLIRV 57
            +  L      +     + S+    C L           +A     + L+  R   +   
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDF 280

Query: 58  TVAEQRQMRRLQQVQG-------------WLS-RVQDVEEEVRRREQEVICLDGLRYRSS 103
             A       L                  +L  R QD+  EV       + +     R  
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG 340

Query: 104 IKSYKYGKRVV---------KSLKNVQGLRKEGDFKDVAQTV-PENPVDERPLPPTVVGM 153
           + ++   K V           SL  ++       F  ++  V P +      +P  +   
Sbjct: 341 LATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS--VFPPS-A---HIPTIL--- 391

Query: 154 QSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ 213
              L  +W  + +  V +V    +  + K +L+ +       +       +   +  +  
Sbjct: 392 ---LSLIWFDVIKSDVMVV----VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444

Query: 214 L-GKIQESIAKKIGLYNES-----WDNKSFD---------EKAQEIFKTMRNRKIVLLLD 258
           L   I +         ++       D   +          E  +      R     + LD
Sbjct: 445 LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPER-MTLFRM----VFLD 499

Query: 259 DIWELFDLAQVGLPVPSRASASKVVFTTREFE--VCGLMDAHKSFKVECLGYEDAWRLFE 316
             +    +        +  S    +   + ++  +C   D    ++       D    F 
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC---DNDPKYERLVNAILD----FL 552

Query: 317 EKVGRDILDS-HPDIPELA 334
            K+  +++ S + D+  +A
Sbjct: 553 PKIEENLICSKYTDLLRIA 571

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 83.0 bits (205), Expect = 5e-17
 Identities = 57/298 (19%), Positives = 107/298 (35%), Gaps = 30/298 (10%)

Query: 145 PLPPTVVGMQSTLDRVWRCL--TEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDF-D 201
             P   V  +  +  + + L       G V +YGM G GK+ L  +           F  
Sbjct: 121 QRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSG 180

Query: 202 FVIWEVV--SRDLQLGKIQESIAKKIGLYNESWDN--KSFDEKAQEIFKTMRNR--KIVL 255
            V W  +       L    +++  ++            + +E    +   M  +  + +L
Sbjct: 181 GVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLL 240

Query: 256 LLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVC-GLMDAHKSFKVE-CLGYEDAWR 313
           +LDD+W+ + L           +  +++ TTR+  V   +M       VE  LG E    
Sbjct: 241 ILDDVWDPWVLKAFD-------NQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLE 293

Query: 314 LFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRS 373
           +    V         D+P  A ++ +EC G PL +  +G  +  +  P  WA+ +  L++
Sbjct: 294 ILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLIGALL--RDFPNRWAYYLRQLQN 347

Query: 374 SA----SKFSGMEKKALSR-LKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCW 426
                  K S  + +AL   +  S + L  +             +D  +  + L   W
Sbjct: 348 KQFKRIRKSSSYDYEALDEAMSISVEMLREDIKD-YYTDLSILQKDVKVPTKVLCVLW 404

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	427
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.73
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.72
2fna_A	357	Conserved hypothetical protein; structural genomic	99.71
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.6
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.6
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.59
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.55
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.47
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.44
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.3
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.28
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.16
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.1
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.1
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.03
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.03
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.9
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.88
3bos_A	242	Putative DNA replication factor; P-loop containing	98.88
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.85
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.85
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.84
3pvs_A	447	Replication-associated recombination protein A; ma	98.8
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.78
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.75
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.72
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.69
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.66
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.66
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.66
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.62
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.59
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.58
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.58
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.58
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.57
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.55
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.55
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.52
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.48
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.47
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.41
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	98.39
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.35
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.35
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.28
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.27
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.27
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.26
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.25
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.23
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.22
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.2
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.19
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.18
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.16
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.09
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.07
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.06
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.03
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.02
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.99
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.98
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.97
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.88
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.87
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.86
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.81
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.76
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.76
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.73
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.59
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.55
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.54
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.49
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.48
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.46
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.43
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.36
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.32
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.29
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	97.26
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.25
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.24
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.24
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.23
3io5_A	333	Recombination and repair protein; storage dimer, i	97.21
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.16
3co5_A	143	Putative two-component system transcriptional RES	97.16
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.12
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.12
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.02
2qgz_A	308	Helicase loader, putative primosome component; str	96.97
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.96
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.83
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.81
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.8
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.78
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.74
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.7
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.69
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.68
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.63
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.6
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.59
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.53
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.51
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.51
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.49
3ice_A	422	Transcription termination factor RHO; transcriptio	96.49
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	96.47
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.47
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.46
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.43
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.41
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.39
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.38
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	96.35
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.31
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.27
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.26
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.25
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.23
2hf9_A	226	Probable hydrogenase nickel incorporation protein	96.23
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.22
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.22
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.21
2xxa_A	433	Signal recognition particle protein; protein trans	96.21
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.21
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	96.21
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	96.2
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.2
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.2
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.19
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.19
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.16
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.12
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.11
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.11
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	96.1
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.09
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.09
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.08
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.07
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.06
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.05
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	96.05
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	96.04
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.03
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.99
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.99
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.99
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.98
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.97
1via_A	175	Shikimate kinase; structural genomics, transferase	95.96
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.95
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.93
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.93
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.92
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.92
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.92
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.91
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.89
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.89
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.89
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.88
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.88
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.86
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.86
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.84
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.83
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.82
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.82
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.82
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.8
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.8
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.78
3l0o_A	427	Transcription termination factor RHO; helicase, RH	95.77
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.77
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.76
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.74
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.74
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.73
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.72
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.69
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.68
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.67
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.67
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.66
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.66
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.65
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.65
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.63
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.63
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.62
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.61
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.61
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.61
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.59
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.58
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.56
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.55
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	95.54
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.53
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.51
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.51
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.48
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.47
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.47
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.46
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.42
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.4
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.39
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.38
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.36
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.36
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.35
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.31
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.3
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.3
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.28
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.26
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.21
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.21
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.15
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	95.15
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.12
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.12
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.11
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	95.1
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.1
3end_A	307	Light-independent protochlorophyllide reductase ir	95.09
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.07
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.06
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.06
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.06
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.98
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.97
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.96
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.96
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.95
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.94
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.93
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	94.92
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.91
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.89
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.89
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	94.88
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.88
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.88
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.87
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.86
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.85
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.83
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.83
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.81
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.79
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.77
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.75
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	94.71
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.7
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.69
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.66
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.63
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.61
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.57
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.57
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	94.56
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	94.52
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	94.51
2og2_A	359	Putative signal recognition particle receptor; nuc	94.51
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	94.51
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.5
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.49
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.49
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.48
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.46
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.46
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.45
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.42
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.42
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.42
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.4
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	94.4
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.4
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	94.39
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.37
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.37
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.36
1g6h_A	257	High-affinity branched-chain amino acid transport	94.36
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.36
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.34
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.33
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.32
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.3
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.3
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.3
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.28
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.27
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.22
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.21
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.21
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	94.19
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.19
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.17
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.16
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	94.16
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	94.15
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.13
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	94.13
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	94.11
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.1
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.09
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.09
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	94.07
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	94.05
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.03
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	94.03
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.92
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	93.88
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.87
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	93.85
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.84
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.83
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	93.79
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	93.79
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	93.78
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.78
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.75
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.73
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.73
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.72
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	93.69
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.65
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.65
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	93.65
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.64
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.64
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.61
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.61
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.55
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.54
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	93.54
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.54
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	93.53
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.53
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.53
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.52
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.51
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.51
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.5
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.49
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.49
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.48
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.46
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.46
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.46
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.43
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.4
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	93.4
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.39
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.39
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.39
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	93.38
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	93.38
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	93.36
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.36
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.35
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.35
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	93.34
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.32
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.28
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	93.28
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.26
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	93.25
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.22
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	93.22
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	93.22
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	93.21
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.2
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	93.18
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	93.17
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	93.17
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	93.17
2ewv_A	372	Twitching motility protein PILT; pilus retraction	93.16
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	93.15
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.14
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.13
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	93.11
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	93.1
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	93.08
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.08
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.06
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	93.05
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	93.05
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	93.04
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.04
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	93.02
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	93.01
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	92.97
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	92.95
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	92.93
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.93
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.92
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	92.92
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.86
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	92.86
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	92.84
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	92.84
3llu_A	196	RAS-related GTP-binding protein C; structural geno	92.84
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	92.83
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	92.82
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	92.81
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.81
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	92.79
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	92.79
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	92.78
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	92.76
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	92.75
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	92.73
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	92.73
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	92.72
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.72
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	92.7
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	92.69
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	92.68
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	92.68
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.67
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	92.67
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.67
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	92.66
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.65
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	92.63
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	92.58
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	92.58
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	92.58
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	92.56
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	92.56
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	92.55
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.54
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	92.53
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	92.53
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.53
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.52
2fh5_B	214	SR-beta, signal recognition particle receptor beta	92.49
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	92.49
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	92.46
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	92.46
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	92.43
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	92.41
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	92.41
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	92.41
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	92.4
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	92.39
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	92.35
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	92.33
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	92.32
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	92.31
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	92.31
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	92.3
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	92.29
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	92.26
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	92.26
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	92.24
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	92.21
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	92.2
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	92.15
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	92.13
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	92.08
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	92.06
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	92.04
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.04
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	92.03
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	92.02
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	92.02
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	92.0
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	91.99
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	91.96
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	91.92
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	91.9
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.86
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	91.84
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	91.84
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	91.82
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	91.76
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	91.75
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	91.74
3cwq_A	209	Para family chromosome partitioning protein; alpha	91.74
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	91.72
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	91.66
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	91.65
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	91.62
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	91.58
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	91.42
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	91.4
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	91.4

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=9.7e-43  Score=351.15  Aligned_cols=256  Identities=15%  Similarity=0.187  Sum_probs=208.2

Q ss_pred             ccchhhHHHHHHHhccC---CCeEEEEEecCCCcHHHHHHHHHh--hccCCCCCCcEEEEEEeCCCC--CHHHHHHHHHH
Q 042645          151 VGMQSTLDRVWRCLTEE---PVGIVGLYGMGGVGKTTLLTQINN--SFLHTPNDFDFVIWEVVSRDL--QLGKIQESIAK  223 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~~---~~~vi~I~G~gGiGKTtLa~~v~~--~~~~~~~~f~~~~wv~~~~~~--~~~~l~~~i~~  223 (427)
                      +||+.++++|.++|..+   +.++|+|+||||+||||||+++|+  +. ....+|+.++|+++++.+  ++..++..|+.
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~-~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~  209 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQ-LIGINYDSIVWLKDSGTAPKSTFDLFTDILL  209 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSS-TBTTTBSEEEEEECCCCSTTHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhH-HHhccCCcEEEEEECCCCCCCHHHHHHHHHH
Confidence            59999999999999754   679999999999999999999998  33 457899999999999875  78999999999


Q ss_pred             HhCCCCC-----CCCCCCHHHHHHHHHHHhcCC-cEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhhcC-
Q 042645          224 KIGLYNE-----SWDNKSFDEKAQEIFKTMRNR-KIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGLMD-  296 (427)
Q Consensus       224 ~l~~~~~-----~~~~~~~~~~~~~l~~~L~~k-~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~~~-  296 (427)
                      +++....     .....+...+...+++.|+++ |+||||||||+...+ .+    + ..+||+||||||+..++..+. 
T Consensus       210 ~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~----~-~~~gs~ilvTTR~~~v~~~~~~  283 (549)
T 2a5y_B          210 MLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RW----A-QELRLRCLVTTRDVEISNAASQ  283 (549)
T ss_dssp             HHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HH----H-HHTTCEEEEEESBGGGGGGCCS
T ss_pred             HHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cc----c-ccCCCEEEEEcCCHHHHHHcCC
Confidence            9986522     112334567789999999996 999999999997654 11    1 127899999999999988775 


Q ss_pred             CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHhhccc
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRSSAS  376 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~~~~~  376 (427)
                      ....|+|++|+.+++|+||.+.++...  .++.+.+++.+|+++|+|+||||+++|+.|+.+ +   |+.+ +.+.+..+
T Consensus       284 ~~~~~~l~~L~~~ea~~Lf~~~a~~~~--~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~-~---w~~~-~~l~~~l~  356 (549)
T 2a5y_B          284 TCEFIEVTSLEIDECYDFLEAYGMPMP--VGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK-T---FEKM-AQLNNKLE  356 (549)
T ss_dssp             CEEEEECCCCCHHHHHHHHHHTSCCCC----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS-S---HHHH-HHHHHHHH
T ss_pred             CCeEEECCCCCHHHHHHHHHHHhcCCC--CchhHHHHHHHHHHHhCCChHHHHHHHHHhccc-h---HHHH-HHhHHHhh
Confidence            336799999999999999999987543  246778899999999999999999999999764 2   5543 44544433


Q ss_pred             cCCCChHHHHHHHhhhcCCCCCChHhHHHh-----------hhcCCCCCccccHHHHHhhcC
Q 042645          377 KFSGMEKKALSRLKFSYDFLPSNETRFCLL-----------YCGFFPEDYSISIEDLIDCWI  427 (427)
Q Consensus       377 ~~~~~~~~~~~~l~~sy~~L~~~~~k~cf~-----------~~s~fp~~~~i~~~~Li~~Wi  427 (427)
                      ...  ...+..+|.+||+.||+ ++|.||+           |||+||+++.|+    +++||
T Consensus       357 ~~~--~~~i~~~l~~Sy~~L~~-~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~  411 (549)
T 2a5y_B          357 SRG--LVGVECITPYSYKSLAM-ALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWS  411 (549)
T ss_dssp             HHC--SSTTCCCSSSSSSSHHH-HHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHH
T ss_pred             ccc--HHHHHHHHhcccccccH-HHHHHHhccchhhhhHhhheeeeCCCCeee----eeeee
Confidence            211  13677889999999999 9999999           999999999999    66774

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=100.00  E-value=1e-37  Score=320.55  Aligned_cols=248  Identities=17%  Similarity=0.204  Sum_probs=197.1

Q ss_pred             CccccchhhHHHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcE-EEEEEeCCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDF-VIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~-~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      +..|||+.++++|.++|.. ++.++|+|+||||+||||||+.++++. .+..+|+. ++|+++++.++...++..|+..+
T Consensus       128 k~~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~-rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL  206 (1221)
T 1vt4_I          128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSY-KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL  206 (1221)
T ss_dssp             CSCCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHC-HHHHHHSSCEEEEECCCSSSHHHHHHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhh-HHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4459999999999999976 567899999999999999999999865 34567886 89999999999888888888764


Q ss_pred             CCCCCC---C-C-----CCCHHHHHHHHHHHh---cCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHh
Q 042645          226 GLYNES---W-D-----NKSFDEKAQEIFKTM---RNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       226 ~~~~~~---~-~-----~~~~~~~~~~l~~~L---~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                      +.....   . .     ..+.+.+...++..|   .++|+||||||+|+...|..+       .+||+||||||+..++.
T Consensus       207 ~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f-------~pGSRILVTTRd~~Va~  279 (1221)
T 1vt4_I          207 YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF-------NLSCKILLTTRFKQVTD  279 (1221)
T ss_dssp             HHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHH-------HSSCCEEEECSCSHHHH
T ss_pred             hhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhh-------CCCeEEEEeccChHHHH
Confidence            321100   0 0     012344566677765   689999999999998777664       26899999999999876


Q ss_pred             hcCCCcceecc------CCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCC-ChHHHHH
Q 042645          294 LMDAHKSFKVE------CLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKK-APREWAH  366 (427)
Q Consensus       294 ~~~~~~~~~l~------~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~-~~~~w~~  366 (427)
                      .+.....+.++      +|+.+|+++||.+.++..    .   .++..+|   |+|+||||.++|+.|+.+. +..+|+.
T Consensus       280 ~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~----~---eeL~~eI---CgGLPLALkLaGs~Lr~k~~s~eeW~~  349 (1221)
T 1vt4_I          280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR----P---QDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKH  349 (1221)
T ss_dssp             HHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCC----T---TTHHHHH---CCCCHHHHHHHHHHHHHSCSSHHHHHH
T ss_pred             hcCCCeEEEecCccccCCcCHHHHHHHHHHHcCCC----H---HHHHHHH---hCCCHHHHHHHHHHHhCCCCCHHHHhc
Confidence            44433456677      999999999999986432    1   2223443   9999999999999999863 6778864


Q ss_pred             HHHHHhhccccCCCChHHHHHHHhhhcCCCCCChH-hHHHhhhcCCCCCccccHHHHHhhcC
Q 042645          367 AIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNET-RFCLLYCGFFPEDYSISIEDLIDCWI  427 (427)
Q Consensus       367 ~l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~-k~cf~~~s~fp~~~~i~~~~Li~~Wi  427 (427)
                      .            . ...+..+|.+||+.||+ +. |+||++||+||+++.|+++.|+.+|+
T Consensus       350 ~------------~-~~~I~aaLelSYd~Lp~-eelK~cFL~LAIFPed~~I~~elLa~LW~  397 (1221)
T 1vt4_I          350 V------------N-CDKLTTIIESSLNVLEP-AEYRKMFDRLSVFPPSAHIPTILLSLIWF  397 (1221)
T ss_dssp             C------------S-CHHHHHHHHHHHHHSCT-THHHHHHHHTTSSCTTSCEEHHHHHHHHC
T ss_pred             C------------C-hhHHHHHHHHHHHhCCH-HHHHHHHHHHhCCCCCCCCCHHHHHHHhc
Confidence            2            1 25899999999999999 78 99999999999999999999999996

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=100.00  E-value=1.4e-36  Score=335.37  Aligned_cols=270  Identities=20%  Similarity=0.286  Sum_probs=217.7

Q ss_pred             CCCCCccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhccCCCC-CCcEEEEEEeCCCCC--HHHHH
Q 042645          144 RPLPPTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPN-DFDFVIWEVVSRDLQ--LGKIQ  218 (427)
Q Consensus       144 ~~~~~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~f~~~~wv~~~~~~~--~~~l~  218 (427)
                      |+.++.||||+.++++|.++|..  ++.++|+|+||||+||||||++++++...... .++.++|+++++..+  ....+
T Consensus       120 p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  199 (1249)
T 3sfz_A          120 PQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKL  199 (1249)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHH
T ss_pred             CCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHH
Confidence            34456799999999999999953  57889999999999999999999988522233 556788999988543  44456


Q ss_pred             HHHHHHhCCCCC--CCCCCCHHHHHHHHHHHhcCC--cEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhh
Q 042645          219 ESIAKKIGLYNE--SWDNKSFDEKAQEIFKTMRNR--KIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL  294 (427)
Q Consensus       219 ~~i~~~l~~~~~--~~~~~~~~~~~~~l~~~L~~k--~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~  294 (427)
                      ..++..+.....  .....+.+.+...++..+.++  |+||||||+|+...|..+       .+||+||||||+..++..
T Consensus       200 ~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~~~~  272 (1249)
T 3sfz_A          200 QNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSVTDS  272 (1249)
T ss_dssp             HHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTTTTT
T ss_pred             HHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHHHHh
Confidence            677777765432  123456788889999999877  999999999998776654       568999999999998854


Q ss_pred             -cCCCcceeccC-CChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHh
Q 042645          295 -MDAHKSFKVEC-LGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLR  372 (427)
Q Consensus       295 -~~~~~~~~l~~-L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~  372 (427)
                       +.....+.+++ |+++|+++||...++...    +...+++++|+++|+|+||||.++|++|+.+.  ..|..+++.+.
T Consensus       273 ~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~----~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~--~~~~~~l~~l~  346 (1249)
T 3sfz_A          273 VMGPKHVVPVESGLGREKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLIGALLRDFP--NRWAYYLRQLQ  346 (1249)
T ss_dssp             CCSCBCCEECCSSCCHHHHHHHHHHHHTSCS----TTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS--SCHHHHHHHHH
T ss_pred             hcCCceEEEecCCCCHHHHHHHHHHhhCCCh----hhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh--hHHHHHHHHHh
Confidence             45567789986 999999999999885432    34456699999999999999999999998854  47999999887


Q ss_pred             hccccC-----CCChHHHHHHHhhhcCCCCCChHhHHHhhhcCCCCCccccHHHHHhhcC
Q 042645          373 SSASKF-----SGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI  427 (427)
Q Consensus       373 ~~~~~~-----~~~~~~~~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~Wi  427 (427)
                      ...+..     ....+.+..+|.+||+.||+ +.|.||+|||+||+++.|+++.++.+|.
T Consensus       347 ~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~-~~~~~~~~l~~f~~~~~i~~~~~~~~~~  405 (1249)
T 3sfz_A          347 NKQFKRIRKSSSYDYEALDEAMSISVEMLRE-DIKDYYTDLSILQKDVKVPTKVLCVLWD  405 (1249)
T ss_dssp             SCCCCCSSCTTCTTHHHHHHHHHHHHHTSCT-TTHHHHHHGGGSCTTCCEEHHHHHHHHT
T ss_pred             hhhhhhcccccccchHHHHHHHHHHHHhCCH-HHHHHHHHhCccCCCCeeCHHHHHHHhC
Confidence            654221     11124799999999999999 8999999999999999999999999994

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=100.00  E-value=9.6e-35  Score=296.50  Aligned_cols=266  Identities=20%  Similarity=0.303  Sum_probs=205.4

Q ss_pred             CCCCccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhccCC-CCCC-cEEEEEEeCCCCCHHHHHHH
Q 042645          145 PLPPTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSFLHT-PNDF-DFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       145 ~~~~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~~f-~~~~wv~~~~~~~~~~l~~~  220 (427)
                      +.++.||||+.++++|.++|..  ++.++|+|+|+||+||||||..++++. .. ..+| +.++|++++.. +...++..
T Consensus       121 ~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~-~~~~~~f~~~v~wv~~~~~-~~~~~~~~  198 (591)
T 1z6t_A          121 QRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDH-SLLEGCFPGGVHWVSVGKQ-DKSGLLMK  198 (591)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCH-HHHHHHCTTCEEEEEEESC-CHHHHHHH
T ss_pred             CCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhch-hHHHhhCCCceEEEECCCC-chHHHHHH
Confidence            3456799999999999999974  467899999999999999999999875 22 4567 57999999765 33344444


Q ss_pred             H---HHHhCCCC--CCCCCCCHHHHHHHHHHHhcC--CcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHh
Q 042645          221 I---AKKIGLYN--ESWDNKSFDEKAQEIFKTMRN--RKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       221 i---~~~l~~~~--~~~~~~~~~~~~~~l~~~L~~--k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                      +   +..++...  ......+.+.....+...+.+  +++||||||+|+...+..+       .+|++||||||+..++.
T Consensus       199 l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l-------~~~~~ilvTsR~~~~~~  271 (591)
T 1z6t_A          199 LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTD  271 (591)
T ss_dssp             HHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTT-------CSSCEEEEEESCGGGGT
T ss_pred             HHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHh-------cCCCeEEEECCCcHHHH
Confidence            4   34554211  112345667788888888876  7999999999986554432       46899999999998876


Q ss_pred             hcCCCcceec---cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHH
Q 042645          294 LMDAHKSFKV---ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEV  370 (427)
Q Consensus       294 ~~~~~~~~~l---~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~  370 (427)
                      .+. ...+.+   ++|+.+|+++||...++...    +...+.+.+|+++|+|+||||.++|+.|+...  ..|..+++.
T Consensus       272 ~~~-~~~~~v~~l~~L~~~ea~~L~~~~~~~~~----~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~--~~w~~~l~~  344 (591)
T 1z6t_A          272 SVM-GPKYVVPVESSLGKEKGLEILSLFVNMKK----ADLPEQAHSIIKECKGSPLVVSLIGALLRDFP--NRWEYYLKQ  344 (591)
T ss_dssp             TCC-SCEEEEECCSSCCHHHHHHHHHHHHTSCG----GGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST--TCHHHHHHH
T ss_pred             hcC-CCceEeecCCCCCHHHHHHHHHHHhCCCc----ccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc--hhHHHHHHH
Confidence            543 334444   58999999999999986532    11234589999999999999999999998753  379988888


Q ss_pred             Hhhcccc-----CCCChHHHHHHHhhhcCCCCCChHhHHHhhhcCCCCCccccHHHHHhhcC
Q 042645          371 LRSSASK-----FSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFFPEDYSISIEDLIDCWI  427 (427)
Q Consensus       371 l~~~~~~-----~~~~~~~~~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~Wi  427 (427)
                      +......     .......+..++..||+.||+ +.|.||.+||+||+++.|+.+.|+.+|.
T Consensus       345 l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~-~~~~~l~~la~f~~~~~i~~~~l~~l~~  405 (591)
T 1z6t_A          345 LQNKQFKRIRKSSSYDYEALDEAMSISVEMLRE-DIKDYYTDLSILQKDVKVPTKVLCILWD  405 (591)
T ss_dssp             HHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSCT-TTHHHHHHGGGCCTTCCEEHHHHHHHHT
T ss_pred             HHHhHHHHhhhccccchHHHHHHHHHHHHhCCH-HHHHHHHHccccCCCCccCHHHHHHHhc
Confidence            8765321     111234899999999999999 8999999999999999999999999884

>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=99.73  E-value=3.5e-17  Score=159.14  Aligned_cols=251  Identities=12%  Similarity=0.083  Sum_probs=157.3

Q ss_pred             CCCccccchhhHHHHHHHh-c----c--CCCeEEEE--EecCCCcHHHHHHHHHhhccCC--CCCCc-EEEEEEeCCCCC
Q 042645          146 LPPTVVGMQSTLDRVWRCL-T----E--EPVGIVGL--YGMGGVGKTTLLTQINNSFLHT--PNDFD-FVIWEVVSRDLQ  213 (427)
Q Consensus       146 ~~~~~vGR~~~~~~l~~~l-~----~--~~~~vi~I--~G~gGiGKTtLa~~v~~~~~~~--~~~f~-~~~wv~~~~~~~  213 (427)
                      .+..|+||+.++++|.+++ .    .  ...+.+.|  +|++|+|||||++.+++.....  ...+. .++|+++....+
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPN   99 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCS
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCC
Confidence            3477999999999999988 4    2  24567778  9999999999999999876210  00122 457888777778


Q ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc--------ccccccCCCC-C--C--C
Q 042645          214 LGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD--------LAQVGLPVPS-R--A--S  278 (427)
Q Consensus       214 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~--------~~~~~~~l~~-~--~--~  278 (427)
                      ...++..++.+++...+. ...+.......+...+.  +++++|||||++....        +..+...+.. .  +  .
T Consensus       100 ~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~  178 (412)
T 1w5s_A          100 LYTILSLIVRQTGYPIQV-RGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVN  178 (412)
T ss_dssp             HHHHHHHHHHHHTCCCCC-TTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCC
T ss_pred             HHHHHHHHHHHhCCCCCC-CCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCc
Confidence            899999999999764321 23345666777777765  7899999999986421        2212122211 1  2  3


Q ss_pred             CcEEEEecCChhHHhhc--------C-CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcC------C
Q 042645          279 ASKVVFTTREFEVCGLM--------D-AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECG------G  343 (427)
Q Consensus       279 gs~IivTtR~~~v~~~~--------~-~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~------G  343 (427)
                      +..+|+||+...+...+        . ....+.+++|+.++++++|...+.... .......+....|++.|+      |
T Consensus       179 ~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~-~~~~~~~~~~~~i~~~~~~~~~~~G  257 (412)
T 1w5s_A          179 RIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGL-RDTVWEPRHLELISDVYGEDKGGDG  257 (412)
T ss_dssp             BEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHB-CTTSCCHHHHHHHHHHHCGGGTSCC
T ss_pred             eEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcC-CCCCCChHHHHHHHHHHHHhccCCC
Confidence            45578788765532111        1 122389999999999999987643111 011122466889999999      9


Q ss_pred             CchHHHHHHHHHc-----CC---CChHHHHHHHHHHhhccccCCCChHHHHHHHhhhcCCCCCChHhHHHhhhcCC
Q 042645          344 LPLALITVGRAMA-----SK---KAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGFF  411 (427)
Q Consensus       344 ~Plai~~~~~~L~-----~~---~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~cf~~~s~f  411 (427)
                      +|..+..++....     ..   -+...+..++....           . ...+.-++..||+ +.+.++..++.+
T Consensus       258 ~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~-----------~-~~~~~~~l~~l~~-~~~~~l~aia~l  320 (412)
T 1w5s_A          258 SARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENE-----------A-ASIQTHELEALSI-HELIILRLIAEA  320 (412)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC------------------CCSSSSSCH-HHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh-----------c-cchHHHHHHcCCH-HHHHHHHHHHHH
Confidence            9976665543321     11   12233332222110           0 2334556788888 788888877764

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.72  E-value=4.2e-17  Score=154.82  Aligned_cols=198  Identities=14%  Similarity=0.096  Sum_probs=134.0

Q ss_pred             CCCccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC------CHHHHHH
Q 042645          146 LPPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL------QLGKIQE  219 (427)
Q Consensus       146 ~~~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~------~~~~l~~  219 (427)
                      .++.|+||+.++++|.+++..+  +++.|+|++|+|||||++.+++..   .     .+|+++....      +...++.
T Consensus        10 ~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~---~-----~~~~~~~~~~~~~~~~~~~~~~~   79 (350)
T 2qen_A           10 RREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNER---P-----GILIDCRELYAERGHITREELIK   79 (350)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHS---S-----EEEEEHHHHHHTTTCBCHHHHHH
T ss_pred             ChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHc---C-----cEEEEeecccccccCCCHHHHHH
Confidence            3467999999999999998764  789999999999999999999875   1     6777765432      5666777


Q ss_pred             HHHHHhCCC--------------C--CCCCCCCHHHHHHHHHHHhcC-CcEEEEEeccCCccc-----ccccccCC---C
Q 042645          220 SIAKKIGLY--------------N--ESWDNKSFDEKAQEIFKTMRN-RKIVLLLDDIWELFD-----LAQVGLPV---P  274 (427)
Q Consensus       220 ~i~~~l~~~--------------~--~~~~~~~~~~~~~~l~~~L~~-k~~LlVlDdv~~~~~-----~~~~~~~l---~  274 (427)
                      .+...+...              .  ......+..++...+.+.... ++++|||||++....     ...+...+   .
T Consensus        80 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~  159 (350)
T 2qen_A           80 ELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAY  159 (350)
T ss_dssp             HHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHH
Confidence            776655320              0  000123455566666665543 499999999987543     11111111   1


Q ss_pred             CCCCCcEEEEecCChhH-Hhh----------cC-CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcC
Q 042645          275 SRASASKVVFTTREFEV-CGL----------MD-AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECG  342 (427)
Q Consensus       275 ~~~~gs~IivTtR~~~v-~~~----------~~-~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~  342 (427)
                      ....+..+|+|++.... ...          .+ ....+.+.+|+.+|+.+++...+...+..   ...+.+..|++.|+
T Consensus       160 ~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~---~~~~~~~~i~~~tg  236 (350)
T 2qen_A          160 DSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLD---VPENEIEEAVELLD  236 (350)
T ss_dssp             HHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCC---CCHHHHHHHHHHHT
T ss_pred             HhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHhC
Confidence            11246889999887653 211          01 12368999999999999998865432211   12456889999999


Q ss_pred             CCchHHHHHHHHHc
Q 042645          343 GLPLALITVGRAMA  356 (427)
Q Consensus       343 G~Plai~~~~~~L~  356 (427)
                      |+|+++..++..+.
T Consensus       237 G~P~~l~~~~~~~~  250 (350)
T 2qen_A          237 GIPGWLVVFGVEYL  250 (350)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999987654

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.71  E-value=2.2e-16  Score=150.20  Aligned_cols=195  Identities=15%  Similarity=0.190  Sum_probs=126.4

Q ss_pred             CCccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-----CCHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-----LQLGKIQESI  221 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-----~~~~~l~~~i  221 (427)
                      +..|+||+++++.|.+ +..   +++.|+|++|+|||||++.+++.. .  .   ..+|+++...     .+...++..+
T Consensus        12 ~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~-~--~---~~~~~~~~~~~~~~~~~~~~~~~~l   81 (357)
T 2fna_A           12 RKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINEL-N--L---PYIYLDLRKFEERNYISYKDFLLEL   81 (357)
T ss_dssp             GGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHH-T--C---CEEEEEGGGGTTCSCCCHHHHHHHH
T ss_pred             HHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhc-C--C---CEEEEEchhhccccCCCHHHHHHHH
Confidence            4679999999999999 765   699999999999999999999886 2  2   2578877642     3445555555


Q ss_pred             HHHhC------------------CCCCCC---------CCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc-----ccccc
Q 042645          222 AKKIG------------------LYNESW---------DNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF-----DLAQV  269 (427)
Q Consensus       222 ~~~l~------------------~~~~~~---------~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~-----~~~~~  269 (427)
                      ...+.                  ...+..         .......+...+.+... ++++|||||++...     ++..+
T Consensus        82 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~~~~~~~  160 (357)
T 2fna_A           82 QKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRGVNLLPA  160 (357)
T ss_dssp             HHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCchhHHHH
Confidence            44331                  000000         12234445544444322 49999999997642     22222


Q ss_pred             ccCCCCCCCCcEEEEecCChhHHh-h---------c-CC-CcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHH
Q 042645          270 GLPVPSRASASKVVFTTREFEVCG-L---------M-DA-HKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETV  337 (427)
Q Consensus       270 ~~~l~~~~~gs~IivTtR~~~v~~-~---------~-~~-~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i  337 (427)
                      ...+.....+..+|+|++...... .         . +. ...+.+.+|+.+|+.+++...+..... ....    ...|
T Consensus       161 l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~-~~~~----~~~i  235 (357)
T 2fna_A          161 LAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADI-DFKD----YEVV  235 (357)
T ss_dssp             HHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTC-CCCC----HHHH
T ss_pred             HHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCC-CCCc----HHHH
Confidence            111111124678999999865321 1         1 11 246899999999999999886532111 1112    2789


Q ss_pred             HHHcCCCchHHHHHHHHHcC
Q 042645          338 ARECGGLPLALITVGRAMAS  357 (427)
Q Consensus       338 ~~~~~G~Plai~~~~~~L~~  357 (427)
                      ++.|+|+|+++..++..+..
T Consensus       236 ~~~t~G~P~~l~~~~~~~~~  255 (357)
T 2fna_A          236 YEKIGGIPGWLTYFGFIYLD  255 (357)
T ss_dssp             HHHHCSCHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHcc
Confidence            99999999999999887654

>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=99.60  E-value=2.2e-14  Score=137.93  Aligned_cols=247  Identities=15%  Similarity=0.031  Sum_probs=156.1

Q ss_pred             CCccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCC----CCC-CcEEEEEEeCCCC-CHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHT----PND-FDFVIWEVVSRDL-QLGK  216 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~~-f~~~~wv~~~~~~-~~~~  216 (427)
                      |..++||+.+++++.+++..    +..+.+.|+|++|+||||||+.+++.....    ... ...++|+++.... +...
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   98 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQA   98 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHH
Confidence            36799999999999877753    346789999999999999999999875211    011 3456788877766 8888


Q ss_pred             HHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--cccc-ccCCCCCCCCcEEEEecCChhHHh
Q 042645          217 IQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQV-GLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       217 l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~-~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                      ++..++..+..........+.......+...+..++.+|||||++....  .... ...+.....+..+|+||+......
T Consensus        99 ~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~~~~~  178 (384)
T 2qby_B           99 VLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRD  178 (384)
T ss_dssp             HHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSSTTTTT
T ss_pred             HHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCCchHh
Confidence            9999998883222222344456777888888887777999999986432  1111 111111115778898988753211


Q ss_pred             hc------CCCcceeccCCChHHHHHHHHHHhCC--CCCCCCCCHHHHHHHHHHHcC---CCchHH-HHHHHH--Hc---
Q 042645          294 LM------DAHKSFKVECLGYEDAWRLFEEKVGR--DILDSHPDIPELAETVARECG---GLPLAL-ITVGRA--MA---  356 (427)
Q Consensus       294 ~~------~~~~~~~l~~L~~~e~~~lf~~~~~~--~~~~~~~~~~~~~~~i~~~~~---G~Plai-~~~~~~--L~---  356 (427)
                      .+      .....+.+++++.++..+++...+..  .....+   .+..+.|++.|+   |.|..+ ..+-..  +.   
T Consensus       179 ~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~---~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~~~  255 (384)
T 2qby_B          179 YMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYD---DEILSYIAAISAKEHGDARKAVNLLFRAAQLASGG  255 (384)
T ss_dssp             TSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCC---SHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTTSS
T ss_pred             hhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcC---HHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhcCC
Confidence            10      11237999999999999999987631  111122   345777888888   988744 333222  22   


Q ss_pred             CCCChHHHHHHHHHHhhccccCCCChHHHHHHHhhhcCCCCCChHhHHHhhhcC
Q 042645          357 SKKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCGF  410 (427)
Q Consensus       357 ~~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~cf~~~s~  410 (427)
                      ..-+.+.+..++.....             ..+..++..|++ +.+..+..++.
T Consensus       256 ~~i~~~~v~~~~~~~~~-------------~~~~~~~~~l~~-~~~~~l~al~~  295 (384)
T 2qby_B          256 GIIRKEHVDKAIVDYEQ-------------ERLIEAVKALPF-HYKLALRSLIE  295 (384)
T ss_dssp             SCCCHHHHHHHHHHHHH-------------HHHHHHHHSSCH-HHHHHHHHHHT
T ss_pred             CccCHHHHHHHHHHHhc-------------chHHHHHHcCCH-HHHHHHHHHHH
Confidence            12356666666554321             234445556665 44544444443

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.60  E-value=4.2e-14  Score=136.00  Aligned_cols=244  Identities=15%  Similarity=0.095  Sum_probs=153.3

Q ss_pred             CCccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCC---CCCcEEEEEEeCCCCCHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTP---NDFDFVIWEVVSRDLQLGKIQE  219 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~~f~~~~wv~~~~~~~~~~l~~  219 (427)
                      |+.++||+.+++++.+++..    ...+.+.|+|++|+||||||+.+++......   +.-..++|+++....+...++.
T Consensus        18 p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~   97 (387)
T 2v1u_A           18 PDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVAS   97 (387)
T ss_dssp             CSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHH
Confidence            47899999999999998843    4567899999999999999999998762110   1123567888888888999999


Q ss_pred             HHHHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCcccc----cccc---cCCCCC--CCCcEEEEecCC
Q 042645          220 SIAKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFDL----AQVG---LPVPSR--ASASKVVFTTRE  288 (427)
Q Consensus       220 ~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~~----~~~~---~~l~~~--~~gs~IivTtR~  288 (427)
                      .++.+++...+. ...+..+....+...+.  +++.+|||||++.....    ..+.   ......  ..+..+|.||+.
T Consensus        98 ~l~~~l~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~  176 (387)
T 2v1u_A           98 AIAEAVGVRVPF-TGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNS  176 (387)
T ss_dssp             HHHHHHSCCCCS-SCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSC
T ss_pred             HHHHHhCCCCCC-CCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECC
Confidence            999999764322 34456666777777774  56899999999865321    1121   111111  345677778776


Q ss_pred             hhH--------HhhcCCCcceeccCCChHHHHHHHHHHhCC--CCCCCCCCHHHHHHHHHHHcC---CCchHHHHHH-HH
Q 042645          289 FEV--------CGLMDAHKSFKVECLGYEDAWRLFEEKVGR--DILDSHPDIPELAETVARECG---GLPLALITVG-RA  354 (427)
Q Consensus       289 ~~v--------~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~--~~~~~~~~~~~~~~~i~~~~~---G~Plai~~~~-~~  354 (427)
                      .+.        ...+ ....+.+++++.++..+++...+..  .....+++   ..+.+++.++   |.|..+..+. ..
T Consensus       177 ~~~~~~l~~~l~~r~-~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~---~~~~l~~~~~~~~G~~r~~~~~l~~a  252 (387)
T 2v1u_A          177 LGFVENLEPRVKSSL-GEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPD---VVPLCAALAAREHGDARRALDLLRVA  252 (387)
T ss_dssp             STTSSSSCHHHHTTT-TSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSS---HHHHHHHHHHSSSCCHHHHHHHHHHH
T ss_pred             CchHhhhCHHHHhcC-CCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHH---HHHHHHHHHHHhccCHHHHHHHHHHH
Confidence            532        1111 1146899999999999999987532  11122333   3677888887   9995443322 22


Q ss_pred             Hc-----C--CCChHHHHHHHHHHhhccccCCCChHHHHHHHhhhcCCCCCChHhHHHhhhc
Q 042645          355 MA-----S--KKAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYCG  409 (427)
Q Consensus       355 L~-----~--~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~cf~~~s  409 (427)
                      ..     .  .-+.+.+..++.....             ..+.-++..||+ +.+..+..+.
T Consensus       253 ~~~a~~~~~~~i~~~~v~~a~~~~~~-------------~~~~~~~~~l~~-~~~~~l~a~~  300 (387)
T 2v1u_A          253 GEIAERRREERVRREHVYSARAEIER-------------DRVSEVVRTLPL-HAKLVLLSIM  300 (387)
T ss_dssp             HHHHHHTTCSCBCHHHHHHHHHHHHH-------------HHHHHHHHSSCH-HHHHHHHHHH
T ss_pred             HHHHHHcCCCCcCHHHHHHHHHHHhh-------------chHHHHHHcCCH-HHHHHHHHHH
Confidence            11     1  1245566655544321             234445667776 4454444333

>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=99.59  E-value=1.3e-14  Score=139.51  Aligned_cols=204  Identities=12%  Similarity=0.140  Sum_probs=134.3

Q ss_pred             CCCccccchhhHHHHHHHhcc----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          146 LPPTVVGMQSTLDRVWRCLTE----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       146 ~~~~~vGR~~~~~~l~~~l~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      .+..|+||+.+++.+.+++..    +..+.+.|+|++|+|||||++.+++...........++|+++....+...++..+
T Consensus        18 ~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i   97 (386)
T 2qby_A           18 IPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADL   97 (386)
T ss_dssp             CCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHH
Confidence            347899999999999998873    4567899999999999999999998762111102356788877667788888888


Q ss_pred             HHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc------ccccccCCCC-CCCCcEEEEecCChhHH
Q 042645          222 AKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD------LAQVGLPVPS-RASASKVVFTTREFEVC  292 (427)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~------~~~~~~~l~~-~~~gs~IivTtR~~~v~  292 (427)
                      +..++..... ...+..+....+...+.  +++.+|||||++....      +..+...+.. ...+..+|+||+..+..
T Consensus        98 ~~~l~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~  176 (386)
T 2qby_A           98 LESLDVKVPF-TGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFV  176 (386)
T ss_dssp             TTTTSCCCCS-SSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGG
T ss_pred             HHHhCCCCCC-CCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChH
Confidence            8877654322 23345666666776665  4589999999976421      1122111111 23356678888866432


Q ss_pred             hhcC-------CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcC---CCchHHHHH
Q 042645          293 GLMD-------AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECG---GLPLALITV  351 (427)
Q Consensus       293 ~~~~-------~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~---G~Plai~~~  351 (427)
                      ..+.       ....+.+++++.++..+++...+.... ....-..+..+.+++.++   |.|..+..+
T Consensus       177 ~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~G~~r~~~~l  244 (386)
T 2qby_A          177 DLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAF-KPGVLPDNVIKLCAALAAREHGDARRALDL  244 (386)
T ss_dssp             GGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHB-CSSCSCHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             hhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhc-cCCCCCHHHHHHHHHHHHHhcCCHHHHHHH
Confidence            2211       114789999999999999998653111 011223456777888887   999855443

>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=99.55  E-value=7.7e-14  Score=134.30  Aligned_cols=202  Identities=14%  Similarity=0.106  Sum_probs=138.6

Q ss_pred             CCccccchhhHHHHHHHhcc----CCCe--EEEEEecCCCcHHHHHHHHHhhccCCCCC-CcEEEEEEeCCCCCHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE----EPVG--IVGLYGMGGVGKTTLLTQINNSFLHTPND-FDFVIWEVVSRDLQLGKIQE  219 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~----~~~~--vi~I~G~gGiGKTtLa~~v~~~~~~~~~~-f~~~~wv~~~~~~~~~~l~~  219 (427)
                      |+.++||+.+++++.+++..    +...  .+.|+|++|+|||||++.+++...   .. -..+++++++...+...++.
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~---~~~~~~~~~i~~~~~~~~~~~~~   92 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYK---DKTTARFVYINGFIYRNFTAIIG   92 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHT---TSCCCEEEEEETTTCCSHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHh---hhcCeeEEEEeCccCCCHHHHHH
Confidence            46799999999999998864    3334  899999999999999999998872   22 23567788777778889999


Q ss_pred             HHHHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCcc--cccccccCCCCC-C---CCcEEEEecCChhH
Q 042645          220 SIAKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELF--DLAQVGLPVPSR-A---SASKVVFTTREFEV  291 (427)
Q Consensus       220 ~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~--~~~~~~~~l~~~-~---~gs~IivTtR~~~v  291 (427)
                      .++..++...+. ...+.......+...+.  +++.+|||||++...  ....+...+... .   .+..+|++|+....
T Consensus        93 ~l~~~l~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~  171 (389)
T 1fnn_A           93 EIARSLNIPFPR-RGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAV  171 (389)
T ss_dssp             HHHHHTTCCCCS-SCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHH
T ss_pred             HHHHHhCccCCC-CCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchH
Confidence            999998754322 23455666666666664  578999999998652  222222222211 1   36678888876644


Q ss_pred             HhhcC-------CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHc---------CCCchHHHHHHH
Q 042645          292 CGLMD-------AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVAREC---------GGLPLALITVGR  353 (427)
Q Consensus       292 ~~~~~-------~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~---------~G~Plai~~~~~  353 (427)
                      ...+.       ....+.+++++.++..+++...+.... ....-..+..+.|++.+         +|.|..+..+..
T Consensus       172 ~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~  248 (389)
T 1fnn_A          172 LNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGL-AEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILY  248 (389)
T ss_dssp             HHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHB-CTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHH
T ss_pred             HHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhc-CCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHH
Confidence            32221       123689999999999999988764211 01122346688899999         798876555443

>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=99.47  E-value=3.7e-13  Score=120.50  Aligned_cols=197  Identities=15%  Similarity=0.162  Sum_probs=117.0

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++||+..++.|..++..+. .+.+.|+|++|+||||||+.+++.... ...+..      ........ ...+.....
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~-~~~~~~------~~~~~~~~-~~~~~~~~~   94 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNC-ETGITA------TPCGVCDN-CREIEQGRF   94 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHC-TTCSCS------SCCSCSHH-HHHHHTTCC
T ss_pred             HHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcC-CCCCCC------CCCcccHH-HHHHhccCC
Confidence            468999999999999997654 457999999999999999999987621 111100      00000000 001100000


Q ss_pred             CCCC--CCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCChhH-H-hhc
Q 042645          227 LYNE--SWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREFEV-C-GLM  295 (427)
Q Consensus       227 ~~~~--~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~~v-~-~~~  295 (427)
                      ....  .............+.+.+     .+++.+||+||++..  ..+..+...+.....+..+|+||+.... . ...
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~  174 (250)
T 1njg_A           95 VDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTIL  174 (250)
T ss_dssp             SSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHH
T ss_pred             cceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHH
Confidence            0000  000001111222222222     346899999999764  2344444444334456788888876432 1 112


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      .....+.+++++.++..+++...+......   -..+..+.|++.|+|+|..+..+...+
T Consensus       175 ~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~---~~~~~~~~l~~~~~G~~~~~~~~~~~~  231 (250)
T 1njg_A          175 SRCLQFHLKALDVEQIRHQLEHILNEEHIA---HEPRALQLLARAAEGSLRDALSLTDQA  231 (250)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHHHHTTCC---BCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHhhhccCCCCCHHHHHHHHHHHHHhcCCC---CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            223578999999999999999877433211   124568899999999999988776544

>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=99.44  E-value=7.5e-13  Score=116.78  Aligned_cols=186  Identities=13%  Similarity=0.082  Sum_probs=116.8

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      ..++|++..++.+.+++.....+.+.|+|++|+|||++|+.+++.... ...-...+.++.+.......+...+......
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFG-ENWRDNFIEMNASDERGIDVVRHKIKEFART   95 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHG-GGGGGGEEEEETTCTTCHHHHHHHHHHHHTS
T ss_pred             HHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhc-cccccceEEeccccccChHHHHHHHHHHhcc
Confidence            468999999999999998776666999999999999999999887521 1111123344444333333222222211111


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChhH--HhhcCCCcceec
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFEV--CGLMDAHKSFKV  303 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~v--~~~~~~~~~~~l  303 (427)
                      ..                 ...+++.+||+||++...  ....+...+.....+..+|+||+....  .........+.+
T Consensus        96 ~~-----------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~  158 (226)
T 2chg_A           96 AP-----------------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRF  158 (226)
T ss_dssp             CC-----------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             cC-----------------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeec
Confidence            00                 012578999999998652  233333333333456788888876532  111122347899


Q ss_pred             cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHH
Q 042645          304 ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRA  354 (427)
Q Consensus       304 ~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~  354 (427)
                      .+++.++..+++.+.+...+..   -..+..+.|++.++|+|..+..+...
T Consensus       159 ~~~~~~~~~~~l~~~~~~~~~~---~~~~~~~~l~~~~~g~~r~l~~~l~~  206 (226)
T 2chg_A          159 KPVPKEAMKKRLLEICEKEGVK---ITEDGLEALIYISGGDFRKAINALQG  206 (226)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCC---BCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            9999999999999876432211   12456788999999999966554433

>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=99.30  E-value=6.5e-12  Score=117.56  Aligned_cols=184  Identities=15%  Similarity=0.140  Sum_probs=114.1

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      ..++|++..++.+.+++..+..+.+.|+|++|+||||+|+.+++.... .......++++.+....... .++++..+..
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~-~~~~~~~~~~~~~~~~~~~~-i~~~~~~~~~   98 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLG-RSYADGVLELNASDDRGIDV-VRNQIKHFAQ   98 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHG-GGHHHHEEEECTTSCCSHHH-HHTHHHHHHH
T ss_pred             HHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcC-CcccCCEEEecCccccChHH-HHHHHHHHHh
Confidence            468999999999999998876666999999999999999999987521 11111233333333222221 1222221110


Q ss_pred             CCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChhH--HhhcCCCccee
Q 042645          228 YNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFEV--CGLMDAHKSFK  302 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~v--~~~~~~~~~~~  302 (427)
                      ..                ..+ .+++.++|+||++...  ....+...+.....++.+|+||+...-  .........+.
T Consensus        99 ~~----------------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~  162 (323)
T 1sxj_B           99 KK----------------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILR  162 (323)
T ss_dssp             BC----------------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEE
T ss_pred             cc----------------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEe
Confidence            00                001 3468999999998642  233343333333456788888876432  11122335789


Q ss_pred             ccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHH-HHHH
Q 042645          303 VECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLAL-ITVG  352 (427)
Q Consensus       303 l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai-~~~~  352 (427)
                      +.+++.++..+++...+...+..   -..+....|++.|+|.|..+ ..+.
T Consensus       163 ~~~~~~~~~~~~l~~~~~~~~~~---~~~~~~~~l~~~~~G~~r~a~~~l~  210 (323)
T 1sxj_B          163 YSKLSDEDVLKRLLQIIKLEDVK---YTNDGLEAIIFTAEGDMRQAINNLQ  210 (323)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTCC---BCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            99999999999999876432211   12456788999999999654 4443

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.28  E-value=4.5e-12  Score=98.82  Aligned_cols=71  Identities=13%  Similarity=0.149  Sum_probs=63.6

Q ss_pred             cchHHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hhChHHHHHHHHHHHHHHHHHH
Q 042645            9 LSCDDTISRCLDCIVSQTGYICHLKDNLDALRTEFQKLIEARNDVLIRVTVAEQRQ-MRRLQQVQGWLSRVQDVEEEVR   86 (427)
Q Consensus         9 ~~~~~~~~~l~~~l~~e~~~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~~ae~~~-~~~~~~v~~wl~~v~~~~~~~~   86 (427)
                      |+++++++||.+++.+|+.++.++++++++|+++|++|+++|.|       ++.+. ...++.++.|+++||+++||+|
T Consensus         1 a~v~~ll~KL~~ll~~E~~l~~gv~~~i~~Lk~eL~~m~a~L~d-------a~~~~~~~~d~~vk~W~~~vrdlaYD~E   72 (115)
T 3qfl_A            1 AAISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESMNAALIK-------IGEVPREQLDSQDKLWADEVRELSYVIE   72 (115)
T ss_dssp             CTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HTTSCGGGCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHH-------HHHhccccCCHHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999988       44442 2357899999999999999999

>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=99.16  E-value=4.9e-11  Score=111.73  Aligned_cols=185  Identities=15%  Similarity=0.080  Sum_probs=114.6

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      ..++|++..++.+.+++..+..+.+.|+|++|+||||+|+.+++.... ...-...+.+..+....... +...+     
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~-~~~~~~~~~~~~~~~~~~~~-~~~~~-----   97 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFG-ENWRHNFLELNASDERGINV-IREKV-----   97 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHG-GGHHHHEEEEETTCHHHHHT-THHHH-----
T ss_pred             HHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcC-CcccCceEEeeccccCchHH-HHHHH-----
Confidence            468999999999999998877667999999999999999999987521 11001223333222111110 01111     


Q ss_pred             CCCCCCCCCHHHHHHHHHH---HhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChhH--HhhcCCCcc
Q 042645          228 YNESWDNKSFDEKAQEIFK---TMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFEV--CGLMDAHKS  300 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~---~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~v--~~~~~~~~~  300 (427)
                                    ..+..   ...+++.++|+||++...  ....+...+.....++++|+||....-  .........
T Consensus        98 --------------~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~  163 (327)
T 1iqp_A           98 --------------KEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAI  163 (327)
T ss_dssp             --------------HHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEE
T ss_pred             --------------HHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcE
Confidence                          11111   112578899999998652  233333333333456788888876432  111112246


Q ss_pred             eeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHc
Q 042645          301 FKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMA  356 (427)
Q Consensus       301 ~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~  356 (427)
                      +.+.+++.++...++...+...+...   ..+..+.|++.++|.|..+..+...+.
T Consensus       164 ~~~~~l~~~~~~~~l~~~~~~~~~~~---~~~~~~~l~~~~~g~~r~~~~~l~~~~  216 (327)
T 1iqp_A          164 FRFRPLRDEDIAKRLRYIAENEGLEL---TEEGLQAILYIAEGDMRRAINILQAAA  216 (327)
T ss_dssp             EECCCCCHHHHHHHHHHHHHTTTCEE---CHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             EEecCCCHHHHHHHHHHHHHhcCCCC---CHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            89999999999999998775433211   245678899999999997665544443

>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=99.10  E-value=4.6e-10  Score=104.66  Aligned_cols=182  Identities=15%  Similarity=0.127  Sum_probs=114.6

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      ..++|++..++.+.+++..+..+.+.|+|++|+|||++|+.+++.... ...-...+.++.+.....             
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~-~~~~~~~~~~~~~~~~~~-------------   82 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFG-ENWRDNFIEMNASDERGI-------------   82 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHT-TCHHHHCEEEETTSTTCT-------------
T ss_pred             HHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcC-CcccCCeEEEeCccccCh-------------
Confidence            468999999999999998776666999999999999999999987521 110011223333321110             


Q ss_pred             CCCCCCCCCHHHHHHHHHHH--h-cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-H-HhhcCCCcc
Q 042645          228 YNESWDNKSFDEKAQEIFKT--M-RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-V-CGLMDAHKS  300 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~--L-~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~~~~~  300 (427)
                             .........+...  + .+++.++|+||++...  ....+...+.....++.+|+||.... + .........
T Consensus        83 -------~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~  155 (319)
T 2chq_A           83 -------DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAV  155 (319)
T ss_dssp             -------TTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEE
T ss_pred             -------HHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeE
Confidence                   0111111111111  1 2568899999997652  23444444444445677888876643 1 111223357


Q ss_pred             eeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          301 FKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       301 ~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      +.+.+++.++..+++...+...+..   -..+....|++.++|.+..+.....
T Consensus       156 i~~~~~~~~~~~~~l~~~~~~~~~~---i~~~~l~~l~~~~~G~~r~~~~~l~  205 (319)
T 2chq_A          156 FRFKPVPKEAMKKRLLEICEKEGVK---ITEDGLEALIYISGGDFRKAINALQ  205 (319)
T ss_dssp             EECCCCCHHHHHHHHHHHHHTTCCC---BCHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             EEecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            8999999999999999887543322   2245678899999999987655443

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.10  E-value=8.9e-10  Score=101.60  Aligned_cols=168  Identities=10%  Similarity=0.057  Sum_probs=105.7

Q ss_pred             cccchhhHHHHHHHhc----cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCC--CC--cEEEEEEeCCCCCHHHHHHHH
Q 042645          150 VVGMQSTLDRVWRCLT----EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPN--DF--DFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--~f--~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      +.||++++++|...|.    .+..+.+.|+|++|+|||++++.+++.+.....  ..  -.++++++....+...++..|
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I  101 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKI  101 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHH
Confidence            7899999999987775    357778999999999999999999998732111  11  135677777778889999999


Q ss_pred             HHHhCCCCCCCCCCCHHHHHHHHHHHh---cCCcEEEEEeccCCcccccccccCC--C-CCCCCcEEEEecCChhH----
Q 042645          222 AKKIGLYNESWDNKSFDEKAQEIFKTM---RNRKIVLLLDDIWELFDLAQVGLPV--P-SRASASKVVFTTREFEV----  291 (427)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~~~~l~~~L---~~k~~LlVlDdv~~~~~~~~~~~~l--~-~~~~gs~IivTtR~~~v----  291 (427)
                      .+++...... .... ......+...+   .+++++++||+++....-+.+...+  + .......||.++...+.    
T Consensus       102 ~~~L~g~~~~-~~~~-~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~  179 (318)
T 3te6_A          102 WFAISKENLC-GDIS-LEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQ  179 (318)
T ss_dssp             HHHHSCCC---CCCC-HHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHH
T ss_pred             HHHhcCCCCC-chHH-HHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccchhh
Confidence            9999643211 1222 23333333333   4678999999998764211121111  1 11112233334433221    


Q ss_pred             -----HhhcCCCcceeccCCChHHHHHHHHHHhC
Q 042645          292 -----CGLMDAHKSFKVECLGYEDAWRLFEEKVG  320 (427)
Q Consensus       292 -----~~~~~~~~~~~l~~L~~~e~~~lf~~~~~  320 (427)
                           ...+. ...+.+++++.+|..+++.+++.
T Consensus       180 L~~~v~SR~~-~~~i~F~pYt~~el~~Il~~Rl~  212 (318)
T 3te6_A          180 INIMPSLKAH-FTEIKLNKVDKNELQQMIITRLK  212 (318)
T ss_dssp             HHTCHHHHTT-EEEEECCCCCHHHHHHHHHHHHH
T ss_pred             cchhhhccCC-ceEEEeCCCCHHHHHHHHHHHHH
Confidence                 11111 14689999999999999998863

>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=99.03  E-value=1.8e-09  Score=103.03  Aligned_cols=195  Identities=15%  Similarity=0.155  Sum_probs=111.7

Q ss_pred             CccccchhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|++..++.+.+++..+. .+.+.|+|++|+||||+|+.+++.... ...+..       ..+........+.....
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~-~~~~~~-------~~~~~~~~~~~~~~~~~   87 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNC-ETGITA-------TPCGVCDNCREIEQGRF   87 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSC-TTCSCS-------SCCSSSHHHHHHHTSCC
T ss_pred             hhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCC-CCCCCC-------CCCcccHHHHHHhccCC
Confidence            458999999999999997754 457899999999999999999987621 111100       00000001111111000


Q ss_pred             -----CCCCC-CCCCCHHHHHHHHHHH-hcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChhH--Hhhc
Q 042645          227 -----LYNES-WDNKSFDEKAQEIFKT-MRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFEV--CGLM  295 (427)
Q Consensus       227 -----~~~~~-~~~~~~~~~~~~l~~~-L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~v--~~~~  295 (427)
                           ..... ........+...+... ..+++.+||+||++...  ....+...+.....+..+|++|....-  ....
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~  167 (373)
T 1jr3_A           88 VDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTIL  167 (373)
T ss_dssp             SSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHH
T ss_pred             CceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHH
Confidence                 00000 0111112222111110 13567899999997642  233333333333445677777765431  1222


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      .....+.+.+++.++..+++...+...+..   ...+....|++.++|.|..+..+..
T Consensus       168 sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~---~~~~a~~~l~~~~~G~~r~~~~~l~  222 (373)
T 1jr3_A          168 SRCLQFHLKALDVEQIRHQLEHILNEEHIA---HEPRALQLLARAAEGSLRDALSLTD  222 (373)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHHHHHTCC---BCHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             hheeEeeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            234578999999999999998776332211   1245578899999999998876543

>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=99.03  E-value=4.2e-09  Score=98.43  Aligned_cols=176  Identities=15%  Similarity=0.083  Sum_probs=107.1

Q ss_pred             CccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..|+|++..+..+..++..     .....+.|+|++|+|||++|+.+++..   ..   ...+++.+......++..   
T Consensus        12 ~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~---~~---~~~~~~~~~~~~~~~l~~---   82 (324)
T 1hqc_A           12 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL---GV---NLRVTSGPAIEKPGDLAA---   82 (324)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHH---TC---CEEEECTTTCCSHHHHHH---
T ss_pred             HHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHh---CC---CEEEEeccccCChHHHHH---
Confidence            5689999999988887752     344678999999999999999999876   22   223444333222222111   


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCC--------C----------CCCCcEE
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVP--------S----------RASASKV  282 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~--------~----------~~~gs~I  282 (427)
                                          .+... ..++.+|+|||++....  ...+...+.        .          ...+..+
T Consensus        83 --------------------~l~~~-~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~  141 (324)
T 1hqc_A           83 --------------------ILANS-LEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTL  141 (324)
T ss_dssp             --------------------HHTTT-CCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEE
T ss_pred             --------------------HHHHh-ccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEE
Confidence                                11110 13566888999876421  111110000        0          0123456


Q ss_pred             EEecCChh-HHhhc-C-CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHc
Q 042645          283 VFTTREFE-VCGLM-D-AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMA  356 (427)
Q Consensus       283 ivTtR~~~-v~~~~-~-~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~  356 (427)
                      |.||.... +...+ . ....+.+.+++.++..+++...+......   -..+....|++.++|+|..+..+...+.
T Consensus       142 i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~---~~~~~~~~l~~~~~G~~r~l~~~l~~~~  215 (324)
T 1hqc_A          142 IGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVR---ITEEAALEIGRRSRGTMRVAKRLFRRVR  215 (324)
T ss_dssp             EEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCC---CCHHHHHHHHHHSCSCHHHHHHHHHHHT
T ss_pred             EEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCC---CCHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            66665432 21111 1 12468999999999999998887543322   2246688999999999998877766553

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.90  E-value=1.4e-09  Score=93.25  Aligned_cols=46  Identities=24%  Similarity=0.372  Sum_probs=41.8

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++||+.+++++.+.+.....+.+.|+|++|+|||+||+.+++..
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~   67 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRI   67 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999988777789999999999999999998876

>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=98.88  E-value=5.5e-09  Score=98.85  Aligned_cols=194  Identities=11%  Similarity=0.084  Sum_probs=111.9

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCC-CCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHT-PNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|++..++.+..++..+..+.+.|+|++|+||||+|+.+++..... ...+ .+..++.+.......+ .+....+.
T Consensus        37 ~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~  114 (353)
T 1sxj_D           37 DEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKS-RILELNASDERGISIV-REKVKNFA  114 (353)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTT-SEEEECSSSCCCHHHH-TTHHHHHH
T ss_pred             HHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCccccc-ceEEEccccccchHHH-HHHHHHHh
Confidence            4689999999999999988755559999999999999999998875210 0111 2233333332232222 22222211


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-H-HhhcCCCccee
Q 042645          227 LYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-V-CGLMDAHKSFK  302 (427)
Q Consensus       227 ~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~~~~~~~  302 (427)
                      ..... .....     .....-.+++-+|++|+++....  ...+...+.......++|++|.... + .........+.
T Consensus       115 ~~~~~-~~~~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~  188 (353)
T 1sxj_D          115 RLTVS-KPSKH-----DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFR  188 (353)
T ss_dssp             HSCCC-CCCTT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEE
T ss_pred             hhccc-ccchh-----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEE
Confidence            00000 00000     00011123567999999876421  2223222322234567777775432 1 11111124688


Q ss_pred             ccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          303 VECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       303 l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      +.+++.++...++...+...+..   -..+..+.|++.++|.|..+..+.
T Consensus       189 ~~~~~~~~~~~~l~~~~~~~~~~---i~~~~l~~l~~~~~G~~r~~~~~l  235 (353)
T 1sxj_D          189 FKALDASNAIDRLRFISEQENVK---CDDGVLERILDISAGDLRRGITLL  235 (353)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCC---CCHHHHHHHHHHTSSCHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHHhCCC---CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999999999999877443322   224668899999999998755443

>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=98.88  E-value=1.1e-09  Score=97.65  Aligned_cols=173  Identities=7%  Similarity=0.025  Sum_probs=102.6

Q ss_pred             Cccccc---hhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          148 PTVVGM---QSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       148 ~~~vGR---~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..|+|.   +..++.+..++..+..+.+.|+|++|+||||||+.+++....   ....+.|++++.....      +.  
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~---~~~~~~~~~~~~~~~~------~~--   96 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANE---LERRSFYIPLGIHASI------ST--   96 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHH---TTCCEEEEEGGGGGGS------CG--
T ss_pred             hhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHH---cCCeEEEEEHHHHHHH------HH--
Confidence            456763   355666666666556778999999999999999999988731   1234556655431110      00  


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----ccccccCCCC-CCCC-cEEEEecCChh--------
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----LAQVGLPVPS-RASA-SKVVFTTREFE--------  290 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----~~~~~~~l~~-~~~g-s~IivTtR~~~--------  290 (427)
                                    .    ....+ .++.+|||||++....    ...+...+.. ...+ .++|+||+...        
T Consensus        97 --------------~----~~~~~-~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~  157 (242)
T 3bos_A           97 --------------A----LLEGL-EQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLP  157 (242)
T ss_dssp             --------------G----GGTTG-GGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCH
T ss_pred             --------------H----HHHhc-cCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhh
Confidence                          0    00011 3467999999976422    1122221110 0112 24777776422        


Q ss_pred             -HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          291 -VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       291 -v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                       +...+.....+.+++++.++..+++...+...+.   .-..+..+.|++.++|.+..+..+..
T Consensus       158 ~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~---~~~~~~~~~l~~~~~g~~r~l~~~l~  218 (242)
T 3bos_A          158 DLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGL---QLPEDVGRFLLNRMARDLRTLFDVLD  218 (242)
T ss_dssp             HHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTC---CCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             hhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHccCCHHHHHHHHH
Confidence             1111122257899999999999999987743221   12246688899999999877665543

>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=98.85  E-value=2.8e-08  Score=96.68  Aligned_cols=182  Identities=16%  Similarity=0.143  Sum_probs=106.6

Q ss_pred             ccc-cchhh--HHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          149 TVV-GMQST--LDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       149 ~~v-GR~~~--~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      .|+ |....  ...+......+. ...+.|+|++|+||||||+.+++........ ..+++++.      ..+...+...
T Consensus       106 ~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~-~~v~~v~~------~~~~~~~~~~  178 (440)
T 2z4s_A          106 NFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPD-LRVMYITS------EKFLNDLVDS  178 (440)
T ss_dssp             GCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCS-SCEEEEEH------HHHHHHHHHH
T ss_pred             hcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCC-CeEEEeeH------HHHHHHHHHH
Confidence            455 64433  333444443433 6789999999999999999999876211111 22345443      2344444444


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----ccccccCCCC-CCCCcEEEEecCChh---------
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----LAQVGLPVPS-RASASKVVFTTREFE---------  290 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----~~~~~~~l~~-~~~gs~IivTtR~~~---------  290 (427)
                      +...       .    ...+...+..++.+|+|||++....    -+.+...+.. ...|..||+||.+..         
T Consensus       179 ~~~~-------~----~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~  247 (440)
T 2z4s_A          179 MKEG-------K----LNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDR  247 (440)
T ss_dssp             HHTT-------C----HHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHH
T ss_pred             HHcc-------c----HHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHH
Confidence            4211       1    1223334444678999999976432    1222222211 134677888887632         


Q ss_pred             HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          291 VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       291 v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      +...+.....+.+++++.++..+++.+.+...+...+++   ....|++.++|.+..+..+
T Consensus       248 L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e---~l~~la~~~~gn~R~l~~~  305 (440)
T 2z4s_A          248 LVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEE---VLNFVAENVDDNLRRLRGA  305 (440)
T ss_dssp             HHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTT---HHHHHHHHCCSCHHHHHHH
T ss_pred             HHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHH---HHHHHHHhcCCCHHHHHHH
Confidence            233333445789999999999999998774322223333   3778899999998766543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.85  E-value=1.9e-08  Score=92.16  Aligned_cols=177  Identities=15%  Similarity=0.181  Sum_probs=103.1

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      ..++|.+..+++|.+.+..             ...+.+.|+|++|+|||+||+.+++..   ..   ..+.+..+.-.. 
T Consensus        17 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~---~~---~~~~v~~~~~~~-   89 (285)
T 3h4m_A           17 EDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET---NA---TFIRVVGSELVK-   89 (285)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHT---TC---EEEEEEGGGGCC-
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHh---CC---CEEEEehHHHHH-
Confidence            5689999999999888742             345679999999999999999999886   22   122233221100 


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc------------c----ccccccCCC--CC
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF------------D----LAQVGLPVP--SR  276 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~------------~----~~~~~~~l~--~~  276 (427)
                                   .   ............+.......+.+|+|||++...            .    +..+...+.  ..
T Consensus        90 -------------~---~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~  153 (285)
T 3h4m_A           90 -------------K---FIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDA  153 (285)
T ss_dssp             -------------C---STTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCS
T ss_pred             -------------h---ccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCC
Confidence                         0   011111122222233334577899999997531            0    111111111  12


Q ss_pred             CCCcEEEEecCChhHHh--hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCC-CchHHHH
Q 042645          277 ASASKVVFTTREFEVCG--LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGG-LPLALIT  350 (427)
Q Consensus       277 ~~gs~IivTtR~~~v~~--~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G-~Plai~~  350 (427)
                      ..+..||.||.......  ...   ....+.+++.+.++..+++...+.......+..    ...|++.+.| .|-.+..
T Consensus       154 ~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~----~~~l~~~~~g~~~~~i~~  229 (285)
T 3h4m_A          154 RGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVN----LEEIAKMTEGCVGAELKA  229 (285)
T ss_dssp             SSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHHCTTCCHHHHHH
T ss_pred             CCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCC----HHHHHHHcCCCCHHHHHH
Confidence            23566777776543211  111   123688999999999999998876543222223    5667778887 4545544


Q ss_pred             H
Q 042645          351 V  351 (427)
Q Consensus       351 ~  351 (427)
                      +
T Consensus       230 l  230 (285)
T 3h4m_A          230 I  230 (285)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=98.84  E-value=2e-08  Score=99.86  Aligned_cols=186  Identities=11%  Similarity=0.103  Sum_probs=107.3

Q ss_pred             CccccchhhHHHHHHHhcc-----------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      ..++|++..+++|.+++..                 +..+.+.|+|++|+||||+|+.+++..   .  + .++.++.+.
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l---~--~-~~i~in~s~  112 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL---G--Y-DILEQNASD  112 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT---T--C-EEEEECTTS
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc---C--C-CEEEEeCCC
Confidence            4689999999999999864                 134789999999999999999999886   1  1 234445444


Q ss_pred             CCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH--HhcCCcEEEEEeccCCccc-----ccccccCCCCCCCCcEEE
Q 042645          211 DLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK--TMRNRKIVLLLDDIWELFD-----LAQVGLPVPSRASASKVV  283 (427)
Q Consensus       211 ~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~--~L~~k~~LlVlDdv~~~~~-----~~~~~~~l~~~~~gs~Ii  283 (427)
                      ..... ++...+.......      +..........  ...+++.+|+||+++....     +..+...+..  .+..||
T Consensus       113 ~~~~~-~~~~~i~~~~~~~------~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~--~~~~iI  183 (516)
T 1sxj_A          113 VRSKT-LLNAGVKNALDNM------SVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLI  183 (516)
T ss_dssp             CCCHH-HHHHTGGGGTTBC------CSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEE
T ss_pred             cchHH-HHHHHHHHHhccc------cHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHh--cCCCEE
Confidence            33332 2222222111000      00000000000  1235789999999976522     1222222211  223455


Q ss_pred             EecCChh---HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH-HHHH
Q 042645          284 FTTREFE---VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA-LITV  351 (427)
Q Consensus       284 vTtR~~~---v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla-i~~~  351 (427)
                      +++.+..   +.........+.+++++.++..+++...+.......+++   ....|++.++|.+.. +..+
T Consensus       184 li~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~---~l~~la~~s~GdiR~~i~~L  252 (516)
T 1sxj_A          184 LICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPN---VIDRLIQTTRGDIRQVINLL  252 (516)
T ss_dssp             EEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTT---HHHHHHHHTTTCHHHHHHHH
T ss_pred             EEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHH---HHHHHHHHcCCcHHHHHHHH
Confidence            5554322   222223345689999999999999988764333223333   378899999995554 4444

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.80  E-value=8.2e-08  Score=93.32  Aligned_cols=177  Identities=16%  Similarity=0.158  Sum_probs=106.9

Q ss_pred             CccccchhhH---HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHH
Q 042645          148 PTVVGMQSTL---DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~---~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~  223 (427)
                      ..++|.+..+   ..|...+..+..+.+.|+|++|+||||||+.+++..   ...|     +.++.. ..... ++.++.
T Consensus        26 ~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~---~~~f-----~~l~a~~~~~~~-ir~~~~   96 (447)
T 3pvs_A           26 AQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYA---NADV-----ERISAVTSGVKE-IREAIE   96 (447)
T ss_dssp             TTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHT---TCEE-----EEEETTTCCHHH-HHHHHH
T ss_pred             HHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHh---CCCe-----EEEEeccCCHHH-HHHHHH
Confidence            4689999888   778888888777889999999999999999999886   2222     222211 11111 111111


Q ss_pred             HhCCCCCCCCCCCHHHHHHHHH-HHhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEE-ecCChhH---HhhcC
Q 042645          224 KIGLYNESWDNKSFDEKAQEIF-KTMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVF-TTREFEV---CGLMD  296 (427)
Q Consensus       224 ~l~~~~~~~~~~~~~~~~~~l~-~~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~Iiv-TtR~~~v---~~~~~  296 (427)
                                         ... ....+++.+|+||+++...  ....+...+.. + ...+|. ||.+...   .....
T Consensus        97 -------------------~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~-~-~v~lI~att~n~~~~l~~aL~s  155 (447)
T 3pvs_A           97 -------------------RARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIED-G-TITFIGATTENPSFELNSALLS  155 (447)
T ss_dssp             -------------------HHHHHHHTTCCEEEEEETTTCC------CCHHHHHT-T-SCEEEEEESSCGGGSSCHHHHT
T ss_pred             -------------------HHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc-C-ceEEEecCCCCcccccCHHHhC
Confidence                               111 1124678999999998652  23333333332 1 233333 5555321   12223


Q ss_pred             CCcceeccCCChHHHHHHHHHHhCCCCC----CCCCCHHHHHHHHHHHcCCCchHHHHHHHH
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVGRDIL----DSHPDIPELAETVARECGGLPLALITVGRA  354 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~~~~~----~~~~~~~~~~~~i~~~~~G~Plai~~~~~~  354 (427)
                      -...+.+.+++.++...++.+.+.....    ....-..+..+.|++.++|.+..+..+...
T Consensus       156 R~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~Le~  217 (447)
T 3pvs_A          156 RARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEM  217 (447)
T ss_dssp             TEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             ceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            3357889999999999999987643110    111223466888999999998876654433

>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=98.78  E-value=2.4e-08  Score=94.49  Aligned_cols=195  Identities=9%  Similarity=0.085  Sum_probs=106.4

Q ss_pred             CccccchhhHHHHHHHh-ccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC-C--CCcE--------------------E
Q 042645          148 PTVVGMQSTLDRVWRCL-TEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP-N--DFDF--------------------V  203 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l-~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~--~f~~--------------------~  203 (427)
                      ..++|.+..++.+.+++ ..+..+.+.|+|++|+||||+++.+++...... +  .++.                    .
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~~   93 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYH   93 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECSSE
T ss_pred             HHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceeeeecccce
Confidence            46899999999999998 666555599999999999999999988541111 1  0000                    0


Q ss_pred             EEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCc
Q 042645          204 IWEVVSRDL-QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASAS  280 (427)
Q Consensus       204 ~wv~~~~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs  280 (427)
                      +.+..+... ......++++..+.....      ..... .+. .+.+++-++|||++.....  ...+...+.....++
T Consensus        94 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~------~~~~~-~ls-~l~~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~  165 (354)
T 1sxj_E           94 LEITPSDMGNNDRIVIQELLKEVAQMEQ------VDFQD-SKD-GLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNI  165 (354)
T ss_dssp             EEECCC----CCHHHHHHHHHHHTTTTC--------------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTE
T ss_pred             EEecHhhcCCcchHHHHHHHHHHHHhcc------ccccc-ccc-ccCCCCeEEEEeCccccCHHHHHHHHHHHHhhcCCC
Confidence            111111000 000012222222211000      00000 000 0234677999999987421  222322222223457


Q ss_pred             EEEEecCChh-H-HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          281 KVVFTTREFE-V-CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       281 ~IivTtR~~~-v-~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      .+|++|.+.. + .........+.+.+++.++..+++...+...+...+.  .+....|++.++|.+..+..+.
T Consensus       166 ~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          166 RLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLET--KDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             EEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECC--SHHHHHHHHHHTTCHHHHHHHH
T ss_pred             EEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCc--HHHHHHHHHHcCCCHHHHHHHH
Confidence            7877776532 2 1222233678999999999999999876433211120  2457889999999998776554

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.75  E-value=1.3e-07  Score=88.94  Aligned_cols=172  Identities=14%  Similarity=0.092  Sum_probs=102.8

Q ss_pred             CccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..++|++..++.+..++..     ...+.+.|+|++|+|||+||+.+++..   ...|   +.++.+.....        
T Consensus        29 ~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~---~~~~---~~~~~~~~~~~--------   94 (338)
T 3pfi_A           29 DGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEM---SANI---KTTAAPMIEKS--------   94 (338)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHT---TCCE---EEEEGGGCCSH--------
T ss_pred             HHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHh---CCCe---EEecchhccch--------
Confidence            4689999999999888863     345678999999999999999998876   2222   22332221111        


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCC------------------CCCCCcEE
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVP------------------SRASASKV  282 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~------------------~~~~gs~I  282 (427)
                                     ......+..  ..+..+|+||+++....  ...+...+.                  ...++..+
T Consensus        95 ---------------~~~~~~~~~--~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (338)
T 3pfi_A           95 ---------------GDLAAILTN--LSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTL  157 (338)
T ss_dssp             ---------------HHHHHHHHT--CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEE
T ss_pred             ---------------hHHHHHHHh--ccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEE
Confidence                           111111111  24567899999876421  111111110                  01113456


Q ss_pred             EEecCChhH-H-hhcC-CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          283 VFTTREFEV-C-GLMD-AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       283 ivTtR~~~v-~-~~~~-~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      |.+|..... . .... ....+.+++++.++...++.+.+......   ...+..+.|++.+.|+|-.+..+..
T Consensus       158 i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~~---~~~~~~~~l~~~~~G~~r~l~~~l~  228 (338)
T 3pfi_A          158 IGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNKT---CEEKAALEIAKRSRSTPRIALRLLK  228 (338)
T ss_dssp             EEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCE---ECHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             EEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCCC---CCHHHHHHHHHHHCcCHHHHHHHHH
Confidence            666655332 1 1111 23578999999999999998876432211   1245678889999999976655443

>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=98.72  E-value=7.5e-07  Score=80.88  Aligned_cols=192  Identities=17%  Similarity=0.119  Sum_probs=104.2

Q ss_pred             CccccchhhHHHHHHH-------hc---cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHH
Q 042645          148 PTVVGMQSTLDRVWRC-------LT---EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~-------l~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l  217 (427)
                      ..++|....++++...       +.   ....+.+.|+|++|+|||+||+.+++..   ...|   +.++.+..      
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~---~~~~---~~i~~~~~------  100 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEES---NFPF---IKICSPDK------  100 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHH---TCSE---EEEECGGG------
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHh---CCCE---EEEeCHHH------
Confidence            4577887776666652       32   3456789999999999999999999876   2221   22222210      


Q ss_pred             HHHHHHHhCCCCCCCCCCCHH----HHHHHHHHHhcCCcEEEEEeccCCcc-----------c-ccccccCCCC---CCC
Q 042645          218 QESIAKKIGLYNESWDNKSFD----EKAQEIFKTMRNRKIVLLLDDIWELF-----------D-LAQVGLPVPS---RAS  278 (427)
Q Consensus       218 ~~~i~~~l~~~~~~~~~~~~~----~~~~~l~~~L~~k~~LlVlDdv~~~~-----------~-~~~~~~~l~~---~~~  278 (427)
                             +       ......    .....+......++.+|+|||++...           . ...+...+..   ...
T Consensus       101 -------~-------~g~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~  166 (272)
T 1d2n_A          101 -------M-------IGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGR  166 (272)
T ss_dssp             -------C-------TTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTC
T ss_pred             -------h-------cCCchHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCC
Confidence                   0       011111    12222233334678999999986531           0 1111111211   222


Q ss_pred             CcEEEEecCChhHHhh---cCC-CcceeccCCCh-HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC------chH
Q 042645          279 ASKVVFTTREFEVCGL---MDA-HKSFKVECLGY-EDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL------PLA  347 (427)
Q Consensus       279 gs~IivTtR~~~v~~~---~~~-~~~~~l~~L~~-~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~------Pla  347 (427)
                      ...||.||........   ... ...+.+++++. ++...++.+...     .   ..+....|++.+.|.      +-+
T Consensus       167 ~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~~~~-----~---~~~~~~~l~~~~~g~~~~g~ir~l  238 (272)
T 1d2n_A          167 KLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLGN-----F---KDKERTTIAQQVKGKKVWIGIKKL  238 (272)
T ss_dssp             EEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHHHHTC-----S---CHHHHHHHHHHHTTSEEEECHHHH
T ss_pred             CEEEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHHHHHhcCC-----C---CHHHHHHHHHHhcCCCccccHHHH
Confidence            3446667766543222   111 34678899988 777777665421     1   134578888888883      333


Q ss_pred             HHHHHHHHcCCCChHHHHHHHHHHhhc
Q 042645          348 LITVGRAMASKKAPREWAHAIEVLRSS  374 (427)
Q Consensus       348 i~~~~~~L~~~~~~~~w~~~l~~l~~~  374 (427)
                      +..+ ...........+..+++.+...
T Consensus       239 ~~~l-~~a~~~~~~~~~~~~~~~l~~~  264 (272)
T 1d2n_A          239 LMLI-EMSLQMDPEYRVRKFLALLREE  264 (272)
T ss_dssp             HHHH-HHHTTSCGGGHHHHHHHHHHHT
T ss_pred             HHHH-HHHhhhchHHHHHHHHHHHHHc
Confidence            3333 2333333445666666666553

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.69  E-value=7e-08  Score=91.81  Aligned_cols=198  Identities=13%  Similarity=0.079  Sum_probs=105.0

Q ss_pred             CCccccchhhHHH---HHHHhccCC--CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEe----CCCCCHHHH
Q 042645          147 PPTVVGMQSTLDR---VWRCLTEEP--VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVV----SRDLQLGKI  217 (427)
Q Consensus       147 ~~~~vGR~~~~~~---l~~~l~~~~--~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~----~~~~~~~~l  217 (427)
                      ...|+|++..+..   +.+.+..+.  .+.+.|+|++|+|||++|+.+++...   .... .+.+..    +........
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~---~~~~-~~~~~~~~~~~~~~~~~~~  118 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALG---PDTP-FTAIAGSEIFSLEMSKTEA  118 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHC---SSCC-EEEEEGGGGSCSSSCHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhc---ccCC-cccccchhhhhcccchhHH
Confidence            3578999988766   455555543  35899999999999999999999872   2111 122221    222334444


Q ss_pred             HHHHHHHhC-C--------------------CC-------CCCCCCCHHHHHHHHHHHh-----cCC----cEEEEEecc
Q 042645          218 QESIAKKIG-L--------------------YN-------ESWDNKSFDEKAQEIFKTM-----RNR----KIVLLLDDI  260 (427)
Q Consensus       218 ~~~i~~~l~-~--------------------~~-------~~~~~~~~~~~~~~l~~~L-----~~k----~~LlVlDdv  260 (427)
                      +........ .                    ..       ..........+...+....     .++    +.+|+||++
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi  198 (368)
T 3uk6_A          119 LTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEV  198 (368)
T ss_dssp             HHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESG
T ss_pred             HHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhc
Confidence            444433311 0                    00       0000011122222222221     133    459999999


Q ss_pred             CCcc--cccccccCCCCCCCCcEEEEecCC-------------hhH-HhhcCCCcceeccCCChHHHHHHHHHHhCCCCC
Q 042645          261 WELF--DLAQVGLPVPSRASASKVVFTTRE-------------FEV-CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDIL  324 (427)
Q Consensus       261 ~~~~--~~~~~~~~l~~~~~gs~IivTtR~-------------~~v-~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~  324 (427)
                      +...  ....+...+...... .++++|..             ..+ .....-...+.+++++.++..+++...+.....
T Consensus       199 ~~l~~~~~~~L~~~le~~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~~~~  277 (368)
T 3uk6_A          199 HMLDIESFSFLNRALESDMAP-VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDV  277 (368)
T ss_dssp             GGSBHHHHHHHHHHTTCTTCC-EEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHHHHHHTTC
T ss_pred             cccChHHHHHHHHHhhCcCCC-eeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHHHHHHcCC
Confidence            8652  122222222222222 34444431             001 111112234799999999999999987743321


Q ss_pred             CCCCCHHHHHHHHHHHcC-CCchHHHHHH
Q 042645          325 DSHPDIPELAETVARECG-GLPLALITVG  352 (427)
Q Consensus       325 ~~~~~~~~~~~~i~~~~~-G~Plai~~~~  352 (427)
                         .-..+..+.|++.+. |.|..+..+.
T Consensus       278 ---~~~~~~l~~l~~~~~~G~~r~~~~ll  303 (368)
T 3uk6_A          278 ---EMSEDAYTVLTRIGLETSLRYAIQLI  303 (368)
T ss_dssp             ---CBCHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             ---CCCHHHHHHHHHHhcCCCHHHHHHHH
Confidence               122456888999998 8887665443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.66  E-value=1.5e-06  Score=80.87  Aligned_cols=179  Identities=14%  Similarity=0.099  Sum_probs=103.7

Q ss_pred             CccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..++.|.+.+..            ...+.+.|+|++|+|||+||+.+++...  ..   ..+.++.+.-..  
T Consensus        12 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~--~~---~~~~i~~~~l~~--   84 (322)
T 1xwi_A           12 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN--NS---TFFSISSSDLVS--   84 (322)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTT--SC---EEEEEECCSSCC--
T ss_pred             HHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcC--CC---cEEEEEhHHHHh--
Confidence            4688999988888877631            1346799999999999999999998761  11   223333332110  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCC---CCCCCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPV---PSRASA  279 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l---~~~~~g  279 (427)
                                     .............+...-..++.+|+||+++....             ...+...+   .....+
T Consensus        85 ---------------~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~  149 (322)
T 1xwi_A           85 ---------------KWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDG  149 (322)
T ss_dssp             ---------------SSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTT
T ss_pred             ---------------hhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCC
Confidence                           00122222222222233346789999999976411             01111111   111234


Q ss_pred             cEEEEecCChhH-----HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc-hHHHHHHH
Q 042645          280 SKVVFTTREFEV-----CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP-LALITVGR  353 (427)
Q Consensus       280 s~IivTtR~~~v-----~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P-lai~~~~~  353 (427)
                      ..||.||.....     ..  .....+.++..+.++-.+++...+.......   .......|++.+.|.. -.|..+..
T Consensus       150 v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l---~~~~l~~la~~t~G~sgadl~~l~~  224 (322)
T 1xwi_A          150 ILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSL---TEADFRELGRKTDGYSGADISIIVR  224 (322)
T ss_dssp             EEEEEEESCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCC---CHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEEEEecCCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCC---CHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            455556644321     12  2335678899999999999998875432111   2355788999999874 44555543

>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=98.66  E-value=2.7e-07  Score=83.22  Aligned_cols=180  Identities=13%  Similarity=0.108  Sum_probs=99.3

Q ss_pred             CccccchhhHHHHHHHhc---c---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLT---E---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~---~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ..++|.+..++.|.+.+.   .         ...+.+.|+|++|+|||++|+.+++..   ...   .+.++.+.-.+. 
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~---~~~---~~~~~~~~~~~~-   78 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEA---QVP---FLAMAGAEFVEV-   78 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHH---TCC---EEEEETTTTSSS-
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHh---CCC---EEEechHHHHhh-
Confidence            468999988877766542   1         234568899999999999999999887   222   233333321110 


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc-------------c----ccccccCCCC--C
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF-------------D----LAQVGLPVPS--R  276 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~-------------~----~~~~~~~l~~--~  276 (427)
                                      ............+.......+.+|+|||++...             .    ...+...+..  .
T Consensus        79 ----------------~~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~  142 (262)
T 2qz4_A           79 ----------------IGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGT  142 (262)
T ss_dssp             ----------------STTHHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCT
T ss_pred             ----------------ccChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCC
Confidence                            011111222223333334568999999998641             0    1111111111  1


Q ss_pred             CCCcEEEEecCChhHH--hhcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch-HHHH
Q 042645          277 ASASKVVFTTREFEVC--GLMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL-ALIT  350 (427)
Q Consensus       277 ~~gs~IivTtR~~~v~--~~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl-ai~~  350 (427)
                      ..+..||.||......  ....   ....+.++..+.++-.+++...+....  ...........+++.+.|.+- .+..
T Consensus       143 ~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~--~~~~~~~~~~~l~~~~~g~~~~~l~~  220 (262)
T 2qz4_A          143 TDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLK--LTQSSTFYSQRLAELTPGFSGADIAN  220 (262)
T ss_dssp             TCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTT--CCBTHHHHHHHHHHTCTTCCHHHHHH
T ss_pred             CCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCC--CCcchhhHHHHHHHHCCCCCHHHHHH
Confidence            2345566666554321  1111   224678899999999999988764322  112222335788888988764 4544


Q ss_pred             HH
Q 042645          351 VG  352 (427)
Q Consensus       351 ~~  352 (427)
                      +.
T Consensus       221 l~  222 (262)
T 2qz4_A          221 IC  222 (262)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.66  E-value=1e-07  Score=88.38  Aligned_cols=151  Identities=13%  Similarity=0.164  Sum_probs=85.3

Q ss_pred             ccccchhhHHHHHHHhc---------------cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCC
Q 042645          149 TVVGMQSTLDRVWRCLT---------------EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ  213 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~---------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~  213 (427)
                      .++|.+..++.|.+.+.               ......+.|+|++|+|||++|+.+++.... .......-++.++..  
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~-~~~~~~~~~~~~~~~--  108 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHR-LGYVRKGHLVSVTRD--  108 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHH-TTSSSSCCEEEECGG--
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHh-cCCcCCCcEEEEcHH--
Confidence            47899988888876653               234457999999999999999988877622 111111112222211  


Q ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc-----------cccccccCCCCCCCCcEE
Q 042645          214 LGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF-----------DLAQVGLPVPSRASASKV  282 (427)
Q Consensus       214 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~-----------~~~~~~~~l~~~~~gs~I  282 (427)
                        .+        ...   ............+...   +..+|+||+++...           ....+...+.....+..|
T Consensus       109 --~l--------~~~---~~g~~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~  172 (309)
T 3syl_A          109 --DL--------VGQ---YIGHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVV  172 (309)
T ss_dssp             --GT--------CCS---STTCHHHHHHHHHHHH---TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEE
T ss_pred             --Hh--------hhh---cccccHHHHHHHHHhc---CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEE
Confidence              00        000   0111112222222222   45699999998441           122232333333445677


Q ss_pred             EEecCChhH----------HhhcCCCcceeccCCChHHHHHHHHHHhC
Q 042645          283 VFTTREFEV----------CGLMDAHKSFKVECLGYEDAWRLFEEKVG  320 (427)
Q Consensus       283 ivTtR~~~v----------~~~~~~~~~~~l~~L~~~e~~~lf~~~~~  320 (427)
                      |.||.....          ...+  ...+.+++++.++...++...+.
T Consensus       173 i~~~~~~~~~~~~~~~~~l~~R~--~~~i~~~~~~~~~~~~il~~~l~  218 (309)
T 3syl_A          173 ILAGYADRMENFFQSNPGFRSRI--AHHIEFPDYSDEELFEIAGHMLD  218 (309)
T ss_dssp             EEEECHHHHHHHHHHSTTHHHHE--EEEEEECCCCHHHHHHHHHHHHH
T ss_pred             EEeCChHHHHHHHhhCHHHHHhC--CeEEEcCCcCHHHHHHHHHHHHH
Confidence            777764322          1221  25689999999999999988764

>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=98.62  E-value=6.9e-07  Score=83.68  Aligned_cols=169  Identities=12%  Similarity=0.110  Sum_probs=102.4

Q ss_pred             chhhHHHHHHHhccCC-CeEEEEEecCCCcHHHHHHHHHhhccCCCC-------------------CCcEEEEEEeCCCC
Q 042645          153 MQSTLDRVWRCLTEEP-VGIVGLYGMGGVGKTTLLTQINNSFLHTPN-------------------DFDFVIWEVVSRDL  212 (427)
Q Consensus       153 R~~~~~~l~~~l~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------~f~~~~wv~~~~~~  212 (427)
                      .+...+.+.+.+..+. .+.+.++|++|+|||++|+.+++.......                   +++. .++....  
T Consensus         7 ~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~-~~~~~~~--   83 (334)
T 1a5t_A            7 LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDY-YTLAPEK--   83 (334)
T ss_dssp             GHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTE-EEECCCT--
T ss_pred             hHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCE-EEEeccc--
Confidence            3566777888887765 456999999999999999999987631110                   1221 1221110  


Q ss_pred             CHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEe
Q 042645          213 QLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFT  285 (427)
Q Consensus       213 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivT  285 (427)
                                        .......++.. .+.+.+     .+++-++|+|+++...  ....+...+.....++.+|++
T Consensus        84 ------------------~~~~~~i~~ir-~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~  144 (334)
T 1a5t_A           84 ------------------GKNTLGVDAVR-EVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLA  144 (334)
T ss_dssp             ------------------TCSSBCHHHHH-HHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEE
T ss_pred             ------------------cCCCCCHHHHH-HHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEE
Confidence                              00111222222 222222     2567899999998653  223333333333456777777


Q ss_pred             cCChh-H-HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          286 TREFE-V-CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       286 tR~~~-v-~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      |.+.+ + .........+.+.+++.++..+++.+...     .   ..+.+..+++.++|.|..+..+
T Consensus       145 t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~~-----~---~~~~~~~l~~~s~G~~r~a~~~  204 (334)
T 1a5t_A          145 TREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT-----M---SQDALLAALRLSAGSPGAALAL  204 (334)
T ss_dssp             ESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC-----C---CHHHHHHHHHHTTTCHHHHHHT
T ss_pred             eCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhcC-----C---CHHHHHHHHHHcCCCHHHHHHH
Confidence            76643 2 22223345789999999999999988751     1   1344678999999999876544

>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=98.59  E-value=5.6e-07  Score=83.88  Aligned_cols=176  Identities=15%  Similarity=0.140  Sum_probs=103.9

Q ss_pred             CccccchhhHHHHHHHhc----------c--CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLT----------E--EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~----------~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ..++|.+..++.|.+.+.          .  ...+.+.|+|++|+|||+||+.+++..   ...   .+.++.+      
T Consensus        18 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~---~~~---~~~v~~~------   85 (322)
T 3eie_A           18 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA---NST---FFSVSSS------   85 (322)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHH---TCE---EEEEEHH------
T ss_pred             HHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHH---CCC---EEEEchH------
Confidence            468999999999988872          1  134579999999999999999999886   222   2223221      


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH-HhcCCcEEEEEeccCCccc-------------ccccccCC---CCCCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFK-TMRNRKIVLLLDDIWELFD-------------LAQVGLPV---PSRAS  278 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l---~~~~~  278 (427)
                      ++..    ..       .. ........+.. .-..++.+|+||+++....             ...+...+   .....
T Consensus        86 ~l~~----~~-------~g-~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  153 (322)
T 3eie_A           86 DLVS----KW-------MG-ESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQ  153 (322)
T ss_dssp             HHHT----TT-------GG-GHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCC
T ss_pred             HHhh----cc-------cc-hHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCC
Confidence            1110    00       01 11222333332 3345778999999975421             11111111   12233


Q ss_pred             CcEEEEecCChhH-----HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC-chHHHHHH
Q 042645          279 ASKVVFTTREFEV-----CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL-PLALITVG  352 (427)
Q Consensus       279 gs~IivTtR~~~v-----~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~-Plai~~~~  352 (427)
                      +..||.||.....     ..  .....+.++..+.++-.+++...+......   ........|++.+.|. +-.|..+.
T Consensus       154 ~v~vi~atn~~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~---~~~~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          154 GVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCV---LTKEDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             CEEEEEEESCGGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCC---CCHHHHHHHHHTTTTCCHHHHHHHH
T ss_pred             ceEEEEecCChhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCC---CCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            4556656665322     22  223467888999999999999987643211   1234578899999884 54555444

>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=98.58  E-value=9.1e-07  Score=83.68  Aligned_cols=179  Identities=13%  Similarity=0.096  Sum_probs=103.8

Q ss_pred             CccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ..++|.+..++.|.+.+..            ...+.+.|+|++|+|||+||+.+++..   ..   ..+.++++.-... 
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~---~~---~~~~i~~~~l~~~-  156 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS---GA---TFFSISASSLTSK-  156 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT---TC---EEEEEEGGGGCCS-
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc---CC---eEEEEehHHhhcc-
Confidence            4689999999999887742            345689999999999999999999876   22   2334444321110 


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH-HhcCCcEEEEEeccCCccc-------------ccccccCCC----CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFK-TMRNRKIVLLLDDIWELFD-------------LAQVGLPVP----SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l~----~~~  277 (427)
                                      ... ........+.. .-..++.+|+||+++....             ...+...+.    ...
T Consensus       157 ----------------~~g-~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~  219 (357)
T 3d8b_A          157 ----------------WVG-EGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSE  219 (357)
T ss_dssp             ----------------STT-HHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CC
T ss_pred             ----------------ccc-hHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCC
Confidence                            000 11222222222 2235789999999964311             111211111    112


Q ss_pred             CCcEEEEecCChh-HHh-hc-CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCC-CchHHHHHHH
Q 042645          278 SASKVVFTTREFE-VCG-LM-DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGG-LPLALITVGR  353 (427)
Q Consensus       278 ~gs~IivTtR~~~-v~~-~~-~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G-~Plai~~~~~  353 (427)
                      .+..||.||.... +.. .. .....+.+...+.++..+++...+......   -..+....|++.+.| .+-.+..+..
T Consensus       220 ~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~---l~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          220 DRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCC---LSEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             CCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBC---CCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCC---ccHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            3445555665432 111 11 122467888999999999998876432211   124567889999999 5556665544

>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=98.58  E-value=2.7e-07  Score=86.73  Aligned_cols=176  Identities=15%  Similarity=0.186  Sum_probs=104.9

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCc-EEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFD-FVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~-~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.|...+..++.+.+.++|++|+||||+|+.+++... . ..+. .+..++.+.....            
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~-~-~~~~~~~~~~~~~~~~~~------------   90 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIY-G-KNYSNMVLELNASDDRGI------------   90 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHH-T-TSHHHHEEEECTTSCCSH------------
T ss_pred             HHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc-C-CCccceEEEEcCcccccH------------
Confidence            34689999999999988887666699999999999999999998862 1 1111 1222222221111            


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHh------cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-H-HhhcC
Q 042645          227 LYNESWDNKSFDEKAQEIFKTM------RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-V-CGLMD  296 (427)
Q Consensus       227 ~~~~~~~~~~~~~~~~~l~~~L------~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~  296 (427)
                                 +.....+....      .+.+-++|+|+++...  ....+...+......+.+|++|.... + .....
T Consensus        91 -----------~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~s  159 (340)
T 1sxj_C           91 -----------DVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLS  159 (340)
T ss_dssp             -----------HHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHT
T ss_pred             -----------HHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHh
Confidence                       11111121111      2346799999997542  12222222222234566777765432 1 11112


Q ss_pred             CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ....+.+.+++.++..+.+...+.......   ..+..+.|++.++|.+.-+..+
T Consensus       160 R~~~~~~~~l~~~~~~~~l~~~~~~~~~~i---~~~~~~~i~~~s~G~~r~~~~~  211 (340)
T 1sxj_C          160 QCTRFRFQPLPQEAIERRIANVLVHEKLKL---SPNAEKALIELSNGDMRRVLNV  211 (340)
T ss_dssp             TSEEEECCCCCHHHHHHHHHHHHHTTTCCB---CHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hceeEeccCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHH
Confidence            234678999999999998888763322112   2355788999999988754433

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.58  E-value=1.9e-06  Score=82.56  Aligned_cols=180  Identities=13%  Similarity=0.058  Sum_probs=101.8

Q ss_pred             CccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ..++|.+..++.|.+.+..            ...+.+.|+|++|+|||+||+.+++..   ..   ..+.++++.-..  
T Consensus       115 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~---~~---~~~~v~~~~l~~--  186 (389)
T 3vfd_A          115 DDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAES---NA---TFFNISAASLTS--  186 (389)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHT---TC---EEEEECSCCC----
T ss_pred             HHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhh---cC---cEEEeeHHHhhc--
Confidence            4689999999999988731            234689999999999999999998876   21   223333322111  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCC---CC-CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPV---PS-RAS  278 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l---~~-~~~  278 (427)
                      ..               ...........+...-...+.+|+||+++....             ...+...+   .. ...
T Consensus       187 ~~---------------~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  251 (389)
T 3vfd_A          187 KY---------------VGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDD  251 (389)
T ss_dssp             --------------------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----
T ss_pred             cc---------------cchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCC
Confidence            00               011112222222222235678999999975410             00111111   11 122


Q ss_pred             CcEEEEecCChhH-H-hhc-CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch-HHHHHHH
Q 042645          279 ASKVVFTTREFEV-C-GLM-DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL-ALITVGR  353 (427)
Q Consensus       279 gs~IivTtR~~~v-~-~~~-~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl-ai~~~~~  353 (427)
                      ...||.||..... . ... .....+.+...+.++..+++...+.....   .-..+....|++.+.|..- .+..+..
T Consensus       252 ~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~---~l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          252 RVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGS---PLTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCC---CSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            3455556654321 1 111 12245788999999999999988754331   1224567889999998655 5555543

>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=98.57  E-value=1.2e-06  Score=82.82  Aligned_cols=177  Identities=15%  Similarity=0.110  Sum_probs=102.4

Q ss_pred             CccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..++.|.+.+..            ...+-|.|+|++|+|||+||+.+++..   ...   .+.++.+      
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~---~~~---~~~v~~~------  118 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA---NST---FFSVSSS------  118 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHH---TCE---EEEEEHH------
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh---CCC---EEEeeHH------
Confidence            4689999999999887731            123468999999999999999999987   221   2223221      


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCC---CCCCCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPV---PSRASA  279 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l---~~~~~g  279 (427)
                      ++..    ..       ...........+...-..++.+|+||+++....             ...+...+   .....+
T Consensus       119 ~l~~----~~-------~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~  187 (355)
T 2qp9_X          119 DLVS----KW-------MGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQG  187 (355)
T ss_dssp             HHHS----CC----------CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CC
T ss_pred             HHhh----hh-------cchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCC
Confidence            1111    00       111222222222223346789999999985421             11111111   111234


Q ss_pred             cEEEEecCChh-----HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC-chHHHHHH
Q 042645          280 SKVVFTTREFE-----VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL-PLALITVG  352 (427)
Q Consensus       280 s~IivTtR~~~-----v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~-Plai~~~~  352 (427)
                      ..||.||....     +..  .....+.++..+.++-.+++...+.......   .......|++.+.|. +-.|..+.
T Consensus       188 v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~---~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          188 VLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVL---TKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             EEEEEEESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCC---CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             eEEEeecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCC---CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            55565665432     122  2335678899999999999998875432111   134578899999984 44455444

>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=98.55  E-value=4.9e-07  Score=84.38  Aligned_cols=181  Identities=9%  Similarity=0.023  Sum_probs=104.5

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ..++|.+..++.+.+++..+.. +++.++|++|+|||++|+.+++..   .   ..++.++.+.. .. ..+...+....
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l---~---~~~~~i~~~~~-~~-~~i~~~~~~~~   97 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV---N---ADMMFVNGSDC-KI-DFVRGPLTNFA   97 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT---T---EEEEEEETTTC-CH-HHHHTHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh---C---CCEEEEccccc-CH-HHHHHHHHHHH
Confidence            5689999999999999987643 567778889999999999999876   1   22344443331 22 22222221110


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc---cccccccCCCCCCCCcEEEEecCChhH-H-hhcCCCcce
Q 042645          227 LYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF---DLAQVGLPVPSRASASKVVFTTREFEV-C-GLMDAHKSF  301 (427)
Q Consensus       227 ~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~---~~~~~~~~l~~~~~gs~IivTtR~~~v-~-~~~~~~~~~  301 (427)
                      ...                 ...+++.+|++||++...   ....+...+.....+..+|+||....- . ........+
T Consensus        98 ~~~-----------------~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i  160 (324)
T 3u61_B           98 SAA-----------------SFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVI  160 (324)
T ss_dssp             HBC-----------------CCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEE
T ss_pred             hhc-----------------ccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEE
Confidence            000                 012477899999998754   222232222222245678887776431 0 011112468


Q ss_pred             eccCCChHHHHHHH-------HHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH
Q 042645          302 KVECLGYEDAWRLF-------EEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM  355 (427)
Q Consensus       302 ~l~~L~~~e~~~lf-------~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L  355 (427)
                      .+++++.++-.+++       ...+...+...++  .+....|++.++|.+..+......+
T Consensus       161 ~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~--~~~~~~l~~~~~gd~R~a~~~L~~~  219 (324)
T 3u61_B          161 TFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIAD--MKVVAALVKKNFPDFRKTIGELDSY  219 (324)
T ss_dssp             ECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSC--HHHHHHHHHHTCSCTTHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCc--HHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            99999988843332       2222222211211  2568889999999887655444444

>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=98.55  E-value=4.4e-07  Score=84.68  Aligned_cols=177  Identities=15%  Similarity=0.166  Sum_probs=99.4

Q ss_pred             Cccc-cchh--hHHHHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVV-GMQS--TLDRVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~v-GR~~--~~~~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..|+ |...  ....+...+..+  ....+.|+|++|+||||||+.+++.....  . ..+++++.      .++...+.
T Consensus        11 ~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~--~-~~~~~i~~------~~~~~~~~   81 (324)
T 1l8q_A           11 ENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR--G-YRVIYSSA------DDFAQAMV   81 (324)
T ss_dssp             SSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT--T-CCEEEEEH------HHHHHHHH
T ss_pred             ccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC--C-CEEEEEEH------HHHHHHHH
Confidence            3454 5433  334444444443  34679999999999999999999876221  1 22344443      33334443


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---c-cccccCCCC-CCCCcEEEEecCChh-------
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---L-AQVGLPVPS-RASASKVVFTTREFE-------  290 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---~-~~~~~~l~~-~~~gs~IivTtR~~~-------  290 (427)
                      ..+...       ...    .+...+ .++.+|+|||++....   + ..+...+.. ...+..||+||.+..       
T Consensus        82 ~~~~~~-------~~~----~~~~~~-~~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~  149 (324)
T 1l8q_A           82 EHLKKG-------TIN----EFRNMY-KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVS  149 (324)
T ss_dssp             HHHHHT-------CHH----HHHHHH-HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSC
T ss_pred             HHHHcC-------cHH----HHHHHh-cCCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhh
Confidence            333210       111    122222 2367999999976532   1 222222211 123556888776432       


Q ss_pred             --HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHH
Q 042645          291 --VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALIT  350 (427)
Q Consensus       291 --v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~  350 (427)
                        +...+.....+.+++ +.++...++...+.......   ..+....|++.+ |.+-.+..
T Consensus       150 ~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l---~~~~l~~l~~~~-g~~r~l~~  206 (324)
T 1l8q_A          150 DRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKEFNLEL---RKEVIDYLLENT-KNVREIEG  206 (324)
T ss_dssp             HHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCC---CHHHHHHHHHHC-SSHHHHHH
T ss_pred             hHhhhcccCceEEEeCC-CHHHHHHHHHHHHHhcCCCC---CHHHHHHHHHhC-CCHHHHHH
Confidence              222233335689999 99999999998874322222   245678889999 87765433

>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=98.52  E-value=2.8e-06  Score=82.69  Aligned_cols=180  Identities=14%  Similarity=0.143  Sum_probs=101.7

Q ss_pred             CccccchhhHHHHHHHhc------------cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLT------------EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..++.|.+.+.            ....+.+.|+|++|+|||+||+.+++...   .  ..  ++.++..    
T Consensus       134 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~---~--~~--~~~v~~~----  202 (444)
T 2zan_A          134 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN---N--ST--FFSISSS----  202 (444)
T ss_dssp             GGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCC---S--SE--EEEECCC----
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcC---C--CC--EEEEeHH----
Confidence            468999999999988763            12346799999999999999999998761   1  11  2333221    


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCCCC---CCCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPVPS---RASA  279 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l~~---~~~g  279 (427)
                      ++....   .+.     ......   ..+...-..++.+|+||+++....             ...+...+..   ...+
T Consensus       203 ~l~~~~---~g~-----~~~~~~---~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~  271 (444)
T 2zan_A          203 DLVSKW---LGE-----SEKLVK---NLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDG  271 (444)
T ss_dssp             -----------------CCCTHH---HHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSS
T ss_pred             HHHhhh---cch-----HHHHHH---HHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCC
Confidence            111110   110     111111   122222235789999999986411             1112122211   2344


Q ss_pred             cEEEEecCChhHH--hhc-CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC-chHHHHHH
Q 042645          280 SKVVFTTREFEVC--GLM-DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL-PLALITVG  352 (427)
Q Consensus       280 s~IivTtR~~~v~--~~~-~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~-Plai~~~~  352 (427)
                      ..||.||......  ... .....+.++..+.++-..+|...+.......   .......|++.+.|. +-.|..+.
T Consensus       272 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l---~~~~l~~la~~t~G~sgadl~~l~  345 (444)
T 2zan_A          272 ILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSL---TEADFQELGRKTDGYSGADISIIV  345 (444)
T ss_dssp             CEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEEC---CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             EEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCC---CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            5666666553221  111 2234677888899999999988875432111   134578899999994 44555444

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.48  E-value=2.9e-06  Score=78.04  Aligned_cols=177  Identities=13%  Similarity=0.098  Sum_probs=102.8

Q ss_pred             CccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ..++|.+..++.|.+.+..            ...+.+.|+|++|+||||+|+.+++..   ..   ..+.++.+.-..  
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~---~~---~~~~i~~~~l~~--   92 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATEC---SA---TFLNISAASLTS--   92 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHT---TC---EEEEEESTTTSS--
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHh---CC---CeEEeeHHHHhh--
Confidence            4689999999999887732            235689999999999999999999876   22   223333322110  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH-HhcCCcEEEEEeccCCcccc-------------cccc---cCCCCC--
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFK-TMRNRKIVLLLDDIWELFDL-------------AQVG---LPVPSR--  276 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVlDdv~~~~~~-------------~~~~---~~l~~~--  276 (427)
                                  .    ...........+.. ....++.+|+||+++....-             ..+.   ..++..  
T Consensus        93 ------------~----~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  156 (297)
T 3b9p_A           93 ------------K----YVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPD  156 (297)
T ss_dssp             ------------S----SCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC----
T ss_pred             ------------c----ccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCC
Confidence                        0    01112233333322 33457889999999754210             0011   011111  


Q ss_pred             CCCcEEEEecCChh-----HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch-HHHH
Q 042645          277 ASASKVVFTTREFE-----VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL-ALIT  350 (427)
Q Consensus       277 ~~gs~IivTtR~~~-----v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl-ai~~  350 (427)
                      ..+..||.||....     +...  ....+.++..+.++...++...+.....   +-.......|++.+.|.+- .+..
T Consensus       157 ~~~v~vi~~tn~~~~l~~~l~~R--~~~~i~~~~p~~~~r~~il~~~~~~~~~---~~~~~~~~~la~~~~g~~~~~l~~  231 (297)
T 3b9p_A          157 GDRIVVLAATNRPQELDEAALRR--FTKRVYVSLPDEQTRELLLNRLLQKQGS---PLDTEALRRLAKITDGYSGSDLTA  231 (297)
T ss_dssp             --CEEEEEEESCGGGBCHHHHHH--CCEEEECCCCCHHHHHHHHHHHHGGGSC---CSCHHHHHHHHHHTTTCCHHHHHH
T ss_pred             CCcEEEEeecCChhhCCHHHHhh--CCeEEEeCCcCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHcCCCCHHHHHH
Confidence            12345666666532     1221  2345778888888888888877643221   1123557889999999886 5545


Q ss_pred             HHH
Q 042645          351 VGR  353 (427)
Q Consensus       351 ~~~  353 (427)
                      +..
T Consensus       232 l~~  234 (297)
T 3b9p_A          232 LAK  234 (297)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.47  E-value=1.8e-07  Score=79.47  Aligned_cols=46  Identities=24%  Similarity=0.351  Sum_probs=41.8

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++||+.+++.+.+.+.....+.+.|+|++|+|||+||+.+++..
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~   67 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKI   67 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999988767788999999999999999998876

>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=98.41  E-value=5.7e-06  Score=76.22  Aligned_cols=173  Identities=16%  Similarity=0.143  Sum_probs=101.0

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .+++|.+..+++|.+++..             ...+.+.|+|++|+|||+||+.+++..   ..   ..+.++      .
T Consensus        15 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~---~~---~~i~v~------~   82 (301)
T 3cf0_A           15 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC---QA---NFISIK------G   82 (301)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHT---TC---EEEEEC------H
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHh---CC---CEEEEE------h
Confidence            4689999988888877642             345679999999999999999999876   22   122222      2


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCC--CC
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SR  276 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~  276 (427)
                      .++....   .+.        ........+.......+.+|+||+++....                ...+...+.  ..
T Consensus        83 ~~l~~~~---~g~--------~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~  151 (301)
T 3cf0_A           83 PELLTMW---FGE--------SEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST  151 (301)
T ss_dssp             HHHHHHH---HTT--------CTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCT
T ss_pred             HHHHhhh---cCc--------hHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccC
Confidence            2333222   121        112223333334446789999999974210                111111111  11


Q ss_pred             CCCcEEEEecCChhHH-h-hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          277 ASASKVVFTTREFEVC-G-LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       277 ~~gs~IivTtR~~~v~-~-~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      ..+..||.||...... . ...   -...+.++..+.++-.+++...+.......+.+    ...++..+.|.|-+
T Consensus       152 ~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~----~~~la~~~~g~sg~  223 (301)
T 3cf0_A          152 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVD----LEFLAKMTNGFSGA  223 (301)
T ss_dssp             TSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCC----HHHHHHTCSSCCHH
T ss_pred             CCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccch----HHHHHHHcCCCCHH
Confidence            2345666677654321 1 112   234678999999999999988775433222223    34566778887754

>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=98.39  E-value=2e-06  Score=79.24  Aligned_cols=147  Identities=11%  Similarity=0.086  Sum_probs=90.8

Q ss_pred             cchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC-CCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCC
Q 042645          152 GMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP-NDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       152 GR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~  229 (427)
                      |-++.++.|.+.+..++.+...++|++|+||||+|..+.+...... .+.+. ..+..+. .....+ .+++.+.+....
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~-~~l~~~~~~~~id~-ir~li~~~~~~p   78 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDD-IRTIKDFLNYSP   78 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHH-HHHHHHHHTSCC
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCE-EEEcCCcCCCCHHH-HHHHHHHHhhcc
Confidence            4456777888888877788999999999999999999987531111 23333 4444332 222222 233444433211


Q ss_pred             CCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCCh-hHHhhcCCCcceeccCC
Q 042645          230 ESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREF-EVCGLMDAHKSFKVECL  306 (427)
Q Consensus       230 ~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~-~v~~~~~~~~~~~l~~L  306 (427)
                                        ..+++-++|+|+++...  ..+.+...+......+.+|++|.+. .+...+... .+++.++
T Consensus        79 ------------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~f~~l  139 (305)
T 2gno_A           79 ------------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFRVVVN  139 (305)
T ss_dssp             ------------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEEEECC
T ss_pred             ------------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEeCCCC
Confidence                              12456799999998652  2344444443334567777776543 333333344 8999999


Q ss_pred             ChHHHHHHHHHHh
Q 042645          307 GYEDAWRLFEEKV  319 (427)
Q Consensus       307 ~~~e~~~lf~~~~  319 (427)
                      ++++..+++.+..
T Consensus       140 ~~~~i~~~L~~~~  152 (305)
T 2gno_A          140 VPKEFRDLVKEKI  152 (305)
T ss_dssp             CCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHh
Confidence            9999999998876

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.35  E-value=2.2e-05  Score=74.26  Aligned_cols=171  Identities=14%  Similarity=0.178  Sum_probs=99.7

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|-++.+++|.+.+.-             ...+-|.++|++|+|||.||+.+++..   ...   .+.++.+.-.+ 
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~---~~~---f~~v~~s~l~s-  220 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHT---DCK---FIRVSGAELVQ-  220 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHH---TCE---EEEEEGGGGSC-
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhh---CCC---ceEEEhHHhhc-
Confidence            3567888888888776531             245679999999999999999999987   222   23333322110 


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH-HhcCCcEEEEEeccCCccc----------------ccccccCCC--C
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFK-TMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--S  275 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~  275 (427)
                                      ...+.+ +..+..+.. .-...+++|++|+++....                ...+...+.  .
T Consensus       221 ----------------k~vGes-e~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~  283 (405)
T 4b4t_J          221 ----------------KYIGEG-SRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFE  283 (405)
T ss_dssp             ----------------SSTTHH-HHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTT
T ss_pred             ----------------cccchH-HHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccC
Confidence                            001111 222222322 3346799999999985411                011111111  1


Q ss_pred             CCCCcEEEEecCChhHH--hhc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          276 RASASKVVFTTREFEVC--GLM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       276 ~~~gs~IivTtR~~~v~--~~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ...+..||.||...+..  ..+   .-...+.++..+.++-.++|+.+........+-+    ...|++.+.|.--
T Consensus       284 ~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvd----l~~lA~~t~G~SG  355 (405)
T 4b4t_J          284 TSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGIN----LRKVAEKMNGCSG  355 (405)
T ss_dssp             CCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCC----HHHHHHHCCSCCH
T ss_pred             CCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCC----HHHHHHHCCCCCH
Confidence            23344556666543321  111   2346788999999999999988775443222233    5677888888654

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.35  E-value=3.3e-06  Score=82.76  Aligned_cols=149  Identities=15%  Similarity=0.160  Sum_probs=82.7

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC--CCC-c-EEEEEEeCCCCCHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP--NDF-D-FVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~~f-~-~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      ..++||+.+++.+++.+.......+.|+|++|+|||++|+.+++......  ... . .++.++++             .
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~-------------~  246 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG-------------T  246 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC-----------------
T ss_pred             CCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCC-------------c
Confidence            35899999999999999876666788999999999999999998762211  011 1 11222222             0


Q ss_pred             HhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHh-------hcC
Q 042645          224 KIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG-------LMD  296 (427)
Q Consensus       224 ~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~-------~~~  296 (427)
                      ..       .+.....+...+...-..++.+|++|  ........+...+.  ....++|.+|.......       ...
T Consensus       247 ~~-------~g~~e~~~~~~~~~~~~~~~~iLfiD--~~~~a~~~L~~~L~--~g~v~vI~at~~~e~~~~~~~~~al~~  315 (468)
T 3pxg_A          247 KY-------RGEFEDRLKKVMDEIRQAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALER  315 (468)
T ss_dssp             -------------CTTHHHHHHHHHTCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHH
T ss_pred             cc-------cchHHHHHHHHHHHHHhcCCeEEEEe--CchhHHHHHHHhhc--CCCEEEEecCCHHHHHHHhhcCHHHHH
Confidence            00       00000112222223333577899999  12222222333332  12345665555443111       111


Q ss_pred             CCcceeccCCChHHHHHHHHHHhC
Q 042645          297 AHKSFKVECLGYEDAWRLFEEKVG  320 (427)
Q Consensus       297 ~~~~~~l~~L~~~e~~~lf~~~~~  320 (427)
                      -...+.+++.+.++...++.....
T Consensus       316 Rf~~i~v~~p~~e~~~~iL~~~~~  339 (468)
T 3pxg_A          316 RFQPIQVDQPSVDESIQILQGLRD  339 (468)
T ss_dssp             SEEEEECCCCCHHHHHHHHHHTTT
T ss_pred             hCccceeCCCCHHHHHHHHHHHHH
Confidence            123589999999999999997664

>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=98.28  E-value=1.8e-05  Score=73.92  Aligned_cols=217  Identities=18%  Similarity=0.178  Sum_probs=114.5

Q ss_pred             CccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ..++|.+..++.+...+..     .....+.|+|++|+||||||+.+++..   ...|.   ..+ +...          
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l---~~~~~---~~s-g~~~----------   87 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL---QTNIH---VTS-GPVL----------   87 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH---TCCEE---EEE-TTTC----------
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHh---CCCEE---EEe-chHh----------
Confidence            4578988888777666643     234679999999999999999999887   22211   111 1110          


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCC--------C----------CCcEE
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSR--------A----------SASKV  282 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~--------~----------~gs~I  282 (427)
                                  ....++.. +...+ .++.++++|+++....  .+.+...+...        .          ....+
T Consensus        88 ------------~~~~~l~~-~~~~~-~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~l  153 (334)
T 1in4_A           88 ------------VKQGDMAA-ILTSL-ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTL  153 (334)
T ss_dssp             ------------CSHHHHHH-HHHHC-CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEE
T ss_pred             ------------cCHHHHHH-HHHHc-cCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeEE
Confidence                        01111111 11112 2345778888765321  11111000000        0          11122


Q ss_pred             E-EecCChhHHhhcC--CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHH----
Q 042645          283 V-FTTREFEVCGLMD--AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAM----  355 (427)
Q Consensus       283 i-vTtR~~~v~~~~~--~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L----  355 (427)
                      + .|++...+...+.  ....+.+++.+.++..+++.+.+.....   ....+.+..|++.+.|.|..+..+...+    
T Consensus       154 i~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~---~~~~~~~~~ia~~~~G~~R~a~~ll~~~~~~a  230 (334)
T 1in4_A          154 VGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV---EIEDAAAEMIAKRSRGTPRIAIRLTKRVRDML  230 (334)
T ss_dssp             EEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC---CBCHHHHHHHHHTSTTCHHHHHHHHHHHHHHH
T ss_pred             EEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCC---CcCHHHHHHHHHhcCCChHHHHHHHHHHHHHH
Confidence            2 3444433322211  1234789999999999999987643221   2224668999999999998665443322    


Q ss_pred             --cCC--CChHHHHHHHHHHhhccccCCCChHHHHHHHhhhcCCCCC
Q 042645          356 --ASK--KAPREWAHAIEVLRSSASKFSGMEKKALSRLKFSYDFLPS  398 (427)
Q Consensus       356 --~~~--~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~l~~sy~~L~~  398 (427)
                        ...  -+.+.-+.++..+......++..+..++..+..+|..=|.
T Consensus       231 ~~~~~~~It~~~v~~al~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~  277 (334)
T 1in4_A          231 TVVKADRINTDIVLKTMEVLNIDDEGLDEFDRKILKTIIEIYRGGPV  277 (334)
T ss_dssp             HHHTCSSBCHHHHHHHHHHHTCCTTCCCHHHHHHHHHHHHHSTTCCB
T ss_pred             HHcCCCCcCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHhCCCcc
Confidence              122  2455556666555432212222223566666666654343

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.27  E-value=2.7e-05  Score=74.68  Aligned_cols=171  Identities=15%  Similarity=0.236  Sum_probs=98.3

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|-++.+++|.+.+.-             ...+-|.++|++|+|||+||+.+++..   ...   .+.++.+.-.+ 
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~---~~~---~~~v~~s~l~s-  253 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATI---GAN---FIFSPASGIVD-  253 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH---TCE---EEEEEGGGTCC-
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHh---CCC---EEEEehhhhcc-
Confidence            3567888888888776531             245789999999999999999999987   222   23333332111 


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH-HHhcCCcEEEEEeccCCccc----------------ccccccCCC--C
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIF-KTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--S  275 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~-~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~  275 (427)
                                      ...+.+ ...+..+. ..-...+++|++|+++....                ...+...+.  .
T Consensus       254 ----------------k~~Ges-e~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~  316 (437)
T 4b4t_L          254 ----------------KYIGES-ARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFD  316 (437)
T ss_dssp             ----------------SSSSHH-HHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSS
T ss_pred             ----------------ccchHH-HHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhccc
Confidence                            001111 22222222 23346899999999985311                011111111  1


Q ss_pred             CCCCcEEEEecCChhHHh--hcCC---CcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          276 RASASKVVFTTREFEVCG--LMDA---HKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       276 ~~~gs~IivTtR~~~v~~--~~~~---~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ...+..||.||.......  .+..   ...|.++..+.++-.++|+.+..........+    ...|++.+.|.--
T Consensus       317 ~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~d----l~~lA~~t~G~sG  388 (437)
T 4b4t_L          317 NLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFD----FEAAVKMSDGFNG  388 (437)
T ss_dssp             CTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCC----HHHHHHTCCSCCH
T ss_pred             CCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccC----HHHHHHhCCCCCH
Confidence            233456677776543211  1112   24678888888888889887764433222233    4667788888654

>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=98.27  E-value=2.4e-06  Score=90.17  Aligned_cols=154  Identities=16%  Similarity=0.230  Sum_probs=84.8

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCC--CCC--CcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHT--PND--FDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~~--f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      ..++||+.++.++++.+.....+.+.|+|++|+|||++|+.+++.....  ...  -..+++++++.-..          
T Consensus       170 d~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~----------  239 (854)
T 1qvr_A          170 DPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA----------  239 (854)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC---------------
T ss_pred             cccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhc----------
Confidence            4589999999999999987666678999999999999999999876211  111  12234443321100          


Q ss_pred             HhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc-------cc---ccccCCCCCCCCcEEEEecCChhH
Q 042645          224 KIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD-------LA---QVGLPVPSRASASKVVFTTREFEV  291 (427)
Q Consensus       224 ~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~-------~~---~~~~~l~~~~~gs~IivTtR~~~v  291 (427)
                        +..    ...........+...+.  +++.+|++|+++....       ++   .+...+.  ..+..+|.+|.....
T Consensus       240 --g~~----~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~--~~~i~~I~at~~~~~  311 (854)
T 1qvr_A          240 --GAK----YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEY  311 (854)
T ss_dssp             ------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHH--TTCCCEEEEECHHHH
T ss_pred             --cCc----cchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHHh--CCCeEEEEecCchHH
Confidence              000    01122333333333332  3689999999976421       11   1111121  123445555544332


Q ss_pred             H------hhcCCCcceeccCCChHHHHHHHHHHh
Q 042645          292 C------GLMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       292 ~------~~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      .      ....-...+.+++++.++..+++....
T Consensus       312 ~~~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~  345 (854)
T 1qvr_A          312 REIEKDPALERRFQPVYVDEPTVEETISILRGLK  345 (854)
T ss_dssp             HHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             hhhccCHHHHhCCceEEeCCCCHHHHHHHHHhhh
Confidence            1      111122458899999999999997543

>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=98.26  E-value=3.2e-06  Score=76.49  Aligned_cols=172  Identities=17%  Similarity=0.151  Sum_probs=91.0

Q ss_pred             CccccchhhHHHHHHHhcc------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ..++|.+..++.+.+.+..            ...+-+.|+|++|+|||+||+.+++...   ..|-   .+..+.-.+. 
T Consensus        11 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~---~~~~---~v~~~~~~~~-   83 (268)
T 2r62_A           11 KDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAH---VPFF---SMGGSSFIEM-   83 (268)
T ss_dssp             TTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHT---CCCC---CCCSCTTTTS-
T ss_pred             HHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhC---CCEE---EechHHHHHh-
Confidence            5689999888777766531            1234488999999999999999998862   2221   1111110000 


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-----------------ccccccCCCC---
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-----------------LAQVGLPVPS---  275 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-----------------~~~~~~~l~~---  275 (427)
                              ..+.     .......   .+......++.+|+|||++....                 ...+...+..   
T Consensus        84 --------~~~~-----~~~~~~~---~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~  147 (268)
T 2r62_A           84 --------FVGL-----GASRVRD---LFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGS  147 (268)
T ss_dssp             --------CSSS-----CSSSSST---THHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSC
T ss_pred             --------hcch-----HHHHHHH---HHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCccc
Confidence                    0000     0011111   12222234678999999965311                 1222222211   


Q ss_pred             CCCCcEEEEecCChhHH--hhcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          276 RASASKVVFTTREFEVC--GLMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       276 ~~~gs~IivTtR~~~v~--~~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ......||.||......  ....   ....+.++..+.++-.+++...+..........    ...|++.+.|.|-
T Consensus       148 ~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~----~~~la~~~~g~~g  219 (268)
T 2r62_A          148 ENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVN----LQEVAKLTAGLAG  219 (268)
T ss_dssp             SCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCC----TTTTTSSSCSSCH
T ss_pred             CCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccC----HHHHHHHcCCCCH
Confidence            11224566666654321  1111   234678889999999999987764332111122    2335666777654

>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=98.25  E-value=1.5e-05  Score=78.19  Aligned_cols=177  Identities=16%  Similarity=0.181  Sum_probs=102.0

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      ..++|.+..+++|.+.+..             ...+-|.|+|++|+|||++|+.+++..   ..   ..+.++++     
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~---~~---~fv~vn~~-----  272 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET---GA---FFFLINGP-----  272 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC---SS---EEEEEEHH-----
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh---CC---CEEEEEch-----
Confidence            3579999999999887742             345579999999999999999998876   22   22333321     


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCCC--CCCCC
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPVP--SRASA  279 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l~--~~~~g  279 (427)
                       ++.    ..+       ...........+.....+++.+|+||+++....             ...+...+.  ....+
T Consensus       273 -~l~----~~~-------~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~  340 (489)
T 3hu3_A          273 -EIM----SKL-------AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAH  340 (489)
T ss_dssp             -HHH----TSC-------TTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSC
T ss_pred             -Hhh----hhh-------cchhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCc
Confidence             111    000       111122233334444457789999999953211             111111111  12234


Q ss_pred             cEEEEecCChh-HHhhc----CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC-chHHHHH
Q 042645          280 SKVVFTTREFE-VCGLM----DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL-PLALITV  351 (427)
Q Consensus       280 s~IivTtR~~~-v~~~~----~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~-Plai~~~  351 (427)
                      ..||.||.... +...+    .....+.+...+.++-.+++...+.......+..    ...+++.+.|. +-.+..+
T Consensus       341 v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~----l~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          341 VIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVD----LEQVANETHGHVGADLAAL  414 (489)
T ss_dssp             EEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCC----HHHHHHTCTTCCHHHHHHH
T ss_pred             eEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhh----HHHHHHHccCCcHHHHHHH
Confidence            45565665542 21111    1234688999999999999998875443222233    45677778775 4444444

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.23  E-value=1.4e-06  Score=70.97  Aligned_cols=45  Identities=24%  Similarity=0.273  Sum_probs=36.0

Q ss_pred             ccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|+...+.++.+.+..  ....-|.|+|++|+|||++|+.+++..
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhC
Confidence            478999999999888753  333457899999999999999998875

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.22  E-value=3.1e-05  Score=69.46  Aligned_cols=177  Identities=16%  Similarity=0.116  Sum_probs=95.5

Q ss_pred             CccccchhhHHHHHHHh---cc---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCL---TE---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l---~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..++++.+.+   ..         ...+-+.|+|++|+||||||+.+++..   ...|   +.++.+.-..  
T Consensus        12 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~---~~~~---~~i~~~~~~~--   83 (257)
T 1lv7_A           12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA---KVPF---FTISGSDFVE--   83 (257)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH---TCCE---EEECSCSSTT--
T ss_pred             HHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHc---CCCE---EEEeHHHHHH--
Confidence            46899988777776543   21         123468899999999999999999876   2222   3333221100  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCC--CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~~  277 (427)
                                     .............+.......+.++++|+++....                ...+...+.  ...
T Consensus        84 ---------------~~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  148 (257)
T 1lv7_A           84 ---------------MFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGN  148 (257)
T ss_dssp             ---------------SCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSS
T ss_pred             ---------------HhhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccC
Confidence                           00112223333334444445678999999853211                001111111  112


Q ss_pred             CCcEEEEecCChh-HHhh-cC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCC-CchHHHHH
Q 042645          278 SASKVVFTTREFE-VCGL-MD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGG-LPLALITV  351 (427)
Q Consensus       278 ~gs~IivTtR~~~-v~~~-~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G-~Plai~~~  351 (427)
                      .+..||.||.... +... ..   -...+.++..+.++-.+++..............    ...++..+.| .+--+..+
T Consensus       149 ~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~----~~~la~~~~G~~~~dl~~l  224 (257)
T 1lv7_A          149 EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDID----AAIIARGTPGFSGADLANL  224 (257)
T ss_dssp             SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCCHHHHHHH
T ss_pred             CCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCcccc----HHHHHHHcCCCCHHHHHHH
Confidence            3455666665543 2111 11   134567888888888888887764332222222    3456777888 66555433

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.20  E-value=1.4e-05  Score=83.21  Aligned_cols=151  Identities=14%  Similarity=0.128  Sum_probs=84.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCC--CCcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPN--DFDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--~f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      ..++||+.+++++...+......-+.|+|++|+|||++|+.+++.......  .....-++.++-               
T Consensus       180 d~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~---------------  244 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM---------------  244 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC-----------------
T ss_pred             CCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc---------------
Confidence            458999999999999998776667899999999999999999987622111  001111111111               


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHh-------hcCCC
Q 042645          226 GLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG-------LMDAH  298 (427)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~-------~~~~~  298 (427)
                      +...   .+.....+...+......++.+|++|.  .......+...+.  ....++|.||.......       ...-.
T Consensus       245 g~~~---~G~~e~~l~~~~~~~~~~~~~iLfiD~--~~~~~~~L~~~l~--~~~v~~I~at~~~~~~~~~~~d~al~rRf  317 (758)
T 3pxi_A          245 GTKY---RGEFEDRLKKVMDEIRQAGNIILFIDA--AIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRF  317 (758)
T ss_dssp             -----------CTTHHHHHHHHHTCCCCEEEECC----------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSE
T ss_pred             cccc---cchHHHHHHHHHHHHHhcCCEEEEEcC--chhHHHHHHHHHh--cCCEEEEeCCChHHHHHHhhccHHHHhhC
Confidence            1000   011111222333333446788999992  2122222333332  22355666665544211       00111


Q ss_pred             cceeccCCChHHHHHHHHHHhC
Q 042645          299 KSFKVECLGYEDAWRLFEEKVG  320 (427)
Q Consensus       299 ~~~~l~~L~~~e~~~lf~~~~~  320 (427)
                      ..+.+++.+.++..+++.....
T Consensus       318 ~~i~v~~p~~~~~~~il~~~~~  339 (758)
T 3pxi_A          318 QPIQVDQPSVDESIQILQGLRD  339 (758)
T ss_dssp             EEEECCCCCHHHHHHHHHHTTT
T ss_pred             cEEEeCCCCHHHHHHHHHHHHH
Confidence            4589999999999999987654

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.19  E-value=4e-05  Score=73.49  Aligned_cols=170  Identities=15%  Similarity=0.179  Sum_probs=97.8

Q ss_pred             ccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++.|-++.+++|.+.+.-             ...+-|.++|++|+|||+||+.+++..   ...   .+.++.+.-.+  
T Consensus       210 DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~---~~~---fi~vs~s~L~s--  281 (467)
T 4b4t_H          210 DVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRT---DAT---FIRVIGSELVQ--  281 (467)
T ss_dssp             SCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHH---TCE---EEEEEGGGGCC--
T ss_pred             HhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhcc---CCC---eEEEEhHHhhc--
Confidence            578888888888776521             356789999999999999999999987   222   23333222110  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCC--CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~~  277 (427)
                                     ...+.+...+...+...-...+++|++|+++....                ...+...+.  ...
T Consensus       282 ---------------k~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~  346 (467)
T 4b4t_H          282 ---------------KYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPR  346 (467)
T ss_dssp             ---------------CSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCT
T ss_pred             ---------------ccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCC
Confidence                           00111112222222233346899999999975311                001111111  122


Q ss_pred             CCcEEEEecCChhHH--hhc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          278 SASKVVFTTREFEVC--GLM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       278 ~gs~IivTtR~~~v~--~~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      .+..||.||......  ..+   .-...+.++..+.++-.++|+.+.........-+    ...|++.|.|.-
T Consensus       347 ~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvd----l~~LA~~T~GfS  415 (467)
T 4b4t_H          347 GNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIR----WELISRLCPNST  415 (467)
T ss_dssp             TTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCC----HHHHHHHCCSCC
T ss_pred             CcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCC----HHHHHHHCCCCC
Confidence            344556666543321  111   2345788888899999999988775443222223    466788888864

>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=98.18  E-value=1.1e-05  Score=74.35  Aligned_cols=46  Identities=20%  Similarity=0.235  Sum_probs=38.6

Q ss_pred             CccccchhhHHHHHHHhcc--------------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--------------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--------------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|.+..++.+...+..              .....+.|+|++|+|||++|+.+++..
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l   74 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999887754              234578899999999999999999887

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.16  E-value=3.9e-05  Score=72.82  Aligned_cols=170  Identities=19%  Similarity=0.229  Sum_probs=96.7

Q ss_pred             ccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++.|-++.+++|.+.+.-             ...+-|.++|++|+|||.||+.+++..   ...   .+.++.+.-.+  
T Consensus       183 DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~---~~~---fi~v~~s~l~s--  254 (437)
T 4b4t_I          183 DIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQT---SAT---FLRIVGSELIQ--  254 (437)
T ss_dssp             GTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHH---TCE---EEEEESGGGCC--
T ss_pred             ecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHh---CCC---EEEEEHHHhhh--
Confidence            467888888888776531             245779999999999999999999987   222   22233221100  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH-HhcCCcEEEEEeccCCccc----------------ccccccCCC--CC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFK-TMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SR  276 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~  276 (427)
                                     ..... .+..+..+.. .-...+++|++|+++....                ...+...+.  ..
T Consensus       255 ---------------k~vGe-sek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~  318 (437)
T 4b4t_I          255 ---------------KYLGD-GPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDD  318 (437)
T ss_dssp             ---------------SSSSH-HHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCC
T ss_pred             ---------------ccCch-HHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCC
Confidence                           00111 1223333333 2346799999999975311                001111111  12


Q ss_pred             CCCcEEEEecCChhHHh--hcCC---CcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          277 ASASKVVFTTREFEVCG--LMDA---HKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       277 ~~gs~IivTtR~~~v~~--~~~~---~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ..+..||.||.......  .+.+   ...+.++.-+.++-.++|+.+........+.+    ...|++.+.|.--
T Consensus       319 ~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvd----l~~LA~~T~GfSG  389 (437)
T 4b4t_I          319 RGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVN----LETLVTTKDDLSG  389 (437)
T ss_dssp             SSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCC----HHHHHHHCCSCCH
T ss_pred             CCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCC----HHHHHHhCCCCCH
Confidence            23445666665544311  1111   24578888888888899988775443222333    4667778887643

>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=98.09  E-value=4.7e-05  Score=74.15  Aligned_cols=171  Identities=15%  Similarity=0.145  Sum_probs=96.7

Q ss_pred             CccccchhhHHHHHHHhc---cC---------CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLT---EE---------PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~---~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..++++.+.+.   .+         ..+-|.|+|++|+|||+||+.+++..   ...|   +.++.+.-... 
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~---~~~f---~~is~~~~~~~-   88 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEA---NVPF---FHISGSDFVEL-   88 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHH---TCCE---EEEEGGGTTTC-
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHc---CCCe---eeCCHHHHHHH-
Confidence            468899887777765542   21         23458899999999999999999876   2222   23333221110 


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCC--CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~~  277 (427)
                                      ............+.......+.+|+||+++....                ...+...+.  ...
T Consensus        89 ----------------~~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~  152 (476)
T 2ce7_A           89 ----------------FVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSK  152 (476)
T ss_dssp             ----------------CTTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGG
T ss_pred             ----------------HhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCC
Confidence                            0011112222334444456899999999975311                111111111  112


Q ss_pred             CCcEEEEecCChhHHh--hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          278 SASKVVFTTREFEVCG--LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       278 ~gs~IivTtR~~~v~~--~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      .+..||.||.......  ...   -...+.++..+.++-.++++.++.......+.+    ...|++.+.|+.
T Consensus       153 ~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~----l~~la~~t~G~s  221 (476)
T 2ce7_A          153 EGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVN----LEIIAKRTPGFV  221 (476)
T ss_dssp             GTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCC
T ss_pred             CCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhh----HHHHHHhcCCCc
Confidence            3456666776654321  122   223678888888888888887765433222222    455788899987

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.07  E-value=3.5e-05  Score=73.81  Aligned_cols=171  Identities=16%  Similarity=0.210  Sum_probs=92.4

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|-++.+++|.+.+.-             ...+-|.++|++|+|||+||+.+++..   ...   .+.++.+.-.+ 
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~---~~~---~~~v~~~~l~~-  244 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANST---KAA---FIRVNGSEFVH-  244 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHH---TCE---EEEEEGGGTCC-
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHh---CCC---eEEEecchhhc-
Confidence            3578899888888776531             245679999999999999999999987   222   23333332110 


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCC--CC
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SR  276 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~  276 (427)
                                      ...+.+...+...+...-...+++|++|+++....                ...+...+.  ..
T Consensus       245 ----------------~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~  308 (428)
T 4b4t_K          245 ----------------KYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQ  308 (428)
T ss_dssp             ----------------SSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCS
T ss_pred             ----------------cccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCC
Confidence                            00111112222222233346799999999964210                011111111  12


Q ss_pred             CCCcEEEEecCChhH--HhhcCC---CcceeccCCC-hHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          277 ASASKVVFTTREFEV--CGLMDA---HKSFKVECLG-YEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       277 ~~gs~IivTtR~~~v--~~~~~~---~~~~~l~~L~-~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      ..+..||.||.....  .....+   ...+.++.++ .++-..+|+.+........+.+    ...|++.+.|.-
T Consensus       309 ~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~d----l~~lA~~t~G~s  379 (428)
T 4b4t_K          309 STNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEAD----LDSLIIRNDSLS  379 (428)
T ss_dssp             SCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCC----HHHHHHHTTTCC
T ss_pred             CCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccC----HHHHHHHCCCCC
Confidence            334556667765332  111122   2356776564 4555566766654332222223    466777888854

>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=98.06  E-value=2.7e-06  Score=72.00  Aligned_cols=116  Identities=16%  Similarity=0.114  Sum_probs=62.2

Q ss_pred             chhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 042645          153 MQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       153 R~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~  229 (427)
                      .+..++.+.+++..   .....+.|+|++|+|||||++.+++......+ . .++++      +..++...+........
T Consensus        19 ~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g-~-~~~~~------~~~~~~~~~~~~~~~~~   90 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKG-I-RGYFF------DTKDLIFRLKHLMDEGK   90 (180)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSC-C-CCCEE------EHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcC-C-eEEEE------EHHHHHHHHHHHhcCch
Confidence            34445555555433   34578999999999999999999987621111 1 12233      34455555544433211


Q ss_pred             CCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCC--ccccc--ccccCCCC-CCCCcEEEEecCC
Q 042645          230 ESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWE--LFDLA--QVGLPVPS-RASASKVVFTTRE  288 (427)
Q Consensus       230 ~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~--~~~~~--~~~~~l~~-~~~gs~IivTtR~  288 (427)
                           .  ......    +. ++-+|||||++.  ...|.  .+...+.. ...|..+|+||..
T Consensus        91 -----~--~~~~~~----~~-~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~  142 (180)
T 3ec2_A           91 -----D--TKFLKT----VL-NSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNY  142 (180)
T ss_dssp             -----C--SHHHHH----HH-TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCC
T ss_pred             -----H--HHHHHH----hc-CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCC
Confidence                 0  122222    22 456899999973  22332  12111111 1246678888865

>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=98.03  E-value=3.4e-05  Score=80.47  Aligned_cols=154  Identities=14%  Similarity=0.256  Sum_probs=90.1

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCC---CCcEEEE-EEeCCCCCHHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPN---DFDFVIW-EVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---~f~~~~w-v~~~~~~~~~~l~~~i~~  223 (427)
                      ..++||+.+++++++.|.......+.|+|++|+|||++|+.+++......-   .....++ +..+.      +      
T Consensus       186 d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~------l------  253 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS------L------  253 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC--------------
T ss_pred             CCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHH------H------
Confidence            458999999999999998776677899999999999999999887621110   1122222 11111      0      


Q ss_pred             HhCCCCCCCCCCCHHHHHHHHHHHhc-CCcEEEEEeccCCcc--------c---ccccccCCCCCCCCcEEEEecCChhH
Q 042645          224 KIGLYNESWDNKSFDEKAQEIFKTMR-NRKIVLLLDDIWELF--------D---LAQVGLPVPSRASASKVVFTTREFEV  291 (427)
Q Consensus       224 ~l~~~~~~~~~~~~~~~~~~l~~~L~-~k~~LlVlDdv~~~~--------~---~~~~~~~l~~~~~gs~IivTtR~~~v  291 (427)
                       +.  ... .....+.....+...+. .++.+|++||++...        .   ...+...+.  ..+..+|.+|.....
T Consensus       254 -~~--~~~-~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~--~~~~~~I~at~~~~~  327 (758)
T 1r6b_X          254 -LA--GTK-YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEF  327 (758)
T ss_dssp             --C--CCC-CSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHH
T ss_pred             -hc--ccc-ccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHh--CCCeEEEEEeCchHH
Confidence             00  000 11233334444444443 467999999998541        1   111222232  234556666654432


Q ss_pred             Hhhc-------CCCcceeccCCChHHHHHHHHHHh
Q 042645          292 CGLM-------DAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       292 ~~~~-------~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      ....       .-...+.+++.+.++..+++....
T Consensus       328 ~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          328 SNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             HCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHH
Confidence            1111       111357899999999988887654

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=98.02  E-value=2.1e-05  Score=72.63  Aligned_cols=46  Identities=28%  Similarity=0.474  Sum_probs=38.0

Q ss_pred             CccccchhhHHHHHHHhccC---------CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEE---------PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..++.+...+...         ....+.|+|++|+|||++|+.+++..
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~   71 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL   71 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHH
Confidence            35789999988888877542         23579999999999999999999876

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.99  E-value=1.6e-05  Score=76.17  Aligned_cols=170  Identities=12%  Similarity=0.155  Sum_probs=95.6

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|-++.+++|.+.+..             ...+-|.+||++|+|||.||+.+++..   ...   .+.++.+.-.+ 
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~---~~~---f~~v~~s~l~~-  253 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQT---NAT---FLKLAAPQLVQ-  253 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH---TCE---EEEEEGGGGCS-
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHh---CCC---EEEEehhhhhh-
Confidence            3578899988888776531             245789999999999999999999987   222   23333222100 


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH-HhcCCcEEEEEeccCCccc----------------ccccccCCCC--
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFK-TMRNRKIVLLLDDIWELFD----------------LAQVGLPVPS--  275 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~~--  275 (427)
                                   .   ..+. .+..+..+.. .-...+++|++|+++....                ...+...+..  
T Consensus       254 -------------~---~vGe-se~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~  316 (434)
T 4b4t_M          254 -------------M---YIGE-GAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFS  316 (434)
T ss_dssp             -------------S---CSSH-HHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSC
T ss_pred             -------------c---ccch-HHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccC
Confidence                         0   0111 1222333332 2235789999999874210                0111111111  


Q ss_pred             CCCCcEEEEecCChhHH-h-hcC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          276 RASASKVVFTTREFEVC-G-LMD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       276 ~~~gs~IivTtR~~~v~-~-~~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      ...+..||.||...... . .+.   -...+.++..+.++-.++|+.+........+-+    ...|++.+.|.-
T Consensus       317 ~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvd----l~~lA~~t~G~s  387 (434)
T 4b4t_M          317 SDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDIN----WQELARSTDEFN  387 (434)
T ss_dssp             SSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCC----HHHHHHHCSSCC
T ss_pred             CCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCC----HHHHHHhCCCCC
Confidence            12344555566554321 1 111   224678888888888888887664322222223    466788888854

>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=97.98  E-value=2.6e-05  Score=76.20  Aligned_cols=46  Identities=24%  Similarity=0.265  Sum_probs=36.3

Q ss_pred             CccccchhhHHHHHHH---hccC--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRC---LTEE--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~---l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.++.++.+...   +..+  ..+-+.++|++|+|||+||+.+++..
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l   87 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQEL   87 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHh
Confidence            5789999887765544   3333  33578999999999999999999877

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.97  E-value=1.9e-05  Score=71.26  Aligned_cols=46  Identities=15%  Similarity=0.187  Sum_probs=34.6

Q ss_pred             CccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..+.++.+.+..  .....|.|+|++|+|||++|+.+++..
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~   53 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLS   53 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTS
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhc
Confidence            4578999988888776643  233568899999999999999999876

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.88  E-value=4.2e-05  Score=70.44  Aligned_cols=46  Identities=13%  Similarity=0.234  Sum_probs=37.7

Q ss_pred             CccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|+...+.++.+.+..  .....|.|+|.+|+|||++|+.+++..
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~   49 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS   49 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHS
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhC
Confidence            3578999999998887754  344568899999999999999999865

>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=97.87  E-value=0.00038  Score=69.35  Aligned_cols=154  Identities=18%  Similarity=0.182  Sum_probs=77.7

Q ss_pred             CccccchhhHHHHHHHhc------cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLT------EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      ..++|-++....+.+.+.      ......+.|+|++|+||||||+.++...   ...|   .-++++...+...+....
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l---~~~~---~~i~~~~~~~~~~~~g~~  154 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSL---GRKF---VRISLGGVRDESEIRGHR  154 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHH---TCEE---EEECCCC-----------
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhc---CCCe---EEEEecccchhhhhhhHH
Confidence            346888877777755442      1245689999999999999999999876   2222   223333222211111111


Q ss_pred             HHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc------ccccccCCCCC---------------CCCc
Q 042645          222 AKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD------LAQVGLPVPSR---------------ASAS  280 (427)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~------~~~~~~~l~~~---------------~~gs  280 (427)
                      ....+        .........+.. .....-+++||+++....      ...+...+...               ....
T Consensus       155 ~~~ig--------~~~~~~~~~~~~-a~~~~~vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v  225 (543)
T 3m6a_A          155 RTYVG--------AMPGRIIQGMKK-AGKLNPVFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKV  225 (543)
T ss_dssp             -----------------CHHHHHHT-TCSSSEEEEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSC
T ss_pred             HHHhc--------cCchHHHHHHHH-hhccCCEEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccce
Confidence            11111        011111112222 222334889999986421      12222222110               0234


Q ss_pred             EEEEecCChh-----HHhhcCCCcceeccCCChHHHHHHHHHHh
Q 042645          281 KVVFTTREFE-----VCGLMDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       281 ~IivTtR~~~-----v~~~~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      .||.||....     +...+   ..+.+++++.++-..++...+
T Consensus       226 ~iI~ttN~~~~l~~aL~~R~---~vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          226 LFIATANNLATIPGPLRDRM---EIINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             EEEEECSSTTTSCHHHHHHE---EEEECCCCCHHHHHHHHHHTH
T ss_pred             EEEeccCccccCCHHHHhhc---ceeeeCCCCHHHHHHHHHHHH
Confidence            5666665432     22333   468899999999988887764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.86  E-value=3.2e-05  Score=66.56  Aligned_cols=112  Identities=23%  Similarity=0.183  Sum_probs=59.8

Q ss_pred             hHHHHHHHhccC----CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC
Q 042645          156 TLDRVWRCLTEE----PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES  231 (427)
Q Consensus       156 ~~~~l~~~l~~~----~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~  231 (427)
                      .++.+.+++...    ....+.|+|++|+|||+||+.+++...   .....+++++++      .+...+.....     
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~---~~~~~~~~~~~~------~~~~~~~~~~~-----  102 (202)
T 2w58_A           37 AIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELA---KRNVSSLIVYVP------ELFRELKHSLQ-----  102 (202)
T ss_dssp             HHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHH---TTTCCEEEEEHH------HHHHHHHHC-------
T ss_pred             HHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHH---HcCCeEEEEEhH------HHHHHHHHHhc-----
Confidence            444555555433    126899999999999999999998873   222345555432      34444433221     


Q ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc--ccccc--ccc-CCCCC-CCCcEEEEecCC
Q 042645          232 WDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL--FDLAQ--VGL-PVPSR-ASASKVVFTTRE  288 (427)
Q Consensus       232 ~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~--~~~~~--~~~-~l~~~-~~gs~IivTtR~  288 (427)
                        ..........+.    . .-+|||||++..  ..|..  +.. .+... ..+..+|+||..
T Consensus       103 --~~~~~~~~~~~~----~-~~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~  158 (202)
T 2w58_A          103 --DQTMNEKLDYIK----K-VPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNF  158 (202)
T ss_dssp             ---CCCHHHHHHHH----H-SSEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESS
T ss_pred             --cchHHHHHHHhc----C-CCEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Confidence              111223333222    2 239999999653  33322  211 11111 234568888875

>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=97.81  E-value=5.2e-05  Score=78.18  Aligned_cols=172  Identities=15%  Similarity=0.143  Sum_probs=97.3

Q ss_pred             ccccchhhHHHHHHHhc----c---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLT----E---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++.|-++.+++|.+.+.    .         ...+-|.++|++|+|||+||+.+++..   ..+   .+.++.+      
T Consensus       205 dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~el---g~~---~~~v~~~------  272 (806)
T 3cf2_A          205 DIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET---GAF---FFLINGP------  272 (806)
T ss_dssp             GCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTT---TCE---EEEEEHH------
T ss_pred             hhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHh---CCe---EEEEEhH------
Confidence            46788888777776652    1         235679999999999999999999887   222   2333321      


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-------------ccccccCCC--CCCCCc
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-------------LAQVGLPVP--SRASAS  280 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-------------~~~~~~~l~--~~~~gs  280 (427)
                      ++.       +.    ........+...+....+..+++|+||+++....             ...+...+.  ....+.
T Consensus       273 ~l~-------sk----~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V  341 (806)
T 3cf2_A          273 EIM-------SK----LAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  341 (806)
T ss_dssp             HHH-------SS----CTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCE
T ss_pred             Hhh-------cc----cchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCE
Confidence            111       10    0111222233333344456899999999975411             011111111  112233


Q ss_pred             EEEEecCChh-HHhhc----CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          281 KVVFTTREFE-VCGLM----DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       281 ~IivTtR~~~-v~~~~----~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      .||.||...+ +-..+    .-...+.++..+.++-.++|+.+........+.+    ...|++++.|.--+
T Consensus       342 ~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvd----l~~lA~~T~Gfsga  409 (806)
T 3cf2_A          342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVD----LEQVANETHGHVGA  409 (806)
T ss_dssp             EEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCC----HHHHHHHCCSCCHH
T ss_pred             EEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccC----HHHHHHhcCCCCHH
Confidence            4455555432 21111    1235688898999999999987765433223333    56678888887543

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.76  E-value=5.8e-05  Score=69.10  Aligned_cols=25  Identities=24%  Similarity=0.355  Sum_probs=22.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+.++|++|+|||+||+.+++..
T Consensus        36 p~~lLl~GppGtGKT~la~aiA~~l   60 (293)
T 3t15_A           36 PLILGIWGGKGQGKSFQCELVFRKM   60 (293)
T ss_dssp             CSEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578899999999999999999987

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.76  E-value=1.6e-05  Score=64.93  Aligned_cols=33  Identities=21%  Similarity=0.249  Sum_probs=26.1

Q ss_pred             HHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          161 WRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       161 ~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..+..-....+.|+|+.|+|||||++.+++..
T Consensus        28 ~~~l~~~~g~~~~l~G~~G~GKTtL~~~i~~~~   60 (149)
T 2kjq_A           28 VYVLRHKHGQFIYVWGEEGAGKSHLLQAWVAQA   60 (149)
T ss_dssp             HHHCCCCCCSEEEEESSSTTTTCHHHHHHHHHH
T ss_pred             HHHHHhcCCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            333333245689999999999999999999877

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.73  E-value=1.7e-05  Score=82.68  Aligned_cols=148  Identities=18%  Similarity=0.194  Sum_probs=81.1

Q ss_pred             CccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQ  218 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~  218 (427)
                      ..++|.+..++.+.+.+..       +  ....+.++|++|+|||++|+.+++...   ..-...+.++++.-....   
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~---~~~~~~i~i~~s~~~~~~---  564 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIF---GDEESMIRIDMSEYMEKH---  564 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHH---SCTTCEEEEEGGGGCSSC---
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc---CCCcceEEEechhccccc---
Confidence            4579999999888887753       1  223699999999999999999998862   222234455544321100   


Q ss_pred             HHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCC-----CC------CCCCcEEEEe
Q 042645          219 ESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPV-----PS------RASASKVVFT  285 (427)
Q Consensus       219 ~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l-----~~------~~~gs~IivT  285 (427)
                                     ......+...+.   +....+|+||+++....  ...+...+     ..      ......||+|
T Consensus       565 ---------------~~~~~~l~~~~~---~~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~t  626 (758)
T 3pxi_A          565 ---------------STSGGQLTEKVR---RKPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMT  626 (758)
T ss_dssp             ---------------CCC---CHHHHH---HCSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEE
T ss_pred             ---------------ccccchhhHHHH---hCCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEe
Confidence                           000011111111   12345999999975421  11111111     11      1234678888


Q ss_pred             cCCh-----hH----Hh-----hcC-CCcceeccCCChHHHHHHHHHHh
Q 042645          286 TREF-----EV----CG-----LMD-AHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       286 tR~~-----~v----~~-----~~~-~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      |...     .+    ..     ... -...+.+.+++.++...++...+
T Consensus       627 tn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l  675 (758)
T 3pxi_A          627 SNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMS  675 (758)
T ss_dssp             ESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHHH
T ss_pred             CCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHH
Confidence            8731     11    01     111 12478899999999888887654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.59  E-value=0.0021  Score=63.00  Aligned_cols=167  Identities=16%  Similarity=0.133  Sum_probs=91.0

Q ss_pred             CccccchhhHHHHHHHh---ccC---------CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCL---TEE---------PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l---~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..+.++.+..   ...         -.+-+.|+|++|+||||||+.+++..   ..   ..+.++.+.-..  
T Consensus        31 ~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~---~~---~~i~i~g~~~~~--  102 (499)
T 2dhr_A           31 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA---RV---PFITASGSDFVE--  102 (499)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHT---TC---CEEEEEGGGGTS--
T ss_pred             HHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHh---CC---CEEEEehhHHHH--
Confidence            56899988776665543   221         12348999999999999999999876   21   223333321100  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc----CCcEEEEEeccCCccc----------------ccccccCCCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR----NRKIVLLLDDIWELFD----------------LAQVGLPVPS  275 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~----~k~~LlVlDdv~~~~~----------------~~~~~~~l~~  275 (427)
                                         .........+...++    ..+.++++|+++....                ...+...+..
T Consensus       103 -------------------~~~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg  163 (499)
T 2dhr_A          103 -------------------MFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDG  163 (499)
T ss_dssp             -------------------SCTTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGG
T ss_pred             -------------------hhhhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcc
Confidence                               000111222333333    2458999999964311                0111111211


Q ss_pred             C--CCCcEEEEecCChhHHh--hc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          276 R--ASASKVVFTTREFEVCG--LM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       276 ~--~~gs~IivTtR~~~v~~--~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                      .  ..+..++.||.......  ..   .....+.++..+.++-.++++.++.......+..    ...|+..+.|+.
T Consensus       164 ~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~----l~~lA~~t~G~~  236 (499)
T 2dhr_A          164 FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVD----LALLAKRTPGFV  236 (499)
T ss_dssp             CCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSST----THHHHTTSCSCC
T ss_pred             cccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHH----HHHHHHhcCCCC
Confidence            1  22334555555544321  11   1234678888899888888887664322111112    456777888876

>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=97.55  E-value=0.0014  Score=58.34  Aligned_cols=170  Identities=16%  Similarity=0.161  Sum_probs=87.5

Q ss_pred             CccccchhhHHHHHHHhc---c---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLT---E---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~---~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..+.++.+...   .         .-.+-+.|+|++|+|||||++.+++.. .  .   ..+.++.      .
T Consensus        16 ~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~-~--~---~~i~~~~------~   83 (254)
T 1ixz_A           16 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA-R--V---PFITASG------S   83 (254)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT-T--C---CEEEEEH------H
T ss_pred             HHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHh-C--C---CEEEeeH------H
Confidence            467888876666654432   1         112238999999999999999999876 2  1   1222221      1


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCccc----------------ccccccCCCCCC-
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFD----------------LAQVGLPVPSRA-  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~----------------~~~~~~~l~~~~-  277 (427)
                      .+.    .. .      .. ........+.+.. ...+.++++||++....                ...+...+..+. 
T Consensus        84 ~~~----~~-~------~~-~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~  151 (254)
T 1ixz_A           84 DFV----EM-F------VG-VGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK  151 (254)
T ss_dssp             HHH----HS-C------TT-HHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCT
T ss_pred             HHH----HH-H------hh-HHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCC
Confidence            111    10 0      00 0111222233332 24578999999953210                011111121111 


Q ss_pred             -CCcEEEEecCChhHHh--hc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          278 -SASKVVFTTREFEVCG--LM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       278 -~gs~IivTtR~~~v~~--~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                       ...-++.||.......  ..   .....+.++..+.++-.++++..........+..    ...|++.+.|.-
T Consensus       152 ~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~----~~~la~~~~G~~  221 (254)
T 1ixz_A          152 DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVD----LALLAKRTPGFV  221 (254)
T ss_dssp             TCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCC
T ss_pred             CCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccC----HHHHHHHcCCCC
Confidence             1233444555544321  11   1234678888898888888887664322122222    345777777754

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.54  E-value=0.0032  Score=56.90  Aligned_cols=170  Identities=15%  Similarity=0.139  Sum_probs=88.4

Q ss_pred             CccccchhhHHHHHHHhc---c---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCLT---E---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~---~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.+..+.++.+...   .         .-.+-+.|+|++|+|||||++.++... .  .   ..+.+...      
T Consensus        40 ~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~-~--~---~~i~~~~~------  107 (278)
T 1iy2_A           40 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA-R--V---PFITASGS------  107 (278)
T ss_dssp             GGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHT-T--C---CEEEEEHH------
T ss_pred             HHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHc-C--C---CEEEecHH------
Confidence            568898877666655432   1         112238999999999999999999876 2  1   22333211      


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH-hcCCcEEEEEeccCCcc------------cc----cccccCCCCCCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKT-MRNRKIVLLLDDIWELF------------DL----AQVGLPVPSRAS  278 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~-L~~k~~LlVlDdv~~~~------------~~----~~~~~~l~~~~~  278 (427)
                      .+.    ...       .. ........+.+. -...+.++++||++...            .+    ..+...+..+..
T Consensus       108 ~~~----~~~-------~~-~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~  175 (278)
T 1iy2_A          108 DFV----EMF-------VG-VGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK  175 (278)
T ss_dssp             HHH----HST-------TT-HHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCT
T ss_pred             HHH----HHH-------hh-HHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCC
Confidence            111    100       00 011112222222 23467899999995321            00    111111221111


Q ss_pred             --CcEEEEecCChhHH-----hhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCc
Q 042645          279 --ASKVVFTTREFEVC-----GLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLP  345 (427)
Q Consensus       279 --gs~IivTtR~~~v~-----~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  345 (427)
                        ...++.||......     ........+.++..+.++-.+++...+.......+..    ...++..+.|+.
T Consensus       176 ~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~----~~~la~~~~G~~  245 (278)
T 1iy2_A          176 DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVD----LALLAKRTPGFV  245 (278)
T ss_dssp             TCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCC
T ss_pred             CCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccC----HHHHHHHcCCCC
Confidence              22344455544331     1112335688899999988888887764322122222    445777787765

>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=97.48  E-value=0.00043  Score=60.09  Aligned_cols=89  Identities=21%  Similarity=0.191  Sum_probs=54.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC----------CCCCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN----------ESWDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~----------~~~~~~~~  237 (427)
                      ...++.|+|++|+|||||+..++. . .    -..++|++.....+...+.. +...++...          ........
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~-~-~----~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL-L-S----GKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQ   91 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH-H-H----CSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-H-c----CCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHH
Confidence            456899999999999999999987 2 1    23678887766555554443 333322210          00011112


Q ss_pred             HHHHHHHHHHhcCCcEEEEEeccCCc
Q 042645          238 DEKAQEIFKTMRNRKIVLLLDDIWEL  263 (427)
Q Consensus       238 ~~~~~~l~~~L~~k~~LlVlDdv~~~  263 (427)
                      ......+...+..++-+||+|.+...
T Consensus        92 ~~~~~~~~~l~~~~~~lliiD~~~~~  117 (220)
T 2cvh_A           92 RRVIGSLKKTVDSNFALVVVDSITAH  117 (220)
T ss_dssp             HHHHHHHHHHCCTTEEEEEEECCCCC
T ss_pred             HHHHHHHHHHhhcCCCEEEEcCcHHH
Confidence            33455555555445789999998643

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=97.46  E-value=0.0027  Score=57.24  Aligned_cols=149  Identities=13%  Similarity=0.103  Sum_probs=79.8

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|-++.+++|.+.+..             .-.+-+.|+|++|+|||||++.++... .  .   ..+.+....-.+.
T Consensus        10 ~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~-~--~---~~i~i~g~~l~~~   83 (274)
T 2x8a_A           10 ADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANES-G--L---NFISVKGPELLNM   83 (274)
T ss_dssp             --CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHT-T--C---EEEEEETTTTCSS
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHc-C--C---CEEEEEcHHHHhh
Confidence            4567888877777765421             112239999999999999999999876 1  1   2334432211100


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh-cCCcEEEEEeccCCcccc-------------cccccCCCCC--CC
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM-RNRKIVLLLDDIWELFDL-------------AQVGLPVPSR--AS  278 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVlDdv~~~~~~-------------~~~~~~l~~~--~~  278 (427)
                                        ........+..+.+.. ...+.++++|+++.....             ..+...+..+  ..
T Consensus        84 ------------------~~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~  145 (274)
T 2x8a_A           84 ------------------YVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQ  145 (274)
T ss_dssp             ------------------TTHHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCSTT
T ss_pred             ------------------hhhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccC
Confidence                              0000111222222222 346889999999753110             0000111111  12


Q ss_pred             CcEEEEecCChhHHh--hc---CCCcceeccCCChHHHHHHHHHHhC
Q 042645          279 ASKVVFTTREFEVCG--LM---DAHKSFKVECLGYEDAWRLFEEKVG  320 (427)
Q Consensus       279 gs~IivTtR~~~v~~--~~---~~~~~~~l~~L~~~e~~~lf~~~~~  320 (427)
                      ..-++.+|....+..  ..   .-...+.++..+.++-.++|+....
T Consensus       146 ~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~  192 (274)
T 2x8a_A          146 QVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITK  192 (274)
T ss_dssp             CEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTT
T ss_pred             CEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHh
Confidence            334555666554421  11   2345678899999999999987763

>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=97.43  E-value=8.5e-05  Score=67.89  Aligned_cols=71  Identities=23%  Similarity=0.375  Sum_probs=46.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEe--CCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVV--SRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~--~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~  245 (427)
                      ..+++.|+|++|+|||+||.+++... .     ..++|++.  .+..+             .     ...+.+.....+.
T Consensus       122 ~gsviLI~GpPGsGKTtLAlqlA~~~-G-----~~VlyIs~~~eE~v~-------------~-----~~~~le~~l~~i~  177 (331)
T 2vhj_A          122 ASGMVIVTGKGNSGKTPLVHALGEAL-G-----GKDKYATVRFGEPLS-------------G-----YNTDFNVFVDDIA  177 (331)
T ss_dssp             ESEEEEEECSCSSSHHHHHHHHHHHH-H-----TTSCCEEEEBSCSST-------------T-----CBCCHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhC-C-----CCEEEEEecchhhhh-------------h-----hhcCHHHHHHHHH
Confidence            34678899999999999999998752 1     12345555  22211             0     0134566666677


Q ss_pred             HHhcCCcEEEEEeccCCc
Q 042645          246 KTMRNRKIVLLLDDIWEL  263 (427)
Q Consensus       246 ~~L~~k~~LlVlDdv~~~  263 (427)
                      +.+...+ +||+|++...
T Consensus       178 ~~l~~~~-LLVIDsI~aL  194 (331)
T 2vhj_A          178 RAMLQHR-VIVIDSLKNV  194 (331)
T ss_dssp             HHHHHCS-EEEEECCTTT
T ss_pred             HHHhhCC-EEEEeccccc
Confidence            7776666 9999998654

>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=97.36  E-value=0.0006  Score=63.72  Aligned_cols=88  Identities=18%  Similarity=0.148  Sum_probs=59.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ...++.|+|++|+|||||+.+++.....   .-..++|++....++..     .++.++......   ...+.++....+
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~~~---~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~  131 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEAQK---MGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIV  131 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHHHH---TTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHH
Confidence            4579999999999999999999887621   22356788776666543     556666543211   234556666666


Q ss_pred             HHHhc-CCcEEEEEeccCCc
Q 042645          245 FKTMR-NRKIVLLLDDIWEL  263 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~~  263 (427)
                      ...++ .+.-++|+|.+...
T Consensus       132 ~~l~~~~~~dlvVIDSi~~l  151 (356)
T 3hr8_A          132 DELVRSGVVDLIVVDSVAAL  151 (356)
T ss_dssp             HHHHHTSCCSEEEEECTTTC
T ss_pred             HHHhhhcCCCeEEehHhhhh
Confidence            66554 45669999997543

>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=97.32  E-value=0.0011  Score=58.52  Aligned_cols=95  Identities=15%  Similarity=0.161  Sum_probs=56.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCC---CCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC----C---CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTP---NDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE----S---WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~----~---~~~~~~  237 (427)
                      ...++.|+|++|+|||||+..++.......   ..-..++|++....+....+. .++..++....    .   ....+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~  101 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNT  101 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCH
Confidence            456899999999999999999987531110   123578888876655544433 34455544310    0   012223


Q ss_pred             HHH---HHHHHHHhc-CCcEEEEEeccCCc
Q 042645          238 DEK---AQEIFKTMR-NRKIVLLLDDIWEL  263 (427)
Q Consensus       238 ~~~---~~~l~~~L~-~k~~LlVlDdv~~~  263 (427)
                      .+.   ...+.+.+. .+.-+||+|++...
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~lliiD~~~~~  131 (243)
T 1n0w_A          102 DHQTQLLYQASAMMVESRYALLIVDSATAL  131 (243)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSSGG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEeCchHH
Confidence            332   333444443 47789999998643

>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=97.29  E-value=0.00035  Score=73.64  Aligned_cols=45  Identities=29%  Similarity=0.489  Sum_probs=36.9

Q ss_pred             ccccchhhHHHHHHHhccC---------CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLTEE---------PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.+..++.+...+...         ....+.|+|++|+|||++|+.+++..
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~  612 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL  612 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            4789999888887777431         22579999999999999999999876

>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=97.26  E-value=0.0013  Score=61.56  Aligned_cols=164  Identities=10%  Similarity=-0.081  Sum_probs=99.3

Q ss_pred             HHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHH
Q 042645          160 VWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDE  239 (427)
Q Consensus       160 l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~  239 (427)
                      +.+.+...-.++..++|+.|.||++.+..+.+...  ...|+....+.+....++.++.                     
T Consensus         9 l~~~l~~~~~~~yl~~G~e~~~~~~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~~~l~---------------------   65 (343)
T 1jr3_D            9 LRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAA--AQGFEEHHTFSIDPNTDWNAIF---------------------   65 (343)
T ss_dssp             HHHHHHHCCCSEEEEEESCHHHHHHHHHHHHHHHH--HHTCCEEEEEECCTTCCHHHHH---------------------
T ss_pred             HHHHHhcCCCcEEEEECCcHHHHHHHHHHHHHHHH--hCCCCeeEEEEecCCCCHHHHH---------------------
Confidence            33444434567899999999999999999887652  1123221111222223333332                     


Q ss_pred             HHHHHHH-HhcCCcEEEEEeccCC-c--ccccccccCCCCCCCCcEEEEecCC-------hhHHhh-cCCCcceeccCCC
Q 042645          240 KAQEIFK-TMRNRKIVLLLDDIWE-L--FDLAQVGLPVPSRASASKVVFTTRE-------FEVCGL-MDAHKSFKVECLG  307 (427)
Q Consensus       240 ~~~~l~~-~L~~k~~LlVlDdv~~-~--~~~~~~~~~l~~~~~gs~IivTtR~-------~~v~~~-~~~~~~~~l~~L~  307 (427)
                        +.+.. -+-+++-++|+|+++. .  ..++.+...+.....++.+|++|..       ..+... ......++..+++
T Consensus        66 --~~~~~~plf~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~  143 (343)
T 1jr3_D           66 --SLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPE  143 (343)
T ss_dssp             --HHHHHHHHCCSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCC
T ss_pred             --HHhcCcCCccCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCC
Confidence              22221 1335677889999876 3  3345554445444556777766643       123332 2344678999999


Q ss_pred             hHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          308 YEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       308 ~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      .++...++.+.+...+...+   .+.+..|++.++|.+..+...
T Consensus       144 ~~~l~~~l~~~~~~~g~~i~---~~a~~~l~~~~~gdl~~~~~e  184 (343)
T 1jr3_D          144 QAQLPRWVAARAKQLNLELD---DAANQVLCYCYEGNLLALAQA  184 (343)
T ss_dssp             TTHHHHHHHHHHHHTTCEEC---HHHHHHHHHSSTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHhchHHHHHHHH
Confidence            99999988887743332222   355888999999988877653

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.25  E-value=0.0018  Score=60.49  Aligned_cols=94  Identities=14%  Similarity=0.171  Sum_probs=58.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCC---CCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTP---NDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNE----------SWDN  234 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~----------~~~~  234 (427)
                      ...++.|+|++|+||||||.+++.......   +.-..++|++....++...+. .++..++....          ....
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g~~~~~~l~~l~~~~~~~~  199 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFNVDHDAVLDNVLYARAYTS  199 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCST
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcCCCHHHHHhceeEeecCCH
Confidence            457899999999999999999987642111   123578899888777766654 34455554321          0011


Q ss_pred             CCHHHHHHHHHHHhc---CCcEEEEEeccCC
Q 042645          235 KSFDEKAQEIFKTMR---NRKIVLLLDDIWE  262 (427)
Q Consensus       235 ~~~~~~~~~l~~~L~---~k~~LlVlDdv~~  262 (427)
                      ....++...+...++   .+.-+||+|.+..
T Consensus       200 e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          200 EHQMELLDYVAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             THHHHHHHHHHHHHHHSCSSEEEEEEETSGG
T ss_pred             HHHHHHHHHHHHHHHhcCCCccEEEEechHH
Confidence            112233344445443   4567999999854

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.24  E-value=0.0018  Score=60.00  Aligned_cols=94  Identities=16%  Similarity=0.237  Sum_probs=59.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCC---CCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTP---NDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~~  237 (427)
                      ...++.|+|++|+||||||.+++.......   ..-..++|++....++...+. .++..++.....       ....+.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~~~~~~~~l~~~~~~~~  184 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLDIDNVMNNIYYIRAINT  184 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCCHHHHhccEEEEeCCCH
Confidence            456899999999999999999987652110   113478899888777766655 345556543210       012233


Q ss_pred             H---HHHHHHHHHhc--CCcEEEEEeccCC
Q 042645          238 D---EKAQEIFKTMR--NRKIVLLLDDIWE  262 (427)
Q Consensus       238 ~---~~~~~l~~~L~--~k~~LlVlDdv~~  262 (427)
                      +   ++...+...++  .+.-+||+|.+..
T Consensus       185 ~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          185 DHQIAIVDDLQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHHHHHHHHHHHHHHHCTTEEEEEETTTTH
T ss_pred             HHHHHHHHHHHHHHHhccCCCEEEEeCcHH
Confidence            3   23445555554  4667999999853

>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=97.24  E-value=0.00012  Score=61.90  Aligned_cols=115  Identities=17%  Similarity=0.131  Sum_probs=63.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC---CCCHHHHHHHHHHHhCCC----CCCCCCCC-----
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR---DLQLGKIQESIAKKIGLY----NESWDNKS-----  236 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~---~~~~~~l~~~i~~~l~~~----~~~~~~~~-----  236 (427)
                      ...|.|++..|.||||.|--..-+..   ++-..+.++..-+   ......++..+    +..    ...+....     
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~---g~G~rV~~vQF~Kg~~~~gE~~~l~~L----~v~~~~~g~gf~~~~~~~~~  100 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAV---GHGKNVGVVQFIKGTWPNGERNLLEPH----GVEFQVMATGFTWETQNREA  100 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHH---HTTCCEEEEESSCCSSCCHHHHHHGGG----TCEEEECCTTCCCCGGGHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHH---HCCCeEEEEEeeCCCCCccHHHHHHhC----CcEEEEcccccccCCCCcHH
Confidence            35677888888999999988776652   3333455565433   22333444333    210    00111111     


Q ss_pred             ----HHHHHHHHHHHhcCCcE-EEEEeccCCc-----ccccccccCCCCCCCCcEEEEecCChh
Q 042645          237 ----FDEKAQEIFKTMRNRKI-VLLLDDIWEL-----FDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       237 ----~~~~~~~l~~~L~~k~~-LlVlDdv~~~-----~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                          .........+.+.+.+| |||||++-..     ...+++...+........||+|+|+.+
T Consensus       101 ~~~~a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap  164 (196)
T 1g5t_A          101 DTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCH  164 (196)
T ss_dssp             HHHHHHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCC
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCc
Confidence                11223344555655555 9999998432     223334444444455678999999853

>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=97.23  E-value=0.00034  Score=72.84  Aligned_cols=46  Identities=26%  Similarity=0.440  Sum_probs=37.4

Q ss_pred             CccccchhhHHHHHHHhcc---------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE---------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..++.+...+..         .....+.++|++|+|||++|+.+++..
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l  512 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            4578999988888877642         123479999999999999999999876

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=97.21  E-value=0.0021  Score=58.44  Aligned_cols=88  Identities=15%  Similarity=0.212  Sum_probs=58.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHH-HHHHH
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEK-AQEIF  245 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~-~~~l~  245 (427)
                      .++.|+|++|+|||||+.+++..... ...-..++|++....++..     .+++++...+..   ...+.++. ...+.
T Consensus        29 GiteI~G~pGsGKTtL~Lq~~~~~~~-~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~  102 (333)
T 3io5_A           29 GLLILAGPSKSFKSNFGLTMVSSYMR-QYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVN  102 (333)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHHHHH-HCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHh-cCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHH
Confidence            37899999999999999998776621 1113467899887777653     367777654321   13344554 43333


Q ss_pred             HH--h-cCCcEEEEEeccCCc
Q 042645          246 KT--M-RNRKIVLLLDDIWEL  263 (427)
Q Consensus       246 ~~--L-~~k~~LlVlDdv~~~  263 (427)
                      ..  + .+++-|||+|-+...
T Consensus       103 ~l~~i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          103 QLDAIERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             HHHTCCTTCCEEEEEECSTTC
T ss_pred             HHHHhhccCceEEEEeccccc
Confidence            32  3 357889999998654

>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=97.16  E-value=0.0014  Score=61.64  Aligned_cols=88  Identities=18%  Similarity=0.147  Sum_probs=58.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC---CCCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES---WDNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~~~l  244 (427)
                      ...++.|+|.+|+||||||.+++.....   .-..++|++....++..     .+..++.....   ....+.++....+
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~---~g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l  144 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQK---AGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIM  144 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH---TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHH---CCCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHH
Confidence            4568999999999999999998877622   12368899887765543     24555554221   0223556666666


Q ss_pred             HHHhcC-CcEEEEEeccCCc
Q 042645          245 FKTMRN-RKIVLLLDDIWEL  263 (427)
Q Consensus       245 ~~~L~~-k~~LlVlDdv~~~  263 (427)
                      ....+. ..-+||+|.+...
T Consensus       145 ~~l~~~~~~~lVVIDsl~~l  164 (366)
T 1xp8_A          145 ELLVRSGAIDVVVVDSVAAL  164 (366)
T ss_dssp             HHHHTTTCCSEEEEECTTTC
T ss_pred             HHHHhcCCCCEEEEeChHHh
Confidence            666553 4569999998543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.16  E-value=0.00016  Score=58.46  Aligned_cols=45  Identities=16%  Similarity=0.120  Sum_probs=34.3

Q ss_pred             ccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|++..++++.+.+..  ....-|.|+|++|+|||++|+.+++..
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~   51 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG   51 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC
Confidence            578999998888887753  333458899999999999999987764

>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=97.12  E-value=0.00013  Score=63.43  Aligned_cols=113  Identities=15%  Similarity=-0.061  Sum_probs=62.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ...++.|+|..|+||||++..+.++..   .+-..++.++.....  . ....+++.++............++.+.+.+.
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~---~~g~kVli~~~~~d~--r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~   84 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLE---YADVKYLVFKPKIDT--R-SIRNIQSRTGTSLPSVEVESAPEILNYIMSN   84 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHH---HTTCCEEEEEECCCG--G-GCSSCCCCCCCSSCCEEESSTHHHHHHHHST
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHH---hcCCEEEEEEeccCc--h-HHHHHHHhcCCCccccccCCHHHHHHHHHHH
Confidence            457899999999999999998888772   222234444433221  1 1223444444432221222334555555555


Q ss_pred             hcCCc-EEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCCh
Q 042645          248 MRNRK-IVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREF  289 (427)
Q Consensus       248 L~~k~-~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~  289 (427)
                      +.+.+ -+||+|.+...  ...+.+ ..+.+  .|..||+|.+..
T Consensus        85 ~~~~~~dvViIDEaQ~l~~~~ve~l-~~L~~--~gi~Vil~Gl~~  126 (223)
T 2b8t_A           85 SFNDETKVIGIDEVQFFDDRICEVA-NILAE--NGFVVIISGLDK  126 (223)
T ss_dssp             TSCTTCCEEEECSGGGSCTHHHHHH-HHHHH--TTCEEEEECCSB
T ss_pred             hhCCCCCEEEEecCccCcHHHHHHH-HHHHh--CCCeEEEEeccc
Confidence            54444 49999998643  112222 12222  267899999853

>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=97.12  E-value=0.0016  Score=60.97  Aligned_cols=88  Identities=17%  Similarity=0.185  Sum_probs=57.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ...++.|+|++|+||||||.+++.....   .-..++|++....++..     .++.++......   ...+.++....+
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~---~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~  131 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQA---AGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIA  131 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH---TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            4578999999999999999999876522   22457888887665542     355565443211   123455666555


Q ss_pred             HHHhc-CCcEEEEEeccCCc
Q 042645          245 FKTMR-NRKIVLLLDDIWEL  263 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~~  263 (427)
                      ....+ .+.-+||+|.+...
T Consensus       132 ~~l~~~~~~~lIVIDsl~~l  151 (349)
T 2zr9_A          132 DMLVRSGALDIIVIDSVAAL  151 (349)
T ss_dssp             HHHHTTTCCSEEEEECGGGC
T ss_pred             HHHHhcCCCCEEEEcChHhh
Confidence            55554 35679999998643

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=97.02  E-value=0.0027  Score=58.75  Aligned_cols=94  Identities=14%  Similarity=0.212  Sum_probs=58.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC-----------CCCC--cEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC---
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT-----------PNDF--DFVIWEVVSRDLQLGKIQESIAKKIGLYNES---  231 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-----------~~~f--~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~---  231 (427)
                      ...++.|+|.+|+|||+||.+++......           .+..  ..++|++....++...+.. ++..++.....   
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~  175 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLD  175 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhc
Confidence            45799999999999999999988653110           1111  5788998888777766653 45556543210   


Q ss_pred             ----CCCCCHH---HHHHHHHHHhcC--CcEEEEEeccCC
Q 042645          232 ----WDNKSFD---EKAQEIFKTMRN--RKIVLLLDDIWE  262 (427)
Q Consensus       232 ----~~~~~~~---~~~~~l~~~L~~--k~~LlVlDdv~~  262 (427)
                          ....+.+   ++...+...++.  +.-+||+|.+..
T Consensus       176 ~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  215 (322)
T 2i1q_A          176 NTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTS  215 (322)
T ss_dssp             TEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSSH
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence                0122333   234455555543  456999998853

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.97  E-value=0.00098  Score=61.27  Aligned_cols=40  Identities=20%  Similarity=0.326  Sum_probs=29.8

Q ss_pred             hhhHHHHHHHhccC---CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          154 QSTLDRVWRCLTEE---PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       154 ~~~~~~l~~~l~~~---~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+..+.+++...   ....+.|+|++|+|||+||..+++..
T Consensus       134 ~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~  176 (308)
T 2qgz_A          134 MEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHEL  176 (308)
T ss_dssp             HHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            33444555555542   24678999999999999999999877

>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=96.96  E-value=0.0025  Score=59.68  Aligned_cols=87  Identities=20%  Similarity=0.163  Sum_probs=56.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ...++.|.|.+|+||||||.+++.....   .-..++|++....++..     .+..++......   ...+.++....+
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~---~g~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~  133 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEIC  133 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH---TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHH
Confidence            4568999999999999999998877622   12357888887766543     245555432211   122345555555


Q ss_pred             HHHhc-CCcEEEEEeccCC
Q 042645          245 FKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~  262 (427)
                      ....+ .+.-+||+|.+..
T Consensus       134 ~~l~~~~~~~lVVIDsl~~  152 (356)
T 1u94_A          134 DALARSGAVDVIVVDSVAA  152 (356)
T ss_dssp             HHHHHHTCCSEEEEECGGG
T ss_pred             HHHHhccCCCEEEEcCHHH
Confidence            44433 4566999999854

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.83  E-value=0.003  Score=55.09  Aligned_cols=116  Identities=16%  Similarity=0.138  Sum_probs=61.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---------------
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---------------  232 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---------------  232 (427)
                      ...+++|.|++|+|||||+..++.....   .-..++|+....  ....+...+. .++......               
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~---~~~~v~~~~~~~--~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~   95 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGLR---DGDPCIYVTTEE--SRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEK   95 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHH---HTCCEEEEESSS--CHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC---
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHH---CCCeEEEEEccc--CHHHHHHHHH-HhcchHHHHhhCCEEEEecccccc
Confidence            3468999999999999999999866521   112455655433  3444443332 443221100               


Q ss_pred             ------CCCCHHHHHHHHHHHhc-CCc--EEEEEeccCCcc--c---ccccccCCCC--CCCCcEEEEecCCh
Q 042645          233 ------DNKSFDEKAQEIFKTMR-NRK--IVLLLDDIWELF--D---LAQVGLPVPS--RASASKVVFTTREF  289 (427)
Q Consensus       233 ------~~~~~~~~~~~l~~~L~-~k~--~LlVlDdv~~~~--~---~~~~~~~l~~--~~~gs~IivTtR~~  289 (427)
                            ...+..++...+...+. .++  .+||+|.+....  +   ...+...+..  ...|..||++|...
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~~  168 (235)
T 2w0m_A           96 EDQWSLVNLTPEELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQYA  168 (235)
T ss_dssp             -CTTBCSSCCHHHHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC--
T ss_pred             CceeeecCCCHHHHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEeccC
Confidence                  11245555555555443 234  499999986331  1   1111111111  12467788888765

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.81  E-value=0.0014  Score=56.19  Aligned_cols=42  Identities=21%  Similarity=0.419  Sum_probs=33.9

Q ss_pred             cchhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          152 GMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       152 GR~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|++.++.|.+.+..   ....+|+|.|+.|+||||+++.+...+
T Consensus         2 ~~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~   46 (201)
T 1rz3_A            2 ELRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTL   46 (201)
T ss_dssp             CHHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            356677778877764   356799999999999999999998765

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.80  E-value=0.0021  Score=66.29  Aligned_cols=170  Identities=14%  Similarity=0.166  Sum_probs=78.5

Q ss_pred             CccccchhhHHHHHHHhcc-------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .++.|.++.+++|.+.+.-             ...+-|.++|++|+|||.||+.+++..   ...     ++.++    .
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~---~~~-----f~~v~----~  544 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC---QAN-----FISIK----G  544 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTT---TCE-----EEECC----H
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHh---CCc-----eEEec----c
Confidence            4567888888887776531             134568899999999999999999987   221     22222    2


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCCCC-C
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVPSR-A  277 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~~~-~  277 (427)
                      .+++    ...       .+.+...+...+...-+..+++|++|+++....                ..++...+... .
T Consensus       545 ~~l~----s~~-------vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~  613 (806)
T 3cf2_A          545 PELL----TMW-------FGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST  613 (806)
T ss_dssp             HHHH----TTT-------CSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCS
T ss_pred             chhh----ccc-------cchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCC
Confidence            2222    111       223333333333333356899999999975311                01111111111 1


Q ss_pred             CCcEEEE-ecCChhH-H-hhc---CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCC
Q 042645          278 SASKVVF-TTREFEV-C-GLM---DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGL  344 (427)
Q Consensus       278 ~gs~Iiv-TtR~~~v-~-~~~---~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~  344 (427)
                      ....++| ||..... - ..+   .-...+.++.-+.++-.++|+.+........+.+    ...|++.+.|.
T Consensus       614 ~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~d----l~~la~~t~g~  682 (806)
T 3cf2_A          614 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVD----LEFLAKMTNGF  682 (806)
T ss_dssp             SSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC-----------------
T ss_pred             CCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCC----HHHHHHhCCCC
Confidence            1223444 4433221 1 111   2245677777777777788877664433222222    34556666664

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.78  E-value=0.00091  Score=62.16  Aligned_cols=44  Identities=20%  Similarity=0.314  Sum_probs=38.3

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|++..+..+...+..++  .+.++|++|+|||+||+.+++..
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~--~vll~G~pGtGKT~la~~la~~~   70 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG--HILLEGVPGLAKTLSVNTLAKTM   70 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC--CEEEESCCCHHHHHHHHHHHHHT
T ss_pred             cceeCcHHHHHHHHHHHHcCC--eEEEECCCCCcHHHHHHHHHHHh
Confidence            467999999999988887653  58899999999999999999876

>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=96.74  E-value=0.007  Score=58.04  Aligned_cols=26  Identities=31%  Similarity=0.496  Sum_probs=23.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.++|.+|+||||++..++..+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l  124 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYF  124 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHH
Confidence            35799999999999999999998877

>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=96.70  E-value=0.012  Score=55.95  Aligned_cols=94  Identities=16%  Similarity=0.179  Sum_probs=54.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKSF  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~~  237 (427)
                      ...++.|+|++|+|||||+..++-.....   ...-..++|++....+....+ ..+++.++.....       ....+.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl~~~~vleni~~~~~~~~  255 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGLDPDDALNNVAYARAYNA  255 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCCChHhHhhcEEEeccCCh
Confidence            45689999999999999999876333111   113356888887665555443 3466666543210       011222


Q ss_pred             HH---HHHHHHHHh-cCCcEEEEEeccCC
Q 042645          238 DE---KAQEIFKTM-RNRKIVLLLDDIWE  262 (427)
Q Consensus       238 ~~---~~~~l~~~L-~~k~~LlVlDdv~~  262 (427)
                      ..   ....+...+ ..+.-+||+|.+-.
T Consensus       256 ~~~~~~l~~~~~~l~~~~~~llVIDs~t~  284 (400)
T 3lda_A          256 DHQLRLLDAAAQMMSESRFSLIVVDSVMA  284 (400)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETGGG
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEecchhh
Confidence            22   223333333 24678999999753

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.69  E-value=7.7e-05  Score=63.17  Aligned_cols=24  Identities=25%  Similarity=0.181  Sum_probs=20.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++.|+|+.|+||||++..++.+.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~   27 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIY   27 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            578899999999999997776665

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.68  E-value=0.0079  Score=55.37  Aligned_cols=51  Identities=12%  Similarity=0.096  Sum_probs=36.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      ...++.|.|.+|+||||||..++..... .+  ..++|++..  .+..++...+..
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~-~g--~~vl~~slE--~s~~~l~~R~~~  117 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSD-ND--DVVNLHSLE--MGKKENIKRLIV  117 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHT-TT--CEEEEEESS--SCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH-cC--CeEEEEECC--CCHHHHHHHHHH
Confidence            4568999999999999999999876622 22  567787765  345555555554

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.63  E-value=0.0015  Score=64.06  Aligned_cols=44  Identities=14%  Similarity=0.150  Sum_probs=38.2

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|++..++.+...+..+.  .|.|+|++|+|||+||+.+++..
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~--~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC--EEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhhHHHHHHHHHHHHHHhcCC--eeEeecCchHHHHHHHHHHHHHH
Confidence            457999999998888877653  58899999999999999999876

>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=96.60  E-value=0.0092  Score=51.86  Aligned_cols=59  Identities=24%  Similarity=0.284  Sum_probs=36.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC--C-CCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT--P-NDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~-~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      ...+++|+|++|+|||||++.++......  . .....++|+.......... ...+.+..+.
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~-i~~~~~~~~~   85 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRGL   85 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH-HHHHHHHTTS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH-HHHHHHHcCC
Confidence            45799999999999999999998744110  0 1234577777554433332 3344444443

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.59  E-value=0.0018  Score=55.72  Aligned_cols=39  Identities=26%  Similarity=0.322  Sum_probs=30.7

Q ss_pred             hhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          155 STLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       155 ~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.+++|.+.+..  +...+|+|.|+.|+|||||++.+...+
T Consensus         6 ~~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~   46 (208)
T 3c8u_A            6 ALCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAAL   46 (208)
T ss_dssp             HHHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            345566666653  356799999999999999999998776

>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=96.53  E-value=0.0011  Score=62.11  Aligned_cols=46  Identities=20%  Similarity=0.307  Sum_probs=35.4

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..+..+...+..+...-+.|+|++|+|||+||+.+++..
T Consensus        24 ~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~   69 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALL   69 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             hhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhC
Confidence            4589998876665555443333459999999999999999999876

>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=96.51  E-value=0.0071  Score=56.53  Aligned_cols=95  Identities=20%  Similarity=0.239  Sum_probs=54.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCC---CcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-------CCCCC-
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPND---FDFVIWEVVSRDLQLGKIQESIAKKIGLYNES-------WDNKS-  236 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~---f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~-------~~~~~-  236 (427)
                      ...++.|+|++|+|||||+..++.........   -..++|++....+....+ ..+++.++.....       ....+ 
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~  208 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNS  208 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCCh
Confidence            56799999999999999999998765211011   134588877655433333 3344444332100       00111 


Q ss_pred             --HHHHHHHHHHHhc------CCcEEEEEeccCCc
Q 042645          237 --FDEKAQEIFKTMR------NRKIVLLLDDIWEL  263 (427)
Q Consensus       237 --~~~~~~~l~~~L~------~k~~LlVlDdv~~~  263 (427)
                        ..++...+...+.      .++-+||+|.+-..
T Consensus       209 ~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          209 NHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             HHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence              2233444455554      46789999998654

>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=96.51  E-value=0.0086  Score=54.51  Aligned_cols=87  Identities=15%  Similarity=0.103  Sum_probs=46.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK  246 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~  246 (427)
                      ...+++|+|++|+||||++..++..+....+  ..+..+.... .....+.+.......+.+..  ...+...+...+. 
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G--~~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~--~~~~~~~l~~al~-  178 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKH--KKIAFITTDTYRIAAVEQLKTYAELLQAPLE--VCYTKEEFQQAKE-  178 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTC--CCEEEEECCCSSTTHHHHHHHHHTTTTCCCC--BCSSHHHHHHHHH-
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcC--CEEEEEecCcccchHHHHHHHHHHhcCCCeE--ecCCHHHHHHHHH-
Confidence            3468999999999999999999877621112  2344454432 22233334443433443321  1223334433333 


Q ss_pred             HhcCCcEEEEEecc
Q 042645          247 TMRNRKIVLLLDDI  260 (427)
Q Consensus       247 ~L~~k~~LlVlDdv  260 (427)
                      .+ .+.=++|+|-.
T Consensus       179 ~~-~~~dlvIiDT~  191 (296)
T 2px0_A          179 LF-SEYDHVFVDTA  191 (296)
T ss_dssp             HG-GGSSEEEEECC
T ss_pred             Hh-cCCCEEEEeCC
Confidence            33 34457888843

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=96.49  E-value=0.0015  Score=54.49  Aligned_cols=24  Identities=17%  Similarity=0.339  Sum_probs=22.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|.|.|++|+||||+++.+.+.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            579999999999999999999887

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=96.49  E-value=0.014  Score=54.65  Aligned_cols=53  Identities=19%  Similarity=0.083  Sum_probs=34.3

Q ss_pred             HHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC
Q 042645          159 RVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL  212 (427)
Q Consensus       159 ~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~  212 (427)
                      +.++.+.. .....++|+|++|+|||||++.+.+........+.+ +++-+++..
T Consensus       163 raID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~-I~~lIGER~  216 (422)
T 3ice_A          163 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVL-MVLLIDERP  216 (422)
T ss_dssp             HHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEE-EEEEESSCH
T ss_pred             eeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeE-EEEEecCCh
Confidence            34444433 345689999999999999999887765211223333 456676543

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=96.47  E-value=0.026  Score=54.26  Aligned_cols=64  Identities=22%  Similarity=0.366  Sum_probs=45.0

Q ss_pred             HHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHH
Q 042645          159 RVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKK  224 (427)
Q Consensus       159 ~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~  224 (427)
                      +.++.|.. .....++|.|.+|+|||+|+..+.+...  ..+.+.++++-+++.. ...++++++...
T Consensus       142 r~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~~--~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          142 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVA--KAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHTT--TTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EEEecccccccCCeeeeecCCCCChHHHHHHHHHhhH--hhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            34555543 3456799999999999999999988752  2344667788887654 456677777655

>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=96.47  E-value=0.012  Score=56.33  Aligned_cols=26  Identities=31%  Similarity=0.336  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.++|++|+||||++..++..+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l  121 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFY  121 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999998776

>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=96.46  E-value=0.0072  Score=51.85  Aligned_cols=77  Identities=19%  Similarity=0.133  Sum_probs=44.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh---CCC----CCCCCCCCHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI---GLY----NESWDNKSFDEKAQE  243 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l---~~~----~~~~~~~~~~~~~~~  243 (427)
                      +|.|.|++|+||||.|+.+.+.+.     +   ..++      ..+++++-+..-   +..    ...-...+.+-....
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g-----~---~~is------tGdllR~~i~~~t~lg~~~~~~~~~G~lvpd~iv~~l   67 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKG-----F---VHIS------TGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIAL   67 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC-----C---EEEE------HHHHHHHHHHHTCHHHHHHHHHHHHTCCCCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC-----C---eEEc------HHHHHHHHHHhcChhhhhHHHHHhcCCcCCHHHHHHH
Confidence            578999999999999999998871     1   1222      344554433211   000    000012334455666


Q ss_pred             HHHHhcCCcEEEEEeccCC
Q 042645          244 IFKTMRNRKIVLLLDDIWE  262 (427)
Q Consensus       244 l~~~L~~k~~LlVlDdv~~  262 (427)
                      +.+.+..... +|||.+-.
T Consensus        68 v~~~l~~~~~-~ilDGfPR   85 (206)
T 3sr0_A           68 IEEVFPKHGN-VIFDGFPR   85 (206)
T ss_dssp             HHHHCCSSSC-EEEESCCC
T ss_pred             HHHhhccCCc-eEecCCch
Confidence            7777765444 68899853

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=96.43  E-value=0.0016  Score=53.93  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|+|.|++|+||||+++.+.+.+
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999998876

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=96.41  E-value=0.0029  Score=59.60  Aligned_cols=45  Identities=20%  Similarity=0.176  Sum_probs=36.8

Q ss_pred             ccccchhhHHHHHHHhc-------------c--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLT-------------E--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~-------------~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.+..++.+...+.             .  .....+.++|++|+|||++|+.+++..
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~   75 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL   75 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            36899998888888772             1  134578999999999999999999886

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.39  E-value=0.0017  Score=53.79  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=20.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|+|.|++|+||||+++.+ ...
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~~   24 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KER   24 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HHT
T ss_pred             cEEEEECCCCCCHHHHHHHH-HHC
Confidence            47999999999999999999 544

>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=96.38  E-value=0.008  Score=54.94  Aligned_cols=90  Identities=16%  Similarity=0.203  Sum_probs=49.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH--HHHHHHHHHhCCCCCC-CCCCCHHHH-HHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG--KIQESIAKKIGLYNES-WDNKSFDEK-AQE  243 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~--~l~~~i~~~l~~~~~~-~~~~~~~~~-~~~  243 (427)
                      ...+++|+|++|+||||++..++..+.. .  -..+..+... .+...  +-+...++..+++.-. ....++... ...
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~-~--g~kV~lv~~D-~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~a  178 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVD-E--GKSVVLAAAD-TFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDA  178 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHH-T--TCCEEEEEEC-TTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHh-c--CCEEEEEccc-cccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHH
Confidence            3478999999999999999999887721 1  2234444433 22222  2233445555543211 112233332 233


Q ss_pred             HHHHhcCCcEEEEEeccC
Q 042645          244 IFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       244 l~~~L~~k~~LlVlDdv~  261 (427)
                      +...+....-++|+|..-
T Consensus       179 l~~a~~~~~dvvIiDtpg  196 (306)
T 1vma_A          179 VAHALARNKDVVIIDTAG  196 (306)
T ss_dssp             HHHHHHTTCSEEEEEECC
T ss_pred             HHHHHhcCCCEEEEECCC
Confidence            444455555688889764

>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=96.35  E-value=0.0035  Score=59.32  Aligned_cols=46  Identities=20%  Similarity=0.211  Sum_probs=36.3

Q ss_pred             CccccchhhHHHHHHHhc------------------------------cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLT------------------------------EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~------------------------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.+..++.|...+.                              ......+.++|++|+|||++|+.+++..
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l   96 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL   96 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHh
Confidence            357898888888877662                              0124568999999999999999999876

>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=96.31  E-value=0.0026  Score=53.69  Aligned_cols=26  Identities=31%  Similarity=0.307  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|++|+|||||++.+....
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~~   33 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANLP   33 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcc
Confidence            34689999999999999999998753

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.27  E-value=0.0026  Score=53.09  Aligned_cols=22  Identities=27%  Similarity=0.314  Sum_probs=20.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      .+|.|.|++|+||||+|+.+.+
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5799999999999999999987

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.26  E-value=0.0024  Score=54.46  Aligned_cols=26  Identities=31%  Similarity=0.299  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|+|++|+||||+++.+...+
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            34689999999999999999999876

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.25  E-value=0.025  Score=52.24  Aligned_cols=27  Identities=30%  Similarity=0.475  Sum_probs=24.0

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+++|+|+.|+||||+++.++..+
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            356799999999999999999998776

>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=96.23  E-value=0.003  Score=53.95  Aligned_cols=28  Identities=25%  Similarity=0.475  Sum_probs=24.7

Q ss_pred             cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          166 EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       166 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .....+|+|.|++|+||||+++.+...+
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~La~~l   49 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACALNQML   49 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3456799999999999999999998877

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=96.23  E-value=0.0046  Score=53.73  Aligned_cols=40  Identities=23%  Similarity=0.341  Sum_probs=30.8

Q ss_pred             hhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          154 QSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       154 ~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+.+...+.......|+|+|.+|+|||||+..+....
T Consensus        23 ~~~a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           23 KRLADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3344455555555567899999999999999999998875

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.22  E-value=0.0025  Score=53.60  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|.|+|++|+||||+++.+.+.+
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999999999876

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.22  E-value=0.0023  Score=53.15  Aligned_cols=24  Identities=29%  Similarity=0.342  Sum_probs=22.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|+|+|++|+||||+++.+...+
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999999998876

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.21  E-value=0.0029  Score=53.25  Aligned_cols=26  Identities=35%  Similarity=0.445  Sum_probs=23.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|.|++|+||||+++.+...+
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l   37 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLL   37 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            45789999999999999999999887

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.21  E-value=0.033  Score=53.48  Aligned_cols=26  Identities=31%  Similarity=0.542  Sum_probs=23.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.++|.+|+||||++..++..+
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l  124 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFL  124 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45799999999999999999998877

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.21  E-value=0.0027  Score=53.59  Aligned_cols=24  Identities=33%  Similarity=0.545  Sum_probs=22.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|.|.|++|+||||+++.+.+.+
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l   25 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEIL   25 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999999999887

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=96.21  E-value=0.012  Score=66.40  Aligned_cols=86  Identities=20%  Similarity=0.158  Sum_probs=57.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..+.+.|+|++|+|||+||.++.....   ..-..++|+++...++...     ++.++.+....   ...+.++....+
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~---~~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~ 1497 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQ---REGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEIC 1497 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHH---TTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHH
Confidence            567899999999999999999987762   2334577888777665544     55565432211   122334555555


Q ss_pred             HHHhc-CCcEEEEEeccC
Q 042645          245 FKTMR-NRKIVLLLDDIW  261 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~  261 (427)
                      ....+ .+.-+||+|.+.
T Consensus      1498 ~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1498 DALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHHTCCSEEEESCGG
T ss_pred             HHHHhcCCCCEEEEcChh
Confidence            55543 577899999985

>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=96.20  E-value=0.018  Score=54.98  Aligned_cols=25  Identities=28%  Similarity=0.367  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++.|+|++|+||||++..++..+
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~l  122 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALYY  122 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999998877

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.20  E-value=0.048  Score=50.41  Aligned_cols=51  Identities=18%  Similarity=0.076  Sum_probs=35.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      ...++.|.|.+|+||||||..++.....   .-..++|++..  .+..++...++.
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~---~g~~Vl~fSlE--ms~~ql~~Rlls   95 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALN---DDRGVAVFSLE--MSAEQLALRALS   95 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHH---TTCEEEEEESS--SCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCC--CCHHHHHHHHHH
Confidence            4468999999999999999999887632   23456776653  345555555543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.20  E-value=0.009  Score=52.51  Aligned_cols=40  Identities=25%  Similarity=0.130  Sum_probs=28.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      ...++.|.|++|+|||||+.+++.....   .-..++|++...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~---~~~~v~~~~~e~   61 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLK---MGEPGIYVALEE   61 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHH---TTCCEEEEESSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEEccC
Confidence            4468999999999999999888765521   123567776543

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=96.19  E-value=0.0032  Score=53.15  Aligned_cols=25  Identities=24%  Similarity=0.349  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.|.|++|+||||+++.+.+.+
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999998876

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.19  E-value=0.015  Score=55.96  Aligned_cols=99  Identities=16%  Similarity=0.254  Sum_probs=53.8

Q ss_pred             HHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCC
Q 042645          161 WRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDN  234 (427)
Q Consensus       161 ~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~  234 (427)
                      ++.|.. .....++|+|.+|+|||||+..+......  ......+++.+++.. ...+++.++...-.+...    ....
T Consensus       142 ID~L~pi~kGq~~~i~G~sGvGKTtL~~~l~~~~~~--~~~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~  219 (473)
T 1sky_E          142 VDLLAPYIKGGKIGLFGGAGVGKTVLIQELIHNIAQ--EHGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMN  219 (473)
T ss_dssp             HHHHSCEETTCEEEEECCSSSCHHHHHHHHHHHHHH--HTCCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTT
T ss_pred             HHHHhhhccCCEEEEECCCCCCccHHHHHHHhhhhh--ccCcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCC
Confidence            444432 23346899999999999999998876521  122344666676654 344555555432100000    0011


Q ss_pred             CCHHHHH------HHHHHHh---cCCcEEEEEeccC
Q 042645          235 KSFDEKA------QEIFKTM---RNRKIVLLLDDIW  261 (427)
Q Consensus       235 ~~~~~~~------~~l~~~L---~~k~~LlVlDdv~  261 (427)
                      .++....      -.+.+++   +++++||++||+.
T Consensus       220 d~pg~r~~~~~~~ltiAEyFrd~~G~~VLl~~D~it  255 (473)
T 1sky_E          220 EPPGARMRVALTGLTMAEYFRDEQGQDGLLFIDNIF  255 (473)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHSCCEEEEEEECTH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence            1111111      1222332   5899999999984

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.16  E-value=0.0032  Score=52.77  Aligned_cols=25  Identities=20%  Similarity=0.319  Sum_probs=22.3

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++|+|+.|+|||||++.+....
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3589999999999999999998765

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.12  E-value=0.0032  Score=53.76  Aligned_cols=27  Identities=33%  Similarity=0.519  Sum_probs=23.3

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+|+|.|+.|+|||||++.+....
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            345789999999999999999998765

>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=96.11  E-value=0.027  Score=51.18  Aligned_cols=26  Identities=19%  Similarity=0.272  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|++|+|||||+..++...
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            45689999999999999999998776

>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=96.11  E-value=0.0029  Score=53.26  Aligned_cols=24  Identities=29%  Similarity=0.506  Sum_probs=21.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.|.|++|+|||||++.+....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            458899999999999999998776

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=96.10  E-value=0.025  Score=54.57  Aligned_cols=99  Identities=19%  Similarity=0.285  Sum_probs=60.9

Q ss_pred             HHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CC-
Q 042645          161 WRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLY-------NE-  230 (427)
Q Consensus       161 ~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~-------~~-  230 (427)
                      ++.|.. .....++|.|.+|+|||+|+..+.+...  ..+.+.++++-+++.. ...+++.++...=.+.       .. 
T Consensus       156 ID~l~pigkGqr~gIfgg~GvGKT~L~~~l~~~~a--~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtv  233 (498)
T 1fx0_B          156 VNLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIA--KAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVA  233 (498)
T ss_dssp             HHHHSCCCTTCCEEEEECSSSSHHHHHHHHHHHTT--TTCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEE
T ss_pred             eeeecccccCCeEEeecCCCCCchHHHHHHHHHHH--hhCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceE
Confidence            444432 3445799999999999999999988752  2345677888887765 4566777776542222       00 


Q ss_pred             ---CCCCCCHHH------HHHHHHHHhc---CCcEEEEEeccC
Q 042645          231 ---SWDNKSFDE------KAQEIFKTMR---NRKIVLLLDDIW  261 (427)
Q Consensus       231 ---~~~~~~~~~------~~~~l~~~L~---~k~~LlVlDdv~  261 (427)
                         .....+...      ..-.+-++++   ++.+||++||+-
T Consensus       234 vV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~Dsit  276 (498)
T 1fx0_B          234 LVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIF  276 (498)
T ss_dssp             EEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSH
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence               001112111      1222334544   589999999984

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=96.09  E-value=0.0029  Score=52.91  Aligned_cols=25  Identities=36%  Similarity=0.395  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|.|.|++|+||||+++.+.+.+
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            3578999999999999999998876

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.09  E-value=0.0026  Score=54.39  Aligned_cols=25  Identities=24%  Similarity=0.446  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+...+
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999998876

>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=96.08  E-value=0.0025  Score=59.64  Aligned_cols=114  Identities=14%  Similarity=0.146  Sum_probs=62.0

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC-CCCCCCCCCCHHHHHHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG-LYNESWDNKSFDEKAQEIF  245 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~-~~~~~~~~~~~~~~~~~l~  245 (427)
                      ....+++|.|+.|+|||||++.+.......  .-..++.+.-.-.+....       ... ..... ...........+.
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~~l~g~~~~~--~~~~i~t~ed~~e~~~~~-------~~~~v~q~~-~~~~~~~~~~~La  190 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLAAMLDYLNNT--KYHHILTIEDPIEFVHES-------KKCLVNQRE-VHRDTLGFSEALR  190 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHHHHHHHHHHH--CCCEEEEEESSCCSCCCC-------SSSEEEEEE-BTTTBSCHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccCC--CCcEEEEccCcHHhhhhc-------cccceeeee-eccccCCHHHHHH
Confidence            344599999999999999999987765211  011222221111110000       000 00000 0111123344777


Q ss_pred             HHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHh
Q 042645          246 KTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       246 ~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                      ..|...+=+|++|+.-+.+.+..+....   ..|..|++|+...+...
T Consensus       191 ~aL~~~PdvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~~~  235 (356)
T 3jvv_A          191 SALREDPDIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSAAK  235 (356)
T ss_dssp             HHTTSCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSHHH
T ss_pred             HHhhhCcCEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChHHH
Confidence            8888899999999997655444332221   23666888888766543

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=96.07  E-value=0.0032  Score=53.09  Aligned_cols=24  Identities=29%  Similarity=0.371  Sum_probs=22.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|.|.|++|+||||+++.+.+.+
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l   27 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNL   27 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            579999999999999999999876

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.06  E-value=0.0037  Score=54.08  Aligned_cols=26  Identities=23%  Similarity=0.337  Sum_probs=24.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.|.|++|+||||.|+.+.+.+
T Consensus        28 k~kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           28 KAKVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             SCEEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            56899999999999999999999887

>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=96.05  E-value=0.004  Score=53.57  Aligned_cols=26  Identities=27%  Similarity=0.241  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+....
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHST
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            45689999999999999999998876

>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=96.05  E-value=0.005  Score=59.09  Aligned_cols=46  Identities=20%  Similarity=0.235  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHhcc--------------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--------------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--------------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.++.++.|..++..              ...+-|.++|++|+||||+|+.++...
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l   74 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHc
Confidence            4578999888888776632              134569999999999999999999887

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=96.04  E-value=0.0053  Score=53.09  Aligned_cols=41  Identities=22%  Similarity=0.261  Sum_probs=31.5

Q ss_pred             chhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          153 MQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       153 R~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++..+.+...+.....++|+|+|.+|+|||||+..+....
T Consensus        14 ~~~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           14 NKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             HHHHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            34445555555545577899999999999999999998875

>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=96.03  E-value=0.0061  Score=55.31  Aligned_cols=27  Identities=26%  Similarity=0.196  Sum_probs=23.8

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+|+|.|+.|+|||||++.+...+
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l   55 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHL   55 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            356799999999999999999988776

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.99  E-value=0.007  Score=56.10  Aligned_cols=43  Identities=26%  Similarity=0.279  Sum_probs=31.5

Q ss_pred             ccchhhHHHHHHHhc----cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          151 VGMQSTLDRVWRCLT----EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       151 vGR~~~~~~l~~~l~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++-+...+++++.+.    .+....|.|+|++|+||||+++.++...
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHh
Confidence            344455555655553    3456679999999999999999888765

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.99  E-value=0.0041  Score=52.64  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998876

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.99  E-value=0.0036  Score=53.62  Aligned_cols=25  Identities=32%  Similarity=0.549  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|+|++|+|||||++.+....
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhC
Confidence            4679999999999999999998876

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.98  E-value=0.0041  Score=52.56  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=22.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+|+.+.+.+
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999998876

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=95.97  E-value=0.0045  Score=51.42  Aligned_cols=25  Identities=24%  Similarity=0.482  Sum_probs=22.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+....
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999998765

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.96  E-value=0.0034  Score=52.29  Aligned_cols=23  Identities=26%  Similarity=0.444  Sum_probs=21.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+++.+...+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999876

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.95  E-value=0.0067  Score=55.01  Aligned_cols=26  Identities=31%  Similarity=0.241  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|.|++|+||||+++.+....
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35689999999999999999998775

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.93  E-value=0.0041  Score=55.35  Aligned_cols=24  Identities=29%  Similarity=0.295  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|.|.|++|+||||||+.++...
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcC
Confidence            478999999999999999998876

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.93  E-value=0.0046  Score=52.81  Aligned_cols=25  Identities=20%  Similarity=0.384  Sum_probs=22.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++|.|+.|+|||||++.+....
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhC
Confidence            3589999999999999999998764

>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=95.92  E-value=0.0033  Score=52.74  Aligned_cols=24  Identities=25%  Similarity=0.408  Sum_probs=21.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|+|.|++|+||||+|+.+...+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            469999999999999999998876

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.92  E-value=0.006  Score=51.84  Aligned_cols=37  Identities=14%  Similarity=0.091  Sum_probs=27.7

Q ss_pred             HHHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          157 LDRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       157 ~~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..+..++.. +....+.|+|++|+||||+|..+++..
T Consensus        45 ~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l   82 (212)
T 1tue_A           45 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFI   82 (212)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHh
Confidence            4445555543 233479999999999999999998887

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.92  E-value=0.0041  Score=51.31  Aligned_cols=26  Identities=23%  Similarity=0.386  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|++|+||||+++.+.+.+
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999999876

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.91  E-value=0.0042  Score=52.98  Aligned_cols=23  Identities=26%  Similarity=0.629  Sum_probs=21.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|.|+.|+||||+++.+.+.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            68999999999999999999887

>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=95.89  E-value=0.02  Score=52.03  Aligned_cols=90  Identities=14%  Similarity=0.045  Sum_probs=51.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHhCCCCCC-CCCCCHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD-LQLGKIQESIAKKIGLYNES-WDNKSFDEKAQEIFK  246 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~-~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~~~~l~~  246 (427)
                      ..+++++|.+|+||||++..++..+..   .-..+.++..... ....+.+.......+++.-. ....++..+.....+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~---~g~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~  174 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKK---KGFKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVE  174 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHH---TTCCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHH
Confidence            468999999999999999999877631   1223555554322 22233344455555543211 122455555544444


Q ss_pred             Hhc-CCcEEEEEeccC
Q 042645          247 TMR-NRKIVLLLDDIW  261 (427)
Q Consensus       247 ~L~-~k~~LlVlDdv~  261 (427)
                      .++ +.-=++++|-.-
T Consensus       175 ~~~~~~~D~ViIDTpg  190 (297)
T 1j8m_F          175 KFLSEKMEIIIVDTAG  190 (297)
T ss_dssp             HHHHTTCSEEEEECCC
T ss_pred             HHHhCCCCEEEEeCCC
Confidence            454 333378888753

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.89  E-value=0.0054  Score=52.34  Aligned_cols=26  Identities=23%  Similarity=0.400  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|++|+||||+++.+.+.+
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            34689999999999999999998876

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.89  E-value=0.0049  Score=52.85  Aligned_cols=24  Identities=21%  Similarity=0.440  Sum_probs=22.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|.|++|+||||+++.+.+.+
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l   28 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWI   28 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHH
Confidence            579999999999999999999887

>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=95.88  E-value=0.0053  Score=51.61  Aligned_cols=24  Identities=25%  Similarity=0.250  Sum_probs=22.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...|+|+|++|+||||+++.+.+.
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            467999999999999999999887

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.88  E-value=0.0047  Score=52.40  Aligned_cols=25  Identities=24%  Similarity=0.351  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+.+.+
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999999876

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.86  E-value=0.0053  Score=52.44  Aligned_cols=25  Identities=32%  Similarity=0.302  Sum_probs=22.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++|+|+.|+||||+++.+....
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            4589999999999999999998765

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.86  E-value=0.0046  Score=51.35  Aligned_cols=23  Identities=30%  Similarity=0.436  Sum_probs=19.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~  190 (427)
                      ...+++|+|+.|+|||||++.++
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHS
T ss_pred             CCEEEEEECCCCCCHHHHHHHHc
Confidence            34689999999999999999643

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.83  E-value=0.005  Score=51.66  Aligned_cols=24  Identities=25%  Similarity=0.351  Sum_probs=21.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|.|++|+||||+++.+.+.+
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999998776

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=95.82  E-value=0.0053  Score=51.74  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .+++|.|++|+|||||++.+...
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~~   25 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAAQ   25 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhcc
Confidence            47899999999999999999764

>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=95.82  E-value=0.0086  Score=52.84  Aligned_cols=40  Identities=25%  Similarity=0.269  Sum_probs=29.0

Q ss_pred             hhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          154 QSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       154 ~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+.++......  .....|+|.|++|+||||+|+.+.+.+
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           12 IDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             HHHHHHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3444444444322  355689999999999999999998876

>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=95.82  E-value=0.0051  Score=51.45  Aligned_cols=23  Identities=39%  Similarity=0.538  Sum_probs=20.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|+|+.|+|||||++.++...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999998765

>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=95.80  E-value=0.0042  Score=51.42  Aligned_cols=24  Identities=21%  Similarity=0.317  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|.|.|++|+||||+++.+.+.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            469999999999999999999876

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.80  E-value=0.0061  Score=52.37  Aligned_cols=26  Identities=27%  Similarity=0.399  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|+.|+|||||++.+...+
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHh
Confidence            44689999999999999999998865

>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=95.78  E-value=0.0068  Score=51.92  Aligned_cols=26  Identities=31%  Similarity=0.511  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|++|+||||+++.+...+
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            34689999999999999999998764

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=95.77  E-value=0.06  Score=50.33  Aligned_cols=53  Identities=19%  Similarity=0.113  Sum_probs=34.9

Q ss_pred             HHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCC
Q 042645          158 DRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRD  211 (427)
Q Consensus       158 ~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~  211 (427)
                      -++++.+.. .....++|+|.+|+|||+|+..+.+........+.+ +++-+++.
T Consensus       163 iraID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~~-V~~lIGER  216 (427)
T 3l0o_A          163 TRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIR-IILLIDER  216 (427)
T ss_dssp             HHHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSEE-EEEECSCC
T ss_pred             chhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhhcCCCeEE-EEEEeccC
Confidence            355666643 445679999999999999999988865211223333 45666554

>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=95.77  E-value=0.0057  Score=51.54  Aligned_cols=25  Identities=32%  Similarity=0.372  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+.+.+
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999998876

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.76  E-value=0.0038  Score=52.28  Aligned_cols=25  Identities=28%  Similarity=0.359  Sum_probs=18.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.|.|++|+||||+|+.+.+.+
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            3579999999999999999998876

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=95.74  E-value=0.0052  Score=53.42  Aligned_cols=24  Identities=25%  Similarity=0.481  Sum_probs=21.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|+|+|++|+||||+++.+...+
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999998765

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.74  E-value=0.0072  Score=51.41  Aligned_cols=25  Identities=28%  Similarity=0.359  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...+|+|.|+.|+||||+++.+.+.
T Consensus         7 ~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            7 HPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHC
Confidence            4578999999999999999999764

>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=95.73  E-value=0.0058  Score=54.03  Aligned_cols=25  Identities=28%  Similarity=0.376  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+|||||++.+.+.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999999766

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.72  E-value=0.0062  Score=52.26  Aligned_cols=25  Identities=16%  Similarity=0.181  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+.+.+
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l   34 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYL   34 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4589999999999999999999876

>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=95.69  E-value=0.0067  Score=54.15  Aligned_cols=25  Identities=28%  Similarity=0.519  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.|.|++|+||||+|+.+...+
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L   28 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKIL   28 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998874

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=95.68  E-value=0.0062  Score=51.99  Aligned_cols=22  Identities=32%  Similarity=0.462  Sum_probs=20.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      .+|+|.|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3699999999999999999987

>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=95.67  E-value=0.0069  Score=51.40  Aligned_cols=26  Identities=19%  Similarity=0.285  Sum_probs=23.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++++|+|+.|+|||||++.+....
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhC
Confidence            45689999999999999999998765

>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=95.67  E-value=0.0059  Score=52.05  Aligned_cols=25  Identities=28%  Similarity=0.266  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|.|++|+||||+|+.+.+.+
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3479999999999999999998876

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.66  E-value=0.0081  Score=53.35  Aligned_cols=26  Identities=31%  Similarity=0.313  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|.|++|+||||+++.+...+
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            35689999999999999999998876

>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=95.66  E-value=0.0067  Score=52.15  Aligned_cols=25  Identities=20%  Similarity=0.328  Sum_probs=22.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l   33 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEAL   33 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.65  E-value=0.0062  Score=50.14  Aligned_cols=23  Identities=26%  Similarity=0.306  Sum_probs=21.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|.|++|+||||+++.+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999876

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.65  E-value=0.0062  Score=51.41  Aligned_cols=23  Identities=26%  Similarity=0.530  Sum_probs=21.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|++|+||||+++.+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l   24 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYL   24 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999998876

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.63  E-value=0.0069  Score=52.76  Aligned_cols=25  Identities=28%  Similarity=0.401  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|.|++|+||||+++.+.+.+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3579999999999999999998876

>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=95.63  E-value=0.032  Score=50.74  Aligned_cols=88  Identities=15%  Similarity=0.132  Sum_probs=48.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH--HHHHHHHHHhCCCCCCC-CCCCHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG--KIQESIAKKIGLYNESW-DNKSFDEKAQEIF  245 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~--~l~~~i~~~l~~~~~~~-~~~~~~~~~~~l~  245 (427)
                      ..+++|+|.+|+||||++..++..+.. .  -..+.++.... ....  ..+.......++..-.. ...++.++.....
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~-~--~~~v~l~~~d~-~~~~~~~ql~~~~~~~~l~~~~~~~~~~p~~l~~~~l  173 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKG-K--GRRPLLVAADT-QRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVE  173 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHH-T--TCCEEEEECCS-SCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH-c--CCeEEEecCCc-ccHhHHHHHHHhcccCCeEEEEcCCCCCHHHHHHHHH
Confidence            468999999999999999999887621 1  22344444332 2222  12334445555432110 1234555543333


Q ss_pred             HHh-cCCcEEEEEecc
Q 042645          246 KTM-RNRKIVLLLDDI  260 (427)
Q Consensus       246 ~~L-~~k~~LlVlDdv  260 (427)
                      ..+ ....=++|+|-.
T Consensus       174 ~~~~~~~~D~viiDtp  189 (295)
T 1ls1_A          174 EKARLEARDLILVDTA  189 (295)
T ss_dssp             HHHHHHTCCEEEEECC
T ss_pred             HHHHhCCCCEEEEeCC
Confidence            333 244557888976

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.62  E-value=0.0056  Score=52.17  Aligned_cols=24  Identities=38%  Similarity=0.470  Sum_probs=21.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|+|+.|+|||||++.+....
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            579999999999999999998755

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.61  E-value=0.012  Score=54.16  Aligned_cols=43  Identities=23%  Similarity=0.235  Sum_probs=30.8

Q ss_pred             ccchhhHHHHHHHhccC----CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          151 VGMQSTLDRVWRCLTEE----PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~~----~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|....+..+...+...    ...+|+|.|+.|+|||||++.+....
T Consensus        70 ~~~~~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl~~~L~~ll  116 (321)
T 3tqc_A           70 VTARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTTSRVLKALL  116 (321)
T ss_dssp             HHHHHHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hcchHHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            44445555555444332    34599999999999999999998766

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.61  E-value=0.0076  Score=53.48  Aligned_cols=26  Identities=19%  Similarity=0.309  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|++|+||||+|+.+...+
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~~l   46 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQLL   46 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999998865

>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=95.59  E-value=0.0078  Score=51.30  Aligned_cols=25  Identities=28%  Similarity=0.324  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|.|+.|+||||+++.+.+.+
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3579999999999999999998875

>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=95.58  E-value=0.0074  Score=51.64  Aligned_cols=22  Identities=45%  Similarity=0.536  Sum_probs=20.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      .+|+|.|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.56  E-value=0.0068  Score=52.27  Aligned_cols=23  Identities=35%  Similarity=0.488  Sum_probs=20.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|.|++|+||||+|+.+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998876

>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=95.55  E-value=0.0075  Score=52.23  Aligned_cols=25  Identities=28%  Similarity=0.313  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|.|++|+||||+++.+.+.+
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3579999999999999999999876

>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=95.54  E-value=0.048  Score=53.66  Aligned_cols=51  Identities=10%  Similarity=0.006  Sum_probs=35.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ...++.|.|.+|+||||||.+++.+...  .+-..++|++...  +..++...++
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~--~~g~~vl~~s~E~--s~~~l~~r~~  291 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGT--AMGKKVGLAMLEE--SVEETAEDLI  291 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTT--TSCCCEEEEESSS--CHHHHHHHHH
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHH--hcCCcEEEEeccC--CHHHHHHHHH
Confidence            4568999999999999999999887732  1123567776644  4556665554

>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=95.53  E-value=0.0075  Score=52.03  Aligned_cols=23  Identities=30%  Similarity=0.414  Sum_probs=20.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|.|++|+||||+|+.+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998776

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.51  E-value=0.045  Score=52.92  Aligned_cols=52  Identities=12%  Similarity=0.003  Sum_probs=36.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      ...++.|.|.+|+||||||..++......  .-..++|++..  .+..++...++.
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~--~g~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALK--EGVGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHT--TCCCEEEEESS--SCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEECC--CCHHHHHHHHHH
Confidence            45689999999999999999998776321  12356776654  345566666554

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.51  E-value=0.0082  Score=55.15  Aligned_cols=41  Identities=22%  Similarity=0.362  Sum_probs=29.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      ++.++|+|+|-||+||||.+..+.-.+.. .+  ..+.-+.+..
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~-~G--kkVllID~Dp   86 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSI-LG--KRVLQIGCDP   86 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHH-TT--CCEEEEEESS
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHH-CC--CeEEEEecCC
Confidence            46799999999999999999988877732 22  2355555543

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.48  E-value=0.0077  Score=52.24  Aligned_cols=25  Identities=24%  Similarity=0.178  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|.|++|+||||+++.+.+.+
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999999887

>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=95.47  E-value=0.0085  Score=49.46  Aligned_cols=26  Identities=23%  Similarity=0.295  Sum_probs=23.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++++|.|..|+|||||+..+...+
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l   28 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAA   28 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhh
Confidence            35789999999999999999998876

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.47  E-value=0.088  Score=51.45  Aligned_cols=26  Identities=23%  Similarity=0.452  Sum_probs=22.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|+|+|.+|+||||++..++..+
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l  125 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYY  125 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35689999999999999999998776

>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=95.46  E-value=0.0047  Score=53.15  Aligned_cols=23  Identities=30%  Similarity=0.768  Sum_probs=21.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +|+|.|+.|+||||+++.+...+
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l   24 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAF   24 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            68999999999999999998876

>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=95.42  E-value=0.0092  Score=51.19  Aligned_cols=26  Identities=27%  Similarity=0.351  Sum_probs=22.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34689999999999999999998765

>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=95.40  E-value=0.011  Score=48.30  Aligned_cols=27  Identities=37%  Similarity=0.333  Sum_probs=23.5

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+++|.|+.|+|||||++.++.-.
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            345689999999999999999998765

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.39  E-value=0.011  Score=52.30  Aligned_cols=26  Identities=23%  Similarity=0.310  Sum_probs=22.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|+.|+|||||++.+...+
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999998754

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.38  E-value=0.01  Score=52.72  Aligned_cols=26  Identities=27%  Similarity=0.418  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|+.|+||||+++.+.+.+
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhc
Confidence            34689999999999999999999765

>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=95.36  E-value=0.011  Score=54.36  Aligned_cols=26  Identities=27%  Similarity=0.296  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|+.|+|||||++.+..-.
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~gll  114 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQALL  114 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHhhc
Confidence            45799999999999999999998766

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.36  E-value=0.026  Score=56.91  Aligned_cols=43  Identities=21%  Similarity=0.316  Sum_probs=37.5

Q ss_pred             ccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.+..++.+...+..+  ..+.|+|++|+||||||+.++...
T Consensus        42 ~i~G~~~~l~~l~~~i~~g--~~vll~Gp~GtGKTtlar~ia~~l   84 (604)
T 3k1j_A           42 QVIGQEHAVEVIKTAANQK--RHVLLIGEPGTGKSMLGQAMAELL   84 (604)
T ss_dssp             HCCSCHHHHHHHHHHHHTT--CCEEEECCTTSSHHHHHHHHHHTS
T ss_pred             eEECchhhHhhccccccCC--CEEEEEeCCCCCHHHHHHHHhccC
Confidence            5799999888888877766  479999999999999999999876

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.35  E-value=0.0086  Score=51.87  Aligned_cols=26  Identities=35%  Similarity=0.531  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+....
T Consensus        22 ~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           22 NIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34679999999999999999998765

>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=95.31  E-value=0.011  Score=50.83  Aligned_cols=27  Identities=22%  Similarity=0.352  Sum_probs=23.8

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+|.|.|+.|+||||+++.+...+
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l   49 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQL   49 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            345789999999999999999998876

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=95.30  E-value=0.01  Score=50.29  Aligned_cols=26  Identities=27%  Similarity=0.489  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|+|+.|+||||+++.+.+.+
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHhc
Confidence            45689999999999999999998764

>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=95.30  E-value=0.011  Score=51.28  Aligned_cols=26  Identities=15%  Similarity=0.215  Sum_probs=23.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+....
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccC
Confidence            34689999999999999999998765

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.28  E-value=0.046  Score=61.72  Aligned_cols=88  Identities=19%  Similarity=0.157  Sum_probs=59.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ...++.|+|++|+||||||.+++.....   .-..++|++.....+..     .++.++......   ...+.+++...+
T Consensus       382 ~G~lilI~G~pGsGKTtLaLqia~~~a~---~G~~vlyis~E~s~~~~-----~a~~lGvd~~~L~I~~~~~~e~il~~~  453 (2050)
T 3cmu_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEIC  453 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEECTTSCCCHH-----HHHHTTCCTTTCEEECCSSHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHh---cCCeEEEEEcCCCHHHH-----HHHHcCCCHHHeEEeCCCCHHHHHHHH
Confidence            4579999999999999999999887732   22367888877766543     256666543221   234556666666


Q ss_pred             HHHh-cCCcEEEEEeccCCc
Q 042645          245 FKTM-RNRKIVLLLDDIWEL  263 (427)
Q Consensus       245 ~~~L-~~k~~LlVlDdv~~~  263 (427)
                      .... +.+.-+||+|.+...
T Consensus       454 ~~lv~~~~~~lIVIDSL~al  473 (2050)
T 3cmu_A          454 DALARSGAVDVIVVDSVAAL  473 (2050)
T ss_dssp             HHHHHHTCCSEEEESCGGGC
T ss_pred             HHHHHhcCCcEEEECCHHHh
Confidence            6544 346679999998643

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.26  E-value=0.035  Score=53.86  Aligned_cols=50  Identities=12%  Similarity=0.076  Sum_probs=34.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      ...++.|.|.+|+|||||+..++......  .-..++|++...  +..++...+
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~--~g~~Vl~~s~E~--s~~~l~~r~  251 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATK--TNENVAIFSLEM--SAQQLVMRM  251 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHH--SSCCEEEEESSS--CHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEEECCC--CHHHHHHHH
Confidence            44689999999999999999998776211  123567776543  344555544

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=95.21  E-value=0.012  Score=53.83  Aligned_cols=26  Identities=31%  Similarity=0.534  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|++|+|||||+..++..+
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            34689999999999999999998776

>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=95.21  E-value=0.013  Score=48.91  Aligned_cols=25  Identities=32%  Similarity=0.408  Sum_probs=22.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|+.|+||||+++.+...+
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l   29 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYL   29 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998865

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.15  E-value=0.059  Score=52.00  Aligned_cols=50  Identities=12%  Similarity=0.035  Sum_probs=34.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ...++.|.|.+|+||||||.+++.+... .  -..++|++...  +..++...++
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~-~--g~~vl~fSlEm--s~~ql~~R~~  245 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSD-N--DDVVNLHSLEM--GKKENIKRLI  245 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHH-T--TCEEEEECSSS--CTTHHHHHHH
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHH-c--CCEEEEEECCC--CHHHHHHHHH
Confidence            4568999999999999999999887632 2  23577776543  3344444443

>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=95.15  E-value=0.021  Score=55.49  Aligned_cols=40  Identities=25%  Similarity=0.372  Sum_probs=30.0

Q ss_pred             chhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          153 MQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       153 R~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+..+.+.+..++ +.+.|.|.+|+||||++..+...+
T Consensus        30 Q~~av~~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           30 QKNAFNIVMKAIKEKK-HHVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             HHHHHHHHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3344555555555544 489999999999999999998877

>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=95.12  E-value=0.024  Score=53.08  Aligned_cols=37  Identities=24%  Similarity=0.369  Sum_probs=29.0

Q ss_pred             HHHHHHHhc--cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          157 LDRVWRCLT--EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       157 ~~~l~~~l~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++.+.+.  .++..+|+|+|.+|+|||||+..+...+
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            444555554  3567899999999999999999998776

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.12  E-value=0.012  Score=50.88  Aligned_cols=24  Identities=29%  Similarity=0.315  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|.|.|++|+||||+++.+.+.+
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999876

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=95.11  E-value=0.012  Score=50.70  Aligned_cols=23  Identities=26%  Similarity=0.219  Sum_probs=21.0

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|.|++|+||||+++.+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998876

>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=95.10  E-value=0.037  Score=61.54  Aligned_cols=88  Identities=20%  Similarity=0.176  Sum_probs=59.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..+++.|+|++|+||||||.+++.....   .-..++|++.....+..     .++.++......   ...+.++....+
T Consensus       382 ~G~lilI~G~pGsGKTtLaLq~a~~~~~---~G~~vlyis~E~s~~~~-----~a~~lGvd~~~L~i~~~~~~e~~l~~l  453 (1706)
T 3cmw_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEIC  453 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH---TTCCEEEECTTSCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH---hCCCeEEEEccCchHHH-----HHHHcCCCHHHeEEcCCCCHHHHHHHH
Confidence            4578999999999999999999877632   23468888887766643     256666543221   233456666666


Q ss_pred             HHHhc-CCcEEEEEeccCCc
Q 042645          245 FKTMR-NRKIVLLLDDIWEL  263 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~~  263 (427)
                      ....+ .+.-+||+|.+...
T Consensus       454 ~~lv~~~~~~lVVIDSL~al  473 (1706)
T 3cmw_A          454 DALARSGAVDVIVVDSVAAL  473 (1706)
T ss_dssp             HHHHHHTCCSEEEESCSTTC
T ss_pred             HHHHHhcCCCEEEECCHHHh
Confidence            55443 46679999998654

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.10  E-value=0.028  Score=51.68  Aligned_cols=26  Identities=38%  Similarity=0.616  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|+|++|+||||++..++..+
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l  129 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYY  129 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35789999999999999999998877

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.07  E-value=0.012  Score=51.10  Aligned_cols=23  Identities=22%  Similarity=0.427  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+++.+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999998876

>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=95.06  E-value=0.026  Score=49.19  Aligned_cols=26  Identities=23%  Similarity=0.446  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|.|++|+||||+++.+.+.+
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l   50 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRL   50 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999999988

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.06  E-value=0.011  Score=49.85  Aligned_cols=24  Identities=42%  Similarity=0.480  Sum_probs=21.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+++|+|+.|+|||||++.++...
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhhc
Confidence            368999999999999999988765

>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=94.98  E-value=0.014  Score=50.97  Aligned_cols=24  Identities=29%  Similarity=0.357  Sum_probs=22.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|.|.|++|+||||+++.+.+.+
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999999887

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=94.97  E-value=0.016  Score=49.98  Aligned_cols=23  Identities=35%  Similarity=0.375  Sum_probs=20.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999976

>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=94.96  E-value=0.051  Score=52.67  Aligned_cols=26  Identities=31%  Similarity=0.540  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|..|+|||||++.++..+
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHh
Confidence            45699999999999999999998776

>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=94.96  E-value=0.014  Score=51.02  Aligned_cols=25  Identities=20%  Similarity=0.389  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|.|++|+||||+++.+...+
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999998876

>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=94.95  E-value=0.015  Score=48.32  Aligned_cols=25  Identities=28%  Similarity=0.527  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++++|.|+.|+|||||+..+...+
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            5789999999999999999998876

>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=94.94  E-value=0.014  Score=49.80  Aligned_cols=24  Identities=25%  Similarity=0.519  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|+|.|+.|+||||+++.+...+
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            3 GIVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            389999999999999999998876

>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=94.93  E-value=0.043  Score=61.07  Aligned_cols=87  Identities=20%  Similarity=0.161  Sum_probs=62.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..++|-|+|+.|+||||||.++....   +..-...+|+...+..++.-     ++.++++.+..   .....++....+
T Consensus      1430 rg~~iei~g~~~sGkttl~~~~~a~~---~~~g~~~~~i~~e~~~~~~~-----~~~~Gv~~~~l~~~~p~~~e~~l~~~ 1501 (1706)
T 3cmw_A         1430 MGRIVEIYGPESSGKTTLTLQVIAAA---QREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEIC 1501 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHH---HHTTCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHH---HhcCCeEEEEecCCCCCHHH-----HHHcCCCHHHeEEeCCCcHHHHHHHH
Confidence            45799999999999999999998765   33445678888877766552     77888765432   233446666666


Q ss_pred             HHHhc-CCcEEEEEeccCC
Q 042645          245 FKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~  262 (427)
                      ...++ +..-+||+|-|-.
T Consensus      1502 ~~~~~s~~~~~vvvDsv~a 1520 (1706)
T 3cmw_A         1502 DALARSGAVDVIVVDSVAA 1520 (1706)
T ss_dssp             HHHHHHTCCSEEEESCSTT
T ss_pred             HHHHHcCCCCEEEEccHHh
Confidence            66665 5667999998843

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=94.92  E-value=0.0091  Score=59.99  Aligned_cols=46  Identities=17%  Similarity=0.169  Sum_probs=33.7

Q ss_pred             CccccchhhHHHHHHHhccCCCe-----------EEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVG-----------IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~-----------vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.++|.+..+..+.-.+..+..+           -|.++|++|+|||+||+.+++..
T Consensus       295 ~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          295 PSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             STTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTC
T ss_pred             chhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhC
Confidence            44678877666665555444211           58999999999999999998765

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.91  E-value=0.015  Score=53.64  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=22.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|+|.|+.|+||||||..++..+
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l   31 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKF   31 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHc
Confidence            589999999999999999999876

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=94.89  E-value=0.018  Score=52.04  Aligned_cols=22  Identities=27%  Similarity=0.682  Sum_probs=20.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~  190 (427)
                      ..+|+|.|+.|+||||+|+.+.
T Consensus        75 ~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           75 LYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4689999999999999999998

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.89  E-value=0.013  Score=51.75  Aligned_cols=25  Identities=36%  Similarity=0.328  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|+.|+||||+++.+...+
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc
Confidence            3579999999999999999999876

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=94.88  E-value=0.01  Score=49.21  Aligned_cols=24  Identities=33%  Similarity=0.476  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++++|+|..|+|||||++.+..-+
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            579999999999999999998776

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.88  E-value=0.018  Score=52.74  Aligned_cols=26  Identities=23%  Similarity=0.235  Sum_probs=23.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|+.|+|||||++.+....
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~~l  104 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQALL  104 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            45699999999999999999998765

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.88  E-value=0.017  Score=52.67  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++|+|+.|+||||+++.++..+
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998776

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.87  E-value=0.01  Score=51.77  Aligned_cols=25  Identities=28%  Similarity=0.240  Sum_probs=16.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHH-hhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQIN-NSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~-~~~  193 (427)
                      ..+++|+|+.|+|||||++.+. ...
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            4689999999999999999998 544

>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=94.86  E-value=0.015  Score=50.91  Aligned_cols=26  Identities=31%  Similarity=0.363  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            44689999999999999999987654

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.85  E-value=0.016  Score=53.07  Aligned_cols=24  Identities=25%  Similarity=0.350  Sum_probs=22.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|.|+|+.|+|||||+..+++.+
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            589999999999999999999876

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.83  E-value=0.11  Score=50.29  Aligned_cols=97  Identities=13%  Similarity=0.121  Sum_probs=54.9

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHH-HHHHhhccCCCCCCc-EEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----C
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLL-TQINNSFLHTPNDFD-FVIWEVVSRDL-QLGKIQESIAKKIGLYNE----S  231 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~~f~-~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~  231 (427)
                      .++.|.. .....++|.|.+|+|||+|| ..+.+..     ..+ .++++-+++.. ...++...+...=.+...    .
T Consensus       152 aID~l~PigrGQR~~Ifg~~g~GKT~Lal~~I~~~~-----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~a  226 (502)
T 2qe7_A          152 AIDSMIPIGRGQRELIIGDRQTGKTTIAIDTIINQK-----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTA  226 (502)
T ss_dssp             HHHHSSCCBTTCBCEEEECSSSCHHHHHHHHHHGGG-----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEE
T ss_pred             ecccccccccCCEEEEECCCCCCchHHHHHHHHHhh-----cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEE
Confidence            3444432 34456899999999999995 5676664     234 34677777654 455666666543222110    0


Q ss_pred             CCCCCHHHHH------HHHHHHh--cCCcEEEEEeccC
Q 042645          232 WDNKSFDEKA------QEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       232 ~~~~~~~~~~------~~l~~~L--~~k~~LlVlDdv~  261 (427)
                      ....+.....      -.+-+++  +++.+||++||+-
T Consensus       227 tad~p~~~r~~a~~~a~tiAEyfrd~G~dVLl~~Dslt  264 (502)
T 2qe7_A          227 SASEPAPLLYLAPYAGCAMGEYFMYKGKHALVVYDDLS  264 (502)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEECHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEecHH
Confidence            0112211111      1223333  4799999999984

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.83  E-value=0.017  Score=50.85  Aligned_cols=26  Identities=27%  Similarity=0.337  Sum_probs=22.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .. .+++|+|+.|+|||||++.++.-.
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            35 789999999999999999998654

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.81  E-value=0.016  Score=50.40  Aligned_cols=26  Identities=31%  Similarity=0.331  Sum_probs=22.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34689999999999999999987644

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.79  E-value=0.019  Score=52.82  Aligned_cols=25  Identities=28%  Similarity=0.478  Sum_probs=22.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.|.|+.|+|||||+..+++.+
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTS
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHC
Confidence            4689999999999999999999876

>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=94.77  E-value=0.02  Score=52.07  Aligned_cols=25  Identities=24%  Similarity=0.341  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|+|.|+.|+|||||+..++..+
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhC
Confidence            3689999999999999999998775

>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=94.75  E-value=0.049  Score=46.86  Aligned_cols=25  Identities=28%  Similarity=0.256  Sum_probs=22.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|.|+.|+||||+++.+.+.+
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l   30 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERL   30 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3579999999999999999999887

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=94.71  E-value=0.035  Score=53.04  Aligned_cols=94  Identities=11%  Similarity=0.137  Sum_probs=53.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCc-EEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFD-FVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSFDEKA  241 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~-~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~~~  241 (427)
                      ....++|.|..|+|||+|+..+.+......++-+ .++++-+++.. ...++..++...=.+...    .....+.....
T Consensus       150 rGQr~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~  229 (465)
T 3vr4_D          150 RGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERI  229 (465)
T ss_dssp             TTCBCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHH
T ss_pred             cCCEEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHH
Confidence            3445889999999999999999887621112222 45666666543 456666665543111100    00112222111


Q ss_pred             ------HHHHHHh---cCCcEEEEEeccC
Q 042645          242 ------QEIFKTM---RNRKIVLLLDDIW  261 (427)
Q Consensus       242 ------~~l~~~L---~~k~~LlVlDdv~  261 (427)
                            -.+-+++   +++.+||++||+-
T Consensus       230 ~a~~~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          230 ATPRMALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence                  1233444   3789999999984

>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=94.70  E-value=0.012  Score=56.64  Aligned_cols=25  Identities=28%  Similarity=0.449  Sum_probs=22.3

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|+|+|.+|+||||++..++..+
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l  123 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYI  123 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999988776

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=94.69  E-value=0.095  Score=50.71  Aligned_cols=97  Identities=11%  Similarity=0.129  Sum_probs=54.4

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHH-HHHHhhccCCCCCCc-EEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----C
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLL-TQINNSFLHTPNDFD-FVIWEVVSRDL-QLGKIQESIAKKIGLYNE----S  231 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~~f~-~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~  231 (427)
                      .++.|.. .....++|.|.+|+|||+|| ..+.+..     ..+ .++++-+++.. ...++...+...=.+...    .
T Consensus       165 aID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~~~-----~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~a  239 (515)
T 2r9v_A          165 AIDSMIPIGRGQRELIIGDRQTGKTAIAIDTIINQK-----GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVA  239 (515)
T ss_dssp             HHHHHSCEETTCBEEEEEETTSSHHHHHHHHHHTTT-----TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEE
T ss_pred             ccccccccccCCEEEEEcCCCCCccHHHHHHHHHhh-----cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEE
Confidence            3444432 34456999999999999995 5676654     244 34677777654 455666666542111100    0


Q ss_pred             CCCCCHH-HH-----HHHHHHHh--cCCcEEEEEeccC
Q 042645          232 WDNKSFD-EK-----AQEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       232 ~~~~~~~-~~-----~~~l~~~L--~~k~~LlVlDdv~  261 (427)
                      ....+.. ..     .-.+-+++  +++.+||++||+-
T Consensus       240 tad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~DslT  277 (515)
T 2r9v_A          240 SASDPASLQYIAPYAGCAMGEYFAYSGRDALVVYDDLS  277 (515)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEeccHH
Confidence            0111211 11     11223333  4799999999984

>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=94.66  E-value=0.018  Score=50.47  Aligned_cols=26  Identities=27%  Similarity=0.468  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            44689999999999999999997654

>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=94.63  E-value=0.044  Score=47.90  Aligned_cols=25  Identities=20%  Similarity=0.460  Sum_probs=23.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|.|+.|+||||+++.+.+.+
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999887

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=94.61  E-value=0.019  Score=55.01  Aligned_cols=27  Identities=26%  Similarity=0.286  Sum_probs=23.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+|.|+|++|+||||+|+.+....
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            356789999999999999999998765

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.57  E-value=0.02  Score=51.12  Aligned_cols=26  Identities=31%  Similarity=0.423  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999987654

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.57  E-value=0.033  Score=49.57  Aligned_cols=27  Identities=22%  Similarity=0.436  Sum_probs=23.4

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+++|+|+.|+|||||++.+....
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhC
Confidence            455789999999999999999987755

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=94.56  E-value=0.048  Score=50.42  Aligned_cols=44  Identities=23%  Similarity=0.210  Sum_probs=30.6

Q ss_pred             hccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          164 LTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       164 l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      +.+...+++.+.|-||+||||+|..++..+..   .-..++-+....
T Consensus        11 l~~~~~~i~~~sgkGGvGKTt~a~~lA~~la~---~g~~vllid~D~   54 (334)
T 3iqw_A           11 LDQRSLRWIFVGGKGGVGKTTTSCSLAIQLAK---VRRSVLLLSTDP   54 (334)
T ss_dssp             HHCTTCCEEEEECSTTSSHHHHHHHHHHHHTT---SSSCEEEEECCS
T ss_pred             hcCCCeEEEEEeCCCCccHHHHHHHHHHHHHh---CCCcEEEEECCC
Confidence            33445678888999999999999999887732   223445555443

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=94.52  E-value=0.053  Score=46.61  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=22.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|.|.|+.|+||||+++.+.+.+
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999999887

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=94.51  E-value=0.04  Score=51.24  Aligned_cols=30  Identities=27%  Similarity=0.419  Sum_probs=25.0

Q ss_pred             hccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          164 LTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       164 l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..+..+++.+.|.||+||||+|..++..+
T Consensus        13 l~~~~~~i~~~~gkGGvGKTt~a~~lA~~l   42 (348)
T 3io3_A           13 VQHDSLKWIFVGGKGGVGKTTTSSSVAVQL   42 (348)
T ss_dssp             HTCTTCSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             hcCCCcEEEEEeCCCCCcHHHHHHHHHHHH
Confidence            334566899999999999999999888766

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.51  E-value=0.023  Score=53.07  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=22.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++|+|+.|+||||++..++..+
T Consensus       157 g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHHHHhhc
Confidence            4689999999999999999998776

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=94.51  E-value=0.027  Score=53.76  Aligned_cols=94  Identities=11%  Similarity=0.193  Sum_probs=52.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCC-------CCCc-EEEEEEeCCCC-CHHHHHHHHHHHhCCCC-----CCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTP-------NDFD-FVIWEVVSRDL-QLGKIQESIAKKIGLYN-----ESWD  233 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------~~f~-~~~wv~~~~~~-~~~~l~~~i~~~l~~~~-----~~~~  233 (427)
                      ....++|.|.+|+|||+|+..+++......       ++-+ .++++-+++.. ...++..++...=.+..     ...+
T Consensus       146 rGQr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~rtvvv~~t~d  225 (464)
T 3gqb_B          146 RGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKAD  225 (464)
T ss_dssp             TTCBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGGEEEEEEETT
T ss_pred             cCCEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccceEEEEECCC
Confidence            345688999999999999999988762110       1222 45666676543 45556665544210110     0011


Q ss_pred             CCCHHHHH-----HHHHHHh---cCCcEEEEEeccC
Q 042645          234 NKSFDEKA-----QEIFKTM---RNRKIVLLLDDIW  261 (427)
Q Consensus       234 ~~~~~~~~-----~~l~~~L---~~k~~LlVlDdv~  261 (427)
                      ........     -.+-+++   +++.+||++||+-
T Consensus       226 ~p~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlT  261 (464)
T 3gqb_B          226 DPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMT  261 (464)
T ss_dssp             SCTHHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence            12222211     1233444   3789999999984

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.50  E-value=0.015  Score=49.97  Aligned_cols=24  Identities=33%  Similarity=0.180  Sum_probs=21.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..+++|+|+.|+|||||++.++.-
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            357999999999999999998764

>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=94.49  E-value=0.024  Score=51.47  Aligned_cols=25  Identities=24%  Similarity=0.288  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.|.|+.|+||||||..+++.+
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhC
Confidence            4689999999999999999998876

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=94.49  E-value=0.022  Score=51.90  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=21.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|.|.|++|+||||+++.+.+..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~   26 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKN   26 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhC
Confidence            579999999999999999998753

>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=94.48  E-value=0.023  Score=47.84  Aligned_cols=24  Identities=38%  Similarity=0.441  Sum_probs=21.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|+|+|.+|+|||||++.+....
T Consensus        30 ~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           30 FKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            578999999999999999998764

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=94.46  E-value=0.023  Score=50.06  Aligned_cols=26  Identities=27%  Similarity=0.589  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999987644

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.46  E-value=0.022  Score=50.83  Aligned_cols=26  Identities=31%  Similarity=0.318  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            45689999999999999999987654

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.45  E-value=0.019  Score=51.55  Aligned_cols=26  Identities=31%  Similarity=0.524  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            34689999999999999999987644

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.42  E-value=0.022  Score=50.15  Aligned_cols=26  Identities=42%  Similarity=0.492  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34689999999999999999997654

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.42  E-value=0.019  Score=49.51  Aligned_cols=26  Identities=38%  Similarity=0.589  Sum_probs=22.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        34 ~Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           34 KGNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999997654

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.42  E-value=0.028  Score=49.40  Aligned_cols=25  Identities=20%  Similarity=0.371  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|.|..|+||||+++.+.+.+
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3579999999999999999999887

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.40  E-value=0.025  Score=50.56  Aligned_cols=25  Identities=28%  Similarity=0.493  Sum_probs=22.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...+++|+|+.|+|||||++.++.-
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999999874

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=94.40  E-value=0.2  Score=48.28  Aligned_cols=98  Identities=14%  Similarity=0.113  Sum_probs=54.5

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHH-HHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CC
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLL-TQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SW  232 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~  232 (427)
                      .++.|.. .....++|.|..|+|||+|+ ..+.+..    ..-..++++-+++.. ...++...+...=.+...    ..
T Consensus       152 aID~l~PigrGQR~~Ifg~~g~GKT~l~l~~I~n~~----~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~at  227 (513)
T 3oaa_A          152 AVDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQR----DSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVAT  227 (513)
T ss_dssp             HHHHHSCCBTTCBCEEEESSSSSHHHHHHHHHHTTS----SSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEEC
T ss_pred             eeccccccccCCEEEeecCCCCCcchHHHHHHHhhc----cCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEEC
Confidence            3444432 34456899999999999996 5666643    222245778887654 455666665543212110    00


Q ss_pred             CCCCHHHH-H-----HHHHHHh--cCCcEEEEEeccC
Q 042645          233 DNKSFDEK-A-----QEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       233 ~~~~~~~~-~-----~~l~~~L--~~k~~LlVlDdv~  261 (427)
                      ...+.... .     -.+-+++  +++.+||++||+-
T Consensus       228 ad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dslt  264 (513)
T 3oaa_A          228 ASESAALQYLAPYAGCAMGEYFRDRGEDALIIYDDLS  264 (513)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEEEETHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHhcCCCEEEEecChH
Confidence            11121111 1     1122333  5899999999984

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.40  E-value=0.024  Score=50.13  Aligned_cols=25  Identities=28%  Similarity=0.361  Sum_probs=22.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...+++|+|+.|+|||||++.++.-
T Consensus        28 ~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999999874

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=94.39  E-value=0.027  Score=47.95  Aligned_cols=39  Identities=21%  Similarity=0.129  Sum_probs=21.6

Q ss_pred             hhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          155 STLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       155 ~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+.+.+.....+.-.|+|+|.+|+|||||+..+.+..
T Consensus        16 ~~~~~m~~~~~~~~~~ki~vvG~~~~GKSsLi~~l~~~~   54 (204)
T 4gzl_A           16 PRGSHMENLYFQGQAIKCVVVGDGAVGKTCLLISYTTNA   54 (204)
T ss_dssp             --------------CEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             cchhHHHhHhhcCCeEEEEEECcCCCCHHHHHHHHHhCC
Confidence            333334343334455678999999999999999888653

>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=94.37  E-value=0.039  Score=53.96  Aligned_cols=45  Identities=9%  Similarity=-0.033  Sum_probs=33.8

Q ss_pred             ccccchhhHHHHHHHh--ccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCL--TEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l--~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+.|.+..+.+.+..  ......+|.+.|+.|+||||+++.+.+.+
T Consensus       373 ~~f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L  419 (511)
T 1g8f_A          373 EWFSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTF  419 (511)
T ss_dssp             TTTSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHH
T ss_pred             ccccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHH
Confidence            3455655555555554  22355789999999999999999999998

>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=94.37  E-value=0.026  Score=51.43  Aligned_cols=27  Identities=15%  Similarity=0.216  Sum_probs=23.3

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+++|+|+.|+|||||++.+..-.
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            455789999999999999999988654

>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=94.36  E-value=0.024  Score=50.39  Aligned_cols=26  Identities=42%  Similarity=0.519  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.++.-.
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            44689999999999999999997654

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.36  E-value=0.021  Score=50.83  Aligned_cols=26  Identities=27%  Similarity=0.397  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34689999999999999999987654

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.36  E-value=0.023  Score=49.59  Aligned_cols=26  Identities=31%  Similarity=0.449  Sum_probs=22.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34689999999999999999998765

>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=94.34  E-value=0.023  Score=50.84  Aligned_cols=26  Identities=31%  Similarity=0.512  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            45689999999999999999997654

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.33  E-value=0.029  Score=45.33  Aligned_cols=24  Identities=25%  Similarity=0.331  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|+|+|.+|+|||||+..+.+..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            468999999999999999998654

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.32  E-value=0.012  Score=53.43  Aligned_cols=26  Identities=23%  Similarity=0.446  Sum_probs=20.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..+|+|.|+.|+||||+|+.+.+.+
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~l   29 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIF   29 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHH
Confidence            35689999999999999999998765

>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=94.30  E-value=0.024  Score=51.04  Aligned_cols=26  Identities=27%  Similarity=0.369  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++.|+|++|+|||||+..++...
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999988655

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.30  E-value=0.025  Score=50.41  Aligned_cols=26  Identities=23%  Similarity=0.341  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccC
Confidence            44689999999999999999997654

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=94.30  E-value=0.027  Score=49.97  Aligned_cols=26  Identities=35%  Similarity=0.422  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++.+.|.||+||||++..+...+
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l   38 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYL   38 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            35788999999999999999998777

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.28  E-value=0.024  Score=50.08  Aligned_cols=26  Identities=31%  Similarity=0.557  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34689999999999999999987654

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.27  E-value=0.025  Score=50.70  Aligned_cols=26  Identities=31%  Similarity=0.560  Sum_probs=22.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999997654

>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=94.22  E-value=0.029  Score=45.89  Aligned_cols=23  Identities=26%  Similarity=0.430  Sum_probs=20.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..|+|+|.+|+|||||...+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999864

>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=94.21  E-value=0.025  Score=47.92  Aligned_cols=24  Identities=38%  Similarity=0.441  Sum_probs=21.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|+|+|.+|+|||||...+....
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECcCCCCHHHHHHHHhcCC
Confidence            468999999999999999998763

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=94.21  E-value=0.028  Score=47.44  Aligned_cols=25  Identities=24%  Similarity=0.092  Sum_probs=22.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|.|.|+.|+||||||..+....
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhC
Confidence            4679999999999999999998765

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=94.19  E-value=0.027  Score=50.38  Aligned_cols=26  Identities=27%  Similarity=0.286  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            44689999999999999999987654

>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=94.19  E-value=0.053  Score=48.14  Aligned_cols=37  Identities=19%  Similarity=0.254  Sum_probs=28.2

Q ss_pred             HHHHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          157 LDRVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       157 ~~~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-+..++...  ....+.++|++|.|||.+|..+++..
T Consensus        90 ~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A           90 ASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhh
Confidence            34455666543  24579999999999999999998864

>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=94.17  E-value=0.022  Score=47.56  Aligned_cols=22  Identities=41%  Similarity=0.534  Sum_probs=19.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.+|+|||||+..+...
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            4889999999999999999764

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=94.16  E-value=0.081  Score=50.47  Aligned_cols=28  Identities=32%  Similarity=0.417  Sum_probs=24.4

Q ss_pred             cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          166 EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       166 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .....+++|.|+.|+|||||++.+....
T Consensus       164 ~~~ggii~I~GpnGSGKTTlL~allg~l  191 (418)
T 1p9r_A          164 KRPHGIILVTGPTGSGKSTTLYAGLQEL  191 (418)
T ss_dssp             TSSSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             HhcCCeEEEECCCCCCHHHHHHHHHhhc
Confidence            4556799999999999999999998776

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=94.16  E-value=0.048  Score=47.08  Aligned_cols=24  Identities=33%  Similarity=0.167  Sum_probs=21.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|.+.|.||+||||++..++...
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l   30 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQ   30 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHH
Confidence            358889999999999999888877

>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=94.15  E-value=0.027  Score=49.83  Aligned_cols=26  Identities=35%  Similarity=0.484  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        25 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34689999999999999999987654

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.13  E-value=0.031  Score=48.89  Aligned_cols=26  Identities=23%  Similarity=0.326  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|.|+.|+||||+++.+...+
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            45689999999999999999998765

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=94.13  E-value=0.05  Score=52.65  Aligned_cols=87  Identities=15%  Similarity=0.198  Sum_probs=49.1

Q ss_pred             CCeEEEEEecCCCcHHHHH-HHHHhhccCCCCCCc-EEEEEEeCCCC-CHHHHHHHHHHHhCCCC-----CCCCCCCH--
Q 042645          168 PVGIVGLYGMGGVGKTTLL-TQINNSFLHTPNDFD-FVIWEVVSRDL-QLGKIQESIAKKIGLYN-----ESWDNKSF--  237 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~~f~-~~~wv~~~~~~-~~~~l~~~i~~~l~~~~-----~~~~~~~~--  237 (427)
                      ....++|.|.+|+|||+|| ..+.+..   .  .+ .++++-+++.. ...++...+...=.+..     ...+....  
T Consensus       162 rGQR~~Ifg~~g~GKT~Lal~~I~~~~---~--~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r  236 (507)
T 1fx0_A          162 RGQRELIIGDRQTGKTAVATDTILNQQ---G--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQ  236 (507)
T ss_dssp             TTCBCBEEESSSSSHHHHHHHHHHTCC---T--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGT
T ss_pred             cCCEEEEecCCCCCccHHHHHHHHHhh---c--CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHH
Confidence            3456899999999999995 5676654   1  34 45677777654 34455555543211110     00011111  


Q ss_pred             ---H----HHHHHHHHHhcCCcEEEEEeccC
Q 042645          238 ---D----EKAQEIFKTMRNRKIVLLLDDIW  261 (427)
Q Consensus       238 ---~----~~~~~l~~~L~~k~~LlVlDdv~  261 (427)
                         .    ...+.++.  +++.+||++||+-
T Consensus       237 ~~a~~~a~tiAEyfrd--~G~dVLli~Dslt  265 (507)
T 1fx0_A          237 YLAPYTGAALAEYFMY--RERHTLIIYDDLS  265 (507)
T ss_dssp             THHHHHHHHHHHHHHH--TTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHH--cCCcEEEEEecHH
Confidence               1    12233333  5899999999974

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=94.11  E-value=0.13  Score=50.19  Aligned_cols=57  Identities=21%  Similarity=0.212  Sum_probs=40.0

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCC-HHHHHHHH
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ-LGKIQESI  221 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~-~~~l~~~i  221 (427)
                      .++.|.. .....++|.|..|+|||+|+..+.+..     +-+.++++-+++... ..+++.++
T Consensus       217 vID~l~PigkGqr~~I~g~~g~GKT~L~~~ia~~~-----~~~~~V~~~iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          217 VIDTFFPQAKGGTAAIPGPAGSGKTVTQHQLAKWS-----DAQVVIYIGCGERGNEMTDVLEEF  275 (588)
T ss_dssp             HHHHHSCEETTCEEEECSCCSHHHHHHHHHHHHHS-----SCSEEEEEECCSSSSHHHHHHHHT
T ss_pred             hhhccCCcccCCeEEeecCCCCCHHHHHHHHHhcc-----CCCEEEEEEecccHHHHHHHHHHH
Confidence            4455543 345679999999999999999988764     234778888877654 44555554

>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=94.10  E-value=0.029  Score=45.34  Aligned_cols=23  Identities=35%  Similarity=0.548  Sum_probs=20.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.++|.+|+|||||+..+....
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            48899999999999999997654

>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=94.09  E-value=0.031  Score=52.57  Aligned_cols=27  Identities=22%  Similarity=0.039  Sum_probs=23.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+++|+|++|+|||||++.+....
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            455699999999999999999998765

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.09  E-value=0.055  Score=45.88  Aligned_cols=50  Identities=18%  Similarity=0.208  Sum_probs=31.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAK  223 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~  223 (427)
                      .|+|-|.-|+||||.++.+.+.+..   ....++...-.......+..+.++.
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~---~g~~v~~treP~~t~~~~~ir~~l~   51 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEK---RGKKVILKREPGGTETGEKIRKILL   51 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH---TTCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH---CCCcEEEEECCCCCcHHHHHHHHhh
Confidence            4788899999999999999988832   2223333333333334445555443

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=94.07  E-value=0.028  Score=49.85  Aligned_cols=26  Identities=31%  Similarity=0.455  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           30 KGDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34689999999999999999998654

>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=94.05  E-value=0.066  Score=44.60  Aligned_cols=34  Identities=35%  Similarity=0.567  Sum_probs=26.0

Q ss_pred             HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          158 DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       158 ~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..+.+ +.......|+|+|.+|+|||||...+.+.
T Consensus         6 ~~~~~-~~~~~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A            6 TRIWR-LFNHQEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             HHHHH-HHTTSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHH-hcCCCccEEEEECCCCCCHHHHHHHHhcC
Confidence            34555 33445568999999999999999999854

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.03  E-value=0.026  Score=50.81  Aligned_cols=26  Identities=42%  Similarity=0.478  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        46 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           46 KGDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            44689999999999999999997654

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=94.03  E-value=0.031  Score=50.07  Aligned_cols=23  Identities=30%  Similarity=0.466  Sum_probs=20.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|+|+.|+|||||.+.++...
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            58999999999999999998754

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=93.92  E-value=0.032  Score=45.37  Aligned_cols=24  Identities=21%  Similarity=0.375  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcCC
Confidence            458899999999999999998754

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=93.88  E-value=0.028  Score=48.97  Aligned_cols=25  Identities=32%  Similarity=0.243  Sum_probs=21.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...+|+|.|+.|+|||||++.+...
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc
Confidence            4468999999999999999998765

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.87  E-value=0.064  Score=47.78  Aligned_cols=37  Identities=22%  Similarity=0.355  Sum_probs=27.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      ++|+|.|-||+||||++..++..+. ..  -..++-+...
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la-~~--G~~VlliD~D   38 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLH-AM--GKTIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHH-TT--TCCEEEEEEC
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHH-HC--CCcEEEEcCC
Confidence            5788899999999999999988873 22  2245555554

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=93.85  E-value=0.044  Score=45.54  Aligned_cols=25  Identities=36%  Similarity=0.456  Sum_probs=21.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ....|+|+|.+|+|||||...+.+.
T Consensus        15 ~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           15 QEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhcC
Confidence            4567999999999999999998764

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.84  E-value=0.05  Score=53.87  Aligned_cols=26  Identities=27%  Similarity=0.331  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+...+
T Consensus       368 ~G~iI~LiG~sGSGKSTLar~La~~L  393 (552)
T 3cr8_A          368 QGFTVFFTGLSGAGKSTLARALAARL  393 (552)
T ss_dssp             SCEEEEEEESSCHHHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCChHHHHHHHHHHhh
Confidence            45789999999999999999999887

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.83  E-value=0.039  Score=45.96  Aligned_cols=23  Identities=26%  Similarity=0.430  Sum_probs=20.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..|+|+|.+|+|||||...+...
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            46999999999999999999874

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=93.79  E-value=0.17  Score=49.05  Aligned_cols=102  Identities=11%  Similarity=0.114  Sum_probs=55.8

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHH-HHHHhhccC---CCCCCc-EEEEEEeCCCC-CHHHHHHHHHHHhCCCCC--
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLL-TQINNSFLH---TPNDFD-FVIWEVVSRDL-QLGKIQESIAKKIGLYNE--  230 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~---~~~~f~-~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~--  230 (427)
                      .++.|.. .....++|.|.+|+|||+|| ..+.+....   ...+.+ .++++-+++.. ...++.+.+...=.+...  
T Consensus       152 aID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvv  231 (510)
T 2ck3_A          152 AVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIV  231 (510)
T ss_dssp             HHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEE
T ss_pred             eeccccccccCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceE
Confidence            3444432 34456899999999999994 566666520   012334 46777777654 455666666542211100  


Q ss_pred             --CCCCCCHHHHH------HHHHHHh--cCCcEEEEEeccC
Q 042645          231 --SWDNKSFDEKA------QEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       231 --~~~~~~~~~~~------~~l~~~L--~~k~~LlVlDdv~  261 (427)
                        .....+.....      -.+-+++  +++.+||++||+-
T Consensus       232 V~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dslt  272 (510)
T 2ck3_A          232 VSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLS  272 (510)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHH
Confidence              00111211111      1223333  4799999999984

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.79  E-value=0.034  Score=46.04  Aligned_cols=25  Identities=28%  Similarity=0.417  Sum_probs=21.5

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHh
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      .....|+|+|.+|+|||||...+..
T Consensus        16 ~~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           16 NKELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            4556799999999999999998864

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=93.78  E-value=0.12  Score=49.59  Aligned_cols=102  Identities=11%  Similarity=0.076  Sum_probs=57.5

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCC-CCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CC
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPN-DFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SW  232 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~  232 (427)
                      .++.|.. .....++|.|.+|+|||+|+..++++....+. .-+.++++-+++.. ...++..++...=.+...    ..
T Consensus       142 ~ID~l~pigrGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~t  221 (469)
T 2c61_A          142 TIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNL  221 (469)
T ss_dssp             HHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEE
T ss_pred             eeeeeeccccCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEEC
Confidence            3444432 23456888999999999999999988632111 11356677776543 456666666654211110    00


Q ss_pred             CCCCHHHH------HHHHHHHh---cCCcEEEEEeccC
Q 042645          233 DNKSFDEK------AQEIFKTM---RNRKIVLLLDDIW  261 (427)
Q Consensus       233 ~~~~~~~~------~~~l~~~L---~~k~~LlVlDdv~  261 (427)
                      ...+....      .-.+-+++   +++.+||++||+-
T Consensus       222 sd~p~~~r~~~~~~a~tiAEyfrdd~G~dVLl~~Dslt  259 (469)
T 2c61_A          222 ADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDIT  259 (469)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEeCHH
Confidence            11222111      11233344   3799999999973

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=93.78  E-value=0.025  Score=50.44  Aligned_cols=26  Identities=15%  Similarity=0.267  Sum_probs=23.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|.|..|+||||+++.+.+.+
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l   48 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLC   48 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhc
Confidence            45789999999999999999998876

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=93.75  E-value=0.034  Score=45.62  Aligned_cols=24  Identities=38%  Similarity=0.346  Sum_probs=20.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~~   28 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGKQ   28 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC-
T ss_pred             EEEEEECCCCccHHHHHHHHhcCC
Confidence            468999999999999999987654

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.73  E-value=0.072  Score=49.61  Aligned_cols=26  Identities=31%  Similarity=0.401  Sum_probs=22.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..+|+|+|.+|+|||||...+....
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            46799999999999999999998654

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.73  E-value=0.045  Score=45.86  Aligned_cols=26  Identities=27%  Similarity=0.232  Sum_probs=22.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|+|.+|+|||||+..+....
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999998764

>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=93.72  E-value=0.041  Score=51.85  Aligned_cols=24  Identities=33%  Similarity=0.596  Sum_probs=22.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|+|.|+.|+|||||+..++..+
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHHC
Confidence            589999999999999999998876

>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=93.69  E-value=0.17  Score=59.07  Aligned_cols=136  Identities=13%  Similarity=0.027  Sum_probs=73.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCC-CCHHHHHHHHHHHh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDN-KSFDEKAQEIFKTM  248 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~-~~~~~~~~~l~~~L  248 (427)
                      +-+.++|++|+|||++|+.+....    ..+ ....++++...+...+...+-..+......... ..+         .-
T Consensus      1268 ~~vLL~GPpGtGKT~la~~~l~~~----~~~-~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P---------~~ 1333 (2695)
T 4akg_A         1268 RGIILCGPPGSGKTMIMNNALRNS----SLY-DVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLP---------KS 1333 (2695)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC----SSC-EEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEE---------BS
T ss_pred             CeEEEECCCCCCHHHHHHHHHhcC----CCC-ceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccC---------CC
Confidence            468899999999999998776654    122 345677777777777666666554321100000 000         00


Q ss_pred             cCCcEEEEEeccCCc--cc------ccccccCCCC-----CC-------CCcEEEEecCChh------H-HhhcCCCcce
Q 042645          249 RNRKIVLLLDDIWEL--FD------LAQVGLPVPS-----RA-------SASKVVFTTREFE------V-CGLMDAHKSF  301 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~--~~------~~~~~~~l~~-----~~-------~gs~IivTtR~~~------v-~~~~~~~~~~  301 (427)
                      .+++++|.+||+.-.  +.      .+-++..+..     ..       .+..+|.++....      + .........+
T Consensus      1334 ~gk~~VlFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~vi 1413 (2695)
T 4akg_A         1334 DIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAIL 1413 (2695)
T ss_dssp             SSSCEEEEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEEE
T ss_pred             CCceEEEEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeEE
Confidence            367899999996421  11      1111111110     01       1233444443321      1 1111222567


Q ss_pred             eccCCChHHHHHHHHHHh
Q 042645          302 KVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       302 ~l~~L~~~e~~~lf~~~~  319 (427)
                      .++..+.++-..+|....
T Consensus      1414 ~i~~P~~~~l~~I~~~il 1431 (2695)
T 4akg_A         1414 YLGYPSGKSLSQIYEIYY 1431 (2695)
T ss_dssp             ECCCCTTTHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHH
Confidence            889999999888888765

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.65  E-value=0.048  Score=44.86  Aligned_cols=26  Identities=38%  Similarity=0.396  Sum_probs=22.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|+|.+|+|||||+..+.+..
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~~   32 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHSK   32 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            45679999999999999999997643

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=93.65  E-value=0.04  Score=49.87  Aligned_cols=26  Identities=31%  Similarity=0.449  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus        63 ~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            45689999999999999999997654

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=93.65  E-value=0.038  Score=44.76  Aligned_cols=24  Identities=38%  Similarity=0.403  Sum_probs=20.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .-|+|+|.+|+|||||+..+....
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            358899999999999999998654

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.64  E-value=0.034  Score=49.53  Aligned_cols=24  Identities=42%  Similarity=0.436  Sum_probs=21.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl   53 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGL   53 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999998754

>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=93.64  E-value=0.044  Score=51.07  Aligned_cols=26  Identities=38%  Similarity=0.456  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        29 ~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           29 PGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            44689999999999999999998644

>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=93.61  E-value=0.04  Score=45.40  Aligned_cols=24  Identities=25%  Similarity=0.263  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|+|.+|+|||||...+....
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~~   28 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGRE   28 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            468899999999999999998653

>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=93.61  E-value=0.038  Score=46.14  Aligned_cols=24  Identities=33%  Similarity=0.470  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|+|+|.+|+|||||+..+....
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            368899999999999999998654

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.55  E-value=0.051  Score=47.01  Aligned_cols=27  Identities=22%  Similarity=0.288  Sum_probs=24.2

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .....|.|.|+.|+||||+++.+.+.+
T Consensus        19 ~~~~~i~~~G~~g~GKst~~~~l~~~l   45 (223)
T 3ld9_A           19 PGSMFITFEGIDGSGKTTQSHLLAEYL   45 (223)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            456789999999999999999999887

>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=93.54  E-value=0.05  Score=45.59  Aligned_cols=25  Identities=24%  Similarity=0.432  Sum_probs=21.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +...|+|+|.+|+|||||...+.+.
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4467999999999999999999765

>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=93.54  E-value=0.061  Score=54.20  Aligned_cols=25  Identities=28%  Similarity=0.344  Sum_probs=21.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.+.|.|.+|+||||++..+...+
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHH
Confidence            4689999999999999988877655

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=93.54  E-value=0.041  Score=44.53  Aligned_cols=23  Identities=39%  Similarity=0.528  Sum_probs=20.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||+..+....
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            58899999999999999987653

>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=93.53  E-value=0.25  Score=43.04  Aligned_cols=22  Identities=23%  Similarity=0.128  Sum_probs=19.5

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|+|+.|.|||.+|..+....
T Consensus       111 ~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A          111 GCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHc
Confidence            7889999999999998887664

>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=93.53  E-value=0.06  Score=51.23  Aligned_cols=25  Identities=24%  Similarity=0.392  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...+++|+|+.|+|||||.+.+...
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhCC
Confidence            4569999999999999999999873

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=93.53  E-value=0.06  Score=45.52  Aligned_cols=25  Identities=32%  Similarity=0.563  Sum_probs=21.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +...|+|+|.+|+|||||+..+.+.
T Consensus        24 ~~~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           24 KTGKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            3456899999999999999998653

>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=93.52  E-value=0.05  Score=46.65  Aligned_cols=26  Identities=27%  Similarity=0.232  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|.|+|.+|+|||||+..+.+..
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45679999999999999999998764

>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=93.51  E-value=0.049  Score=45.28  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=21.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.+|+|+.|+|||||+..++--+
T Consensus        27 g~~~i~G~NGsGKStll~ai~~~l   50 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILFVL   50 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHH
Confidence            489999999999999999987654

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=93.51  E-value=0.041  Score=44.80  Aligned_cols=24  Identities=38%  Similarity=0.351  Sum_probs=20.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            368899999999999999988653

>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=93.50  E-value=0.043  Score=45.67  Aligned_cols=24  Identities=25%  Similarity=0.275  Sum_probs=20.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus         8 ~ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            8 CKIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            458899999999999999998753

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.49  E-value=0.042  Score=44.66  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=20.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||+..+.+..
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            48899999999999999987654

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=93.49  E-value=0.042  Score=44.56  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=20.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||...+.+..
T Consensus         5 ki~v~G~~~~GKssli~~l~~~~   27 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58899999999999999998653

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.48  E-value=0.042  Score=44.71  Aligned_cols=23  Identities=30%  Similarity=0.430  Sum_probs=20.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||+..+.+..
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            58899999999999999998764

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.46  E-value=0.051  Score=47.21  Aligned_cols=25  Identities=28%  Similarity=0.417  Sum_probs=19.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|.|+.|+||||+++.+.+.+
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4579999999999999999999887

>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=93.46  E-value=0.035  Score=45.11  Aligned_cols=22  Identities=36%  Similarity=0.434  Sum_probs=19.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.+|+|||||+..+.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCc
Confidence            4789999999999999998654

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.46  E-value=0.043  Score=44.72  Aligned_cols=22  Identities=36%  Similarity=0.753  Sum_probs=19.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.+|+|||||+..+...
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            5889999999999999999864

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=93.43  E-value=0.033  Score=50.79  Aligned_cols=26  Identities=31%  Similarity=0.517  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-+
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcCC
Confidence            45689999999999999999987654

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.40  E-value=0.055  Score=45.18  Aligned_cols=25  Identities=36%  Similarity=0.497  Sum_probs=21.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||+..+....
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           23 KGEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             TCEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHcCc
Confidence            3578999999999999999998764

>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=93.40  E-value=0.045  Score=44.30  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=19.5

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+|+|.+|+|||||+..+....
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            7899999999999999987653

>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=93.39  E-value=0.046  Score=44.47  Aligned_cols=24  Identities=33%  Similarity=0.384  Sum_probs=20.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVEDK   27 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            358899999999999999987653

>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=93.39  E-value=0.043  Score=44.73  Aligned_cols=21  Identities=43%  Similarity=0.525  Sum_probs=18.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHh
Q 042645          171 IVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      -|+|+|.+|+|||||+..+..
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            588999999999999999864

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.39  E-value=0.044  Score=45.17  Aligned_cols=25  Identities=36%  Similarity=0.430  Sum_probs=21.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||+..+....
T Consensus         8 ~~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            8 ILKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCc
Confidence            4568999999999999999987654

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=93.38  E-value=0.042  Score=47.66  Aligned_cols=24  Identities=33%  Similarity=0.356  Sum_probs=21.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.|++|+||||+|+.+.+.+
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceeeECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999998876

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=93.38  E-value=0.089  Score=46.11  Aligned_cols=39  Identities=26%  Similarity=0.253  Sum_probs=28.2

Q ss_pred             EEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCC
Q 042645          172 VGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ  213 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~  213 (427)
                      |+|.|-||+||||+|..++..+. ..+  ..++-+......+
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la-~~g--~~VlliD~D~~~~   41 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMA-SDY--DKIYAVDGDPDSC   41 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHT-TTC--SCEEEEEECTTSC
T ss_pred             EEEecCCCCCHHHHHHHHHHHHH-HCC--CeEEEEeCCCCcC
Confidence            66699999999999999998883 222  3466666654444

>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=93.36  E-value=0.045  Score=45.69  Aligned_cols=24  Identities=25%  Similarity=0.259  Sum_probs=20.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        21 ~ki~ivG~~~vGKSsL~~~~~~~~   44 (184)
T 3ihw_A           21 LKVGIVGNLSSGKSALVHRYLTGT   44 (184)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            468899999999999998877653

>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=93.36  E-value=0.047  Score=44.98  Aligned_cols=25  Identities=36%  Similarity=0.511  Sum_probs=21.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-|+|+|.+|+|||||+..+.+..
T Consensus         9 ~~~i~v~G~~~~GKssli~~l~~~~   33 (181)
T 2fn4_A            9 THKLVVVGGGGVGKSALTIQFIQSY   33 (181)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCc
Confidence            3568999999999999999988763

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=93.35  E-value=0.045  Score=44.96  Aligned_cols=24  Identities=38%  Similarity=0.454  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .-|+|+|.+|+|||||...+....
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~~   31 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTNK   31 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999997653

>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=93.35  E-value=0.039  Score=50.75  Aligned_cols=26  Identities=46%  Similarity=0.625  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++++|.|+.|+|||||++.+....
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhhc
Confidence            35799999999999999999998653

>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=93.34  E-value=0.15  Score=43.45  Aligned_cols=24  Identities=25%  Similarity=0.530  Sum_probs=22.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|-|..|+||||+++.+.+.+
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L   26 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRL   26 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHH
Confidence            468899999999999999999988

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.32  E-value=0.05  Score=44.74  Aligned_cols=24  Identities=29%  Similarity=0.290  Sum_probs=20.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~~~   30 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQET   30 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHGGG
T ss_pred             EEEEEECcCCCCHHHHHHHHHhCc
Confidence            358899999999999999987653

>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=93.28  E-value=0.052  Score=50.62  Aligned_cols=26  Identities=35%  Similarity=0.456  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        53 ~Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           53 AGQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHhcCC
Confidence            45689999999999999999987644

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=93.28  E-value=0.046  Score=45.51  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=20.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||+..+.+..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGKK   25 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCcC
Confidence            47899999999999999988654

>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=93.26  E-value=0.053  Score=50.58  Aligned_cols=26  Identities=35%  Similarity=0.471  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           28 DGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            44689999999999999999998644

>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=93.25  E-value=0.07  Score=46.13  Aligned_cols=108  Identities=15%  Similarity=0.043  Sum_probs=51.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTM  248 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L  248 (427)
                      ..+..++|.-|.||||-+.....+.. . ... .++.+....+..  .- ..+.+.++.........+..++.+    ..
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~-~-~g~-kvli~kp~~D~R--yg-~~i~sr~G~~~~a~~i~~~~di~~----~~   88 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQ-I-AQY-KCLVIKYAKDTR--YS-SSFCTHDRNTMEALPACLLRDVAQ----EA   88 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHH-T-TTC-CEEEEEETTCCC--C------------CEEEEESSGGGGHH----HH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHH-H-CCC-eEEEEeecCCcc--ch-HHHHhhcCCeeEEEecCCHHHHHH----Hh
Confidence            46899999999999988777666652 1 222 333333322211  11 234444444322111112222222    22


Q ss_pred             cCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCCh
Q 042645          249 RNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREF  289 (427)
Q Consensus       249 ~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~  289 (427)
                       ++--+|++|++.-.....++...+.+  .|..||+|.++.
T Consensus        89 -~~~dvViIDEaQF~~~v~el~~~l~~--~gi~VI~~GL~~  126 (234)
T 2orv_A           89 -LGVAVIGIDEGQFFPDIVEFCEAMAN--AGKTVIVAALDG  126 (234)
T ss_dssp             -TTCSEEEESSGGGCTTHHHHHHHHHH--TTCEEEEECCSB
T ss_pred             -ccCCEEEEEchhhhhhHHHHHHHHHh--CCCEEEEEeccc
Confidence             23339999998643333333323322  467899999983

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.22  E-value=0.048  Score=50.78  Aligned_cols=26  Identities=42%  Similarity=0.514  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        40 ~Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           40 EGEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34689999999999999999998654

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=93.22  E-value=0.045  Score=47.11  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=21.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|+|.|+.|+||||+++.+...+
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            479999999999999999998765

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=93.22  E-value=0.058  Score=49.99  Aligned_cols=27  Identities=30%  Similarity=0.471  Sum_probs=23.4

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+++|+|++|+|||||...+....
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            456799999999999999999998654

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=93.21  E-value=0.081  Score=47.74  Aligned_cols=38  Identities=21%  Similarity=0.334  Sum_probs=27.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      ++|+|.|-||+||||+|..++..+.. .+  ..++-+....
T Consensus         3 kvIavs~KGGvGKTT~a~nLA~~La~-~G--~rVlliD~D~   40 (289)
T 2afh_E            3 RQCAIYGKGGIGKSTTTQNLVAALAE-MG--KKVMIVGCDP   40 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHH-TT--CCEEEEEECS
T ss_pred             eEEEEeCCCcCcHHHHHHHHHHHHHH-CC--CeEEEEecCC
Confidence            67888999999999999999887732 22  2355555543

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.20  E-value=0.055  Score=50.56  Aligned_cols=26  Identities=35%  Similarity=0.511  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           28 DGEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            44689999999999999999998654

>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=93.18  E-value=0.051  Score=45.57  Aligned_cols=24  Identities=38%  Similarity=0.574  Sum_probs=20.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...|+|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           23 HGKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             -CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            346899999999999999999864

>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=93.17  E-value=0.05  Score=45.49  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=20.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        22 ~ki~vvG~~~vGKTsLi~~l~~~~   45 (187)
T 3c5c_A           22 VNLAILGRRGAGKSALTVKFLTKR   45 (187)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCcHHHHHHHHHhCC
Confidence            468899999999999998887653

>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=93.17  E-value=0.051  Score=44.16  Aligned_cols=24  Identities=25%  Similarity=0.284  Sum_probs=20.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            358899999999999999988643

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=93.17  E-value=1.8  Score=40.10  Aligned_cols=26  Identities=31%  Similarity=0.410  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|+|.+|+|||||...+....
T Consensus       166 ~~~~v~lvG~~gvGKSTLin~L~~~~  191 (357)
T 2e87_A          166 EIPTVVIAGHPNVGKSTLLKALTTAK  191 (357)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHCSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            45689999999999999999987654

>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=93.16  E-value=0.074  Score=50.01  Aligned_cols=113  Identities=14%  Similarity=0.125  Sum_probs=57.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFK  246 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~  246 (427)
                      ....+++|+|+.|+|||||++.+.......  .-..++++.-.-.....       ...+.-.......+.......+..
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~~~--~~g~I~~~e~~~e~~~~-------~~~~~v~Q~~~g~~~~~~~~~l~~  204 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYINQT--KSYHIITIEDPIEYVFK-------HKKSIVNQREVGEDTKSFADALRA  204 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHHHH--SCCEEEEEESSCCSCCC-------CSSSEEEEEEBTTTBSCSHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcCcC--CCcEEEEecccHhhhhc-------cCceEEEeeecCCCHHHHHHHHHH
Confidence            455789999999999999999988765210  01122232211000000       000000000000011122345667


Q ss_pred             HhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhH
Q 042645          247 TMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEV  291 (427)
Q Consensus       247 ~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v  291 (427)
                      .|...+=+|++|++.+...........   ..|..|+.|+...+.
T Consensus       205 ~L~~~pd~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~~~  246 (372)
T 2ewv_A          205 ALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTA  246 (372)
T ss_dssp             HTTSCCSEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCCSH
T ss_pred             HhhhCcCEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcchH
Confidence            777778899999997544333322221   345668888776553

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=93.15  E-value=0.22  Score=43.35  Aligned_cols=104  Identities=16%  Similarity=0.140  Sum_probs=51.3

Q ss_pred             HHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCC-cEEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----
Q 042645          157 LDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDF-DFVIWEVVSRDLQLGKIQESIAKKIGLYNES----  231 (427)
Q Consensus       157 ~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f-~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~----  231 (427)
                      ..+++..+..+  +.+.|.|+.|+||||+.....-+........ ...+.+.........++...+...++.....    
T Consensus        66 q~~~i~~i~~g--~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~  143 (235)
T 3llm_A           66 ESEILEAISQN--SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGY  143 (235)
T ss_dssp             HHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEE
T ss_pred             HHHHHHHHhcC--CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEE
Confidence            44455555444  5799999999999987655432211111211 2223222222222334444444443322100    


Q ss_pred             --------------CCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc
Q 042645          232 --------------WDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL  263 (427)
Q Consensus       232 --------------~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~  263 (427)
                                    ..-.++..+...+...+. +--+||+|+++..
T Consensus       144 ~~~~~~~~~~~~~~Ivv~Tpg~l~~~l~~~l~-~~~~lVlDEah~~  188 (235)
T 3llm_A          144 SVRFESILPRPHASIMFCTVGVLLRKLEAGIR-GISHVIVDEIHER  188 (235)
T ss_dssp             EETTEEECCCSSSEEEEEEHHHHHHHHHHCCT-TCCEEEECCTTSC
T ss_pred             eechhhccCCCCCeEEEECHHHHHHHHHhhhc-CCcEEEEECCccC
Confidence                          001234555565555443 3348899999863

>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=93.14  E-value=0.052  Score=45.43  Aligned_cols=24  Identities=38%  Similarity=0.315  Sum_probs=20.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||++.+.+..
T Consensus        15 ~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhc
Confidence            468899999999999997776554

>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=93.13  E-value=0.057  Score=50.72  Aligned_cols=26  Identities=35%  Similarity=0.351  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        28 ~Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           28 EGEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHcCC
Confidence            44689999999999999999998654

>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=93.11  E-value=0.057  Score=53.24  Aligned_cols=26  Identities=15%  Similarity=0.319  Sum_probs=23.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.++|++|+||||+|+.+...+
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L   59 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYL   59 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999998776

>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=93.10  E-value=0.054  Score=44.96  Aligned_cols=24  Identities=29%  Similarity=0.253  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        11 ~ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           11 FKFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468899999999999999988654

>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=93.08  E-value=0.053  Score=44.17  Aligned_cols=25  Identities=28%  Similarity=0.387  Sum_probs=21.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||+..+....
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~~   31 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVGE   31 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcCC
Confidence            3568999999999999999997643

>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=93.06  E-value=0.053  Score=44.51  Aligned_cols=25  Identities=32%  Similarity=0.305  Sum_probs=21.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-|+|+|.+|+|||||+..+.+..
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcCC
Confidence            3468999999999999999998654

>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=93.05  E-value=0.056  Score=44.40  Aligned_cols=24  Identities=29%  Similarity=0.284  Sum_probs=20.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~~   38 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYDS   38 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            358899999999999999987543

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=93.05  E-value=0.059  Score=50.53  Aligned_cols=26  Identities=35%  Similarity=0.313  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        36 ~Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           36 DGEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            44689999999999999999998644

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=93.04  E-value=0.1  Score=51.68  Aligned_cols=44  Identities=14%  Similarity=0.065  Sum_probs=31.7

Q ss_pred             cccchhhHHHHHHHh--ccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          150 VVGMQSTLDRVWRCL--TEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       150 ~vGR~~~~~~l~~~l--~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|.+....+.+..  ......+|.+.|++|+||||+|+.+...+
T Consensus       351 ~~~r~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L  396 (546)
T 2gks_A          351 WFTRPEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATML  396 (546)
T ss_dssp             TTSCHHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHh
Confidence            344554555555554  22345789999999999999999998876

>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=93.04  E-value=0.084  Score=48.08  Aligned_cols=33  Identities=30%  Similarity=0.405  Sum_probs=26.1

Q ss_pred             HHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          157 LDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       157 ~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +++|.+.+.   ..+++|.|+.|+|||||++.+. ..
T Consensus       156 i~~L~~~l~---G~i~~l~G~sG~GKSTLln~l~-~~  188 (302)
T 2yv5_A          156 IDELVDYLE---GFICILAGPSGVGKSSILSRLT-GE  188 (302)
T ss_dssp             HHHHHHHTT---TCEEEEECSTTSSHHHHHHHHH-SC
T ss_pred             HHHHHhhcc---CcEEEEECCCCCCHHHHHHHHH-Hh
Confidence            455655553   3589999999999999999998 54

>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=93.02  E-value=0.054  Score=44.83  Aligned_cols=24  Identities=33%  Similarity=0.414  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            468999999999999999998653

>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=93.01  E-value=0.054  Score=44.98  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=20.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||+..+.+..
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            58899999999999999998654

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=92.97  E-value=0.043  Score=45.20  Aligned_cols=24  Identities=21%  Similarity=0.313  Sum_probs=20.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus         8 ~ki~~vG~~~vGKTsli~~l~~~~   31 (178)
T 2iwr_A            8 LRLGVLGDARSGKSSLIHRFLTGS   31 (178)
T ss_dssp             EEEEEECCGGGCHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            358899999999999999988653

>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=92.95  E-value=0.049  Score=50.62  Aligned_cols=26  Identities=27%  Similarity=0.277  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        25 ~Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHcCC
Confidence            44689999999999999999998654

>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=92.93  E-value=0.055  Score=50.77  Aligned_cols=26  Identities=35%  Similarity=0.295  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHcCC
Confidence            34689999999999999999998654

>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=92.93  E-value=0.059  Score=44.49  Aligned_cols=25  Identities=24%  Similarity=0.356  Sum_probs=21.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||+..+.+..
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~~   30 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEGQ   30 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            3568999999999999999998543

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=92.92  E-value=0.057  Score=45.02  Aligned_cols=24  Identities=33%  Similarity=0.299  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~~~   35 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTDGK   35 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            468899999999999999998653

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=92.92  E-value=0.046  Score=45.04  Aligned_cols=25  Identities=28%  Similarity=0.409  Sum_probs=21.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-|+|+|.+|+|||||+..+....
T Consensus         9 ~~~i~v~G~~~~GKssl~~~l~~~~   33 (181)
T 3tw8_B            9 LFKLLIIGDSGVGKSSLLLRFADNT   33 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHCSCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcCC
Confidence            3468999999999999999987653

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=92.86  E-value=0.059  Score=44.61  Aligned_cols=23  Identities=35%  Similarity=0.403  Sum_probs=20.0

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||+..+.+..
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~~~   29 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTTNA   29 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58899999999999999987543

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=92.86  E-value=0.13  Score=47.79  Aligned_cols=27  Identities=37%  Similarity=0.479  Sum_probs=24.1

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....+++|.|+.|+|||||++.+.+..
T Consensus        69 ~~Gq~~gIiG~nGaGKTTLl~~I~g~~   95 (347)
T 2obl_A           69 GIGQRIGIFAGSGVGKSTLLGMICNGA   95 (347)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            455689999999999999999999886

>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=92.84  E-value=0.058  Score=45.17  Aligned_cols=24  Identities=42%  Similarity=0.469  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            468999999999999999988754

>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=92.84  E-value=0.059  Score=44.59  Aligned_cols=24  Identities=38%  Similarity=0.403  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .-|+|+|.+|+|||||+..+....
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            468899999999999999998654

>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=92.84  E-value=0.06  Score=45.36  Aligned_cols=25  Identities=16%  Similarity=0.251  Sum_probs=20.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .--|+|+|.+|+|||||+..+.+..
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l~~~~   44 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVVFHKM   44 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHSCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhcC
Confidence            3468899999999999999877654

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=92.83  E-value=0.51  Score=46.29  Aligned_cols=56  Identities=21%  Similarity=0.239  Sum_probs=38.5

Q ss_pred             HHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHH
Q 042645          160 VWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQES  220 (427)
Q Consensus       160 l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~  220 (427)
                      .++.|.. .....++|.|..|+|||+|+..+.+..     +-+.++++-+++.. ...+++.+
T Consensus       222 vID~l~PigrGqr~~Ifgg~g~GKT~L~~~ia~~~-----~~~v~V~~~iGER~~Ev~e~~~~  279 (600)
T 3vr4_A          222 VIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWS-----DVDLVVYVGCGERGNEMTDVVNE  279 (600)
T ss_dssp             HHHHHSCCBTTCEEEEECCTTSCHHHHHHHHHHHS-----SCSEEEEEEEEECHHHHHHHHHH
T ss_pred             hhhccCCccCCCEEeeecCCCccHHHHHHHHHhcc-----CCCEEEEEEecccHHHHHHHHHH
Confidence            4555543 345679999999999999999998864     22567777777652 34444444

>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=92.82  E-value=0.06  Score=44.38  Aligned_cols=24  Identities=25%  Similarity=0.338  Sum_probs=20.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        13 ~ki~v~G~~~~GKSsli~~l~~~~   36 (181)
T 2efe_B           13 AKLVLLGDVGAGKSSLVLRFVKDQ   36 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            468899999999999999988653

>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=92.81  E-value=0.09  Score=52.41  Aligned_cols=26  Identities=15%  Similarity=0.123  Sum_probs=23.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|.|++|+||||+|+.+.+.+
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~~L  420 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQVTL  420 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999998886

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=92.81  E-value=0.061  Score=44.39  Aligned_cols=24  Identities=33%  Similarity=0.288  Sum_probs=20.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~~   32 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSNT   32 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            458899999999999999987653

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=92.79  E-value=0.07  Score=45.41  Aligned_cols=24  Identities=13%  Similarity=0.192  Sum_probs=22.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|.|.|+.|+||||+++.+++.+
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~l   30 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHY   30 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHh
Confidence            589999999999999999999987

>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=92.79  E-value=0.06  Score=50.53  Aligned_cols=25  Identities=24%  Similarity=0.456  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|+|+.|+|||||++.+....
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~  194 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVF  194 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998765

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=92.78  E-value=0.061  Score=45.22  Aligned_cols=23  Identities=39%  Similarity=0.377  Sum_probs=20.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      --|+|+|.+|+|||||...+...
T Consensus         7 ~kv~lvG~~~vGKSsL~~~~~~~   29 (192)
T 2cjw_A            7 YRVVLIGEQGVGKSTLANIFAGV   29 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45889999999999999998753

>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=92.76  E-value=0.065  Score=44.86  Aligned_cols=24  Identities=25%  Similarity=0.271  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        24 ~ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           24 FKLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCcCHHHHHHHHhcCC
Confidence            468899999999999999988754

>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=92.75  E-value=0.063  Score=45.92  Aligned_cols=111  Identities=15%  Similarity=0.052  Sum_probs=51.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      ...+..++|.-|.||||.+.....+.. . ... .++.+.....  ...-...+.+.++.........+..    .+.+.
T Consensus        27 ~G~l~vitG~MgsGKTT~lL~~a~r~~-~-~g~-kVli~k~~~d--~R~ge~~i~s~~g~~~~a~~~~~~~----~~~~~   97 (214)
T 2j9r_A           27 NGWIEVICGSMFSGKSEELIRRVRRTQ-F-AKQ-HAIVFKPCID--NRYSEEDVVSHNGLKVKAVPVSASK----DIFKH   97 (214)
T ss_dssp             SCEEEEEECSTTSCHHHHHHHHHHHHH-H-TTC-CEEEEECC-------------------CCEEECSSGG----GGGGG
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH-H-CCC-EEEEEEeccC--CcchHHHHHhhcCCeeEEeecCCHH----HHHHH
Confidence            346889999999999999988877762 1 222 2333332211  1111223444444332211111211    22233


Q ss_pred             hcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCChh
Q 042645          248 MRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       248 L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                      +.++--+|++|++.-.  +..+.+ ..+.  ..|..||+|.++.+
T Consensus        98 ~~~~~dvViIDEaQF~~~~~V~~l-~~l~--~~~~~Vi~~Gl~~D  139 (214)
T 2j9r_A           98 ITEEMDVIAIDEVQFFDGDIVEVV-QVLA--NRGYRVIVAGLDQD  139 (214)
T ss_dssp             CCSSCCEEEECCGGGSCTTHHHHH-HHHH--HTTCEEEEEECSBC
T ss_pred             HhcCCCEEEEECcccCCHHHHHHH-HHHh--hCCCEEEEEecccc
Confidence            3333349999998643  223222 2211  13678999999643

>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=92.73  E-value=0.062  Score=45.43  Aligned_cols=25  Identities=36%  Similarity=0.411  Sum_probs=21.3

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        14 ~~ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           14 LHKVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCC
Confidence            3568999999999999999987653

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=92.73  E-value=0.071  Score=46.71  Aligned_cols=50  Identities=18%  Similarity=0.109  Sum_probs=31.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      ...++.|.|.+|+|||+||.+++.+..  ...-..+++++...  +..++...+
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~--~~~~~~v~~~s~E~--~~~~~~~~~   78 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGA--EEYGEPGVFVTLEE--RARDLRREM   78 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHH--HHHCCCEEEEESSS--CHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH--HhcCCCceeecccC--CHHHHHHHH
Confidence            456899999999999999988764421  11123455665443  345554443

>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=92.72  E-value=0.071  Score=44.28  Aligned_cols=27  Identities=30%  Similarity=0.351  Sum_probs=22.3

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .....|+|+|.+|+|||||+..+.+..
T Consensus        16 ~~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           16 ERELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            345678999999999999999997654

>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=92.72  E-value=0.064  Score=44.17  Aligned_cols=24  Identities=42%  Similarity=0.458  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            468999999999999999987654

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=92.70  E-value=0.065  Score=45.63  Aligned_cols=25  Identities=24%  Similarity=0.242  Sum_probs=21.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .--|+|+|.+|+|||||+..+....
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~~   52 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKDC   52 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            3468899999999999999998754

>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=92.69  E-value=0.065  Score=44.90  Aligned_cols=24  Identities=29%  Similarity=0.414  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            468999999999999999997654

>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=92.68  E-value=0.081  Score=44.46  Aligned_cols=26  Identities=23%  Similarity=0.427  Sum_probs=22.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..--|+|+|.+|+|||||+..+....
T Consensus        27 ~~~ki~v~G~~~vGKSsli~~l~~~~   52 (196)
T 2atv_A           27 AEVKLAIFGRAGVGKSALVVRFLTKR   52 (196)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhCC
Confidence            34568999999999999999988653

>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=92.68  E-value=0.066  Score=45.44  Aligned_cols=24  Identities=33%  Similarity=0.476  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        27 ~ki~lvG~~~vGKSsLi~~l~~~~   50 (201)
T 2ew1_A           27 FKIVLIGNAGVGKTCLVRRFTQGL   50 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            468999999999999999987654

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=92.67  E-value=0.063  Score=45.43  Aligned_cols=25  Identities=40%  Similarity=0.434  Sum_probs=21.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||+..+....
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            8 LLKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3468999999999999999987654

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=92.67  E-value=0.086  Score=43.32  Aligned_cols=24  Identities=21%  Similarity=0.174  Sum_probs=21.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..-|.|.|.+|+||||||..+..+
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc
Confidence            457899999999999999998764

>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=92.67  E-value=0.046  Score=50.93  Aligned_cols=26  Identities=31%  Similarity=0.365  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            44689999999999999999998643

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=92.66  E-value=0.083  Score=44.74  Aligned_cols=41  Identities=17%  Similarity=0.212  Sum_probs=28.6

Q ss_pred             eEEEEE-ecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCC
Q 042645          170 GIVGLY-GMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQ  213 (427)
Q Consensus       170 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~  213 (427)
                      ++|+|+ +-||+||||++..++..+..   .-..++-+......+
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~---~g~~vlliD~D~~~~   43 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSR---SGYNIAVVDTDPQMS   43 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHH---TTCCEEEEECCTTCH
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHH---CCCeEEEEECCCCCC
Confidence            577787 67999999999999888732   223456666654433

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.65  E-value=0.046  Score=46.49  Aligned_cols=26  Identities=23%  Similarity=0.325  Sum_probs=21.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .....|+|+|.+|+|||||...+...
T Consensus        24 ~~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           24 DTGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            34567999999999999999887654

>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=92.63  E-value=0.052  Score=45.62  Aligned_cols=25  Identities=24%  Similarity=0.331  Sum_probs=21.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..--|+|+|.+|+|||||+..+...
T Consensus        28 ~~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           28 KQMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             CccEEEEECCCCCCHHHHHHHHHhC
Confidence            4457999999999999999998643

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=92.58  E-value=0.069  Score=45.12  Aligned_cols=25  Identities=32%  Similarity=0.278  Sum_probs=21.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-|+|+|.+|+|||||+..+.+..
T Consensus        24 ~~ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           24 YRKVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             cEEEEEECCCCcCHHHHHHHHHhCC
Confidence            4568999999999999999998754

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=92.58  E-value=0.082  Score=49.08  Aligned_cols=27  Identities=26%  Similarity=0.366  Sum_probs=23.4

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+..+|+|+|.+|+|||||+..+....
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            466899999999999999999987654

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=92.58  E-value=0.17  Score=47.09  Aligned_cols=27  Identities=33%  Similarity=0.317  Sum_probs=21.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...++...|-||+||||++..++..+
T Consensus        16 ~~~~i~v~sgKGGvGKTTvaanLA~~l   42 (354)
T 2woj_A           16 TTHKWIFVGGKGGVGKTTSSCSIAIQM   42 (354)
T ss_dssp             SSCCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHHH
Confidence            344566677999999999999888776

>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=92.56  E-value=0.052  Score=45.78  Aligned_cols=23  Identities=39%  Similarity=0.449  Sum_probs=19.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      ..-|+|+|.+|+|||||+..+..
T Consensus        23 ~~ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           23 IFKVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHTCC
T ss_pred             EEEEEEECCCCCCHHHHHHHHHh
Confidence            35689999999999999999853

>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=92.56  E-value=0.067  Score=45.20  Aligned_cols=24  Identities=25%  Similarity=0.281  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADDS   32 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            468999999999999999988654

>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=92.55  E-value=0.069  Score=44.59  Aligned_cols=24  Identities=29%  Similarity=0.290  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        23 ~ki~v~G~~~~GKSsli~~l~~~~   46 (188)
T 1zd9_A           23 MELTLVGLQYSGKTTFVNVIASGQ   46 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHcCC
Confidence            468899999999999999998654

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.54  E-value=0.068  Score=44.93  Aligned_cols=25  Identities=20%  Similarity=0.300  Sum_probs=21.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .--|+|+|.+|+|||||+..+....
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~~   31 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKDT   31 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCc
Confidence            3468899999999999999998764

>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=92.53  E-value=0.069  Score=44.55  Aligned_cols=24  Identities=29%  Similarity=0.279  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999987654

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=92.53  E-value=0.073  Score=48.46  Aligned_cols=24  Identities=33%  Similarity=0.614  Sum_probs=21.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...|+|+|.+|+|||||...+...
T Consensus         8 ~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            8 CGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC
Confidence            458999999999999999999865

>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=92.53  E-value=0.079  Score=50.01  Aligned_cols=25  Identities=44%  Similarity=0.582  Sum_probs=21.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ...+++|.|+.|+|||||++.++.-
T Consensus        46 ~Ge~~~llGpsGsGKSTLLr~iaGl   70 (390)
T 3gd7_A           46 PGQRVGLLGRTGSGKSTLLSAFLRL   70 (390)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCC
Confidence            4568999999999999999998753

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.52  E-value=0.066  Score=50.13  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=22.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...++|+|+.|+|||||++.+....
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~~~  199 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQEI  199 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcC
Confidence            3579999999999999999998866

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=92.49  E-value=0.069  Score=45.58  Aligned_cols=25  Identities=24%  Similarity=0.264  Sum_probs=21.1

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||+..+....
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3568999999999999999998654

>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=92.49  E-value=0.07  Score=44.72  Aligned_cols=24  Identities=33%  Similarity=0.357  Sum_probs=21.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            468899999999999999998764

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=92.46  E-value=0.085  Score=45.40  Aligned_cols=25  Identities=20%  Similarity=0.272  Sum_probs=23.1

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|.|.|+.|+||||+++.+.+.+
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l   29 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKL   29 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999999988

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=92.46  E-value=0.063  Score=48.90  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=18.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|..|+|||||...++..
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g~   41 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFLT   41 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4599999999999999997653

>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=92.43  E-value=0.071  Score=44.15  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=20.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -.|+|+|.+|+|||||...+...
T Consensus        22 ~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           22 HKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999999865

>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=92.41  E-value=0.072  Score=44.57  Aligned_cols=24  Identities=33%  Similarity=0.314  Sum_probs=20.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (191)
T 2a5j_A           22 FKYIIIGDTGVGKSCLLLQFTDKR   45 (191)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            358899999999999999988654

>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=92.41  E-value=0.072  Score=45.03  Aligned_cols=25  Identities=28%  Similarity=0.288  Sum_probs=20.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .--|+|+|.+|+|||||+..+.+..
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~~   49 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIENK   49 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC--
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhCC
Confidence            3468899999999999999987543

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=92.41  E-value=0.073  Score=44.56  Aligned_cols=24  Identities=33%  Similarity=0.384  Sum_probs=21.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            468999999999999999998754

>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=92.40  E-value=0.089  Score=45.54  Aligned_cols=25  Identities=20%  Similarity=0.347  Sum_probs=21.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ....|+|+|.+|+|||||+..+...
T Consensus        28 ~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           28 HKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3467999999999999999998765

>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=92.39  E-value=0.07  Score=44.35  Aligned_cols=21  Identities=14%  Similarity=0.142  Sum_probs=18.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +.|+|.+|+||||+|.+++..
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~   22 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD   22 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            789999999999999998754

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=92.35  E-value=0.094  Score=46.86  Aligned_cols=25  Identities=32%  Similarity=0.425  Sum_probs=21.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||...+....
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~~   27 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGLR   27 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCCC
Confidence            3578999999999999999987653

>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=92.33  E-value=0.076  Score=44.30  Aligned_cols=24  Identities=25%  Similarity=0.146  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .-|+|+|.+|+|||||+..+....
T Consensus        21 ~ki~v~G~~~~GKSsli~~l~~~~   44 (189)
T 1z06_A           21 FKIIVIGDSNVGKTCLTYRFCAGR   44 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            568999999999999999987543

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=92.32  E-value=0.16  Score=46.85  Aligned_cols=28  Identities=29%  Similarity=0.325  Sum_probs=22.9

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      +...++.+.|-||+||||++..++..+.
T Consensus        17 ~~~~i~v~sgkGGvGKTTva~~LA~~lA   44 (329)
T 2woo_A           17 TSLKWIFVGGKGGVGKTTTSCSLAIQMS   44 (329)
T ss_dssp             TTCCEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCcHHHHHHHHHHHHH
Confidence            3456777789999999999999887773

>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=92.31  E-value=0.077  Score=44.94  Aligned_cols=24  Identities=33%  Similarity=0.412  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSDDT   32 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            468999999999999999987654

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=92.31  E-value=0.073  Score=44.88  Aligned_cols=24  Identities=33%  Similarity=0.362  Sum_probs=20.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .--|+|+|.+|+|||||+..+.+.
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346889999999999999998754

>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=92.30  E-value=0.079  Score=44.46  Aligned_cols=25  Identities=32%  Similarity=0.492  Sum_probs=21.3

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .--|+|+|.+|+|||||+..+....
T Consensus         8 ~~ki~vvG~~~~GKSsli~~l~~~~   32 (199)
T 2gf0_A            8 DYRVVVFGAGGVGKSSLVLRFVKGT   32 (199)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCcHHHHHHHHHcCC
Confidence            3468999999999999999997643

>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=92.29  E-value=0.077  Score=44.32  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|+|+|.+|+|||||+..+.+..
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~~   39 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDDT   39 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999998754

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=92.26  E-value=0.16  Score=47.68  Aligned_cols=39  Identities=18%  Similarity=0.184  Sum_probs=28.8

Q ss_pred             CCeEEEEEe-cCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          168 PVGIVGLYG-MGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       168 ~~~vi~I~G-~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      +.++|+|+| -||+||||+|..++..+..   .-..++.+...
T Consensus       142 ~~kvIav~s~KGGvGKTT~a~nLA~~La~---~g~rVlliD~D  181 (373)
T 3fkq_A          142 KSSVVIFTSPCGGVGTSTVAAACAIAHAN---MGKKVFYLNIE  181 (373)
T ss_dssp             SCEEEEEECSSTTSSHHHHHHHHHHHHHH---HTCCEEEEECC
T ss_pred             CceEEEEECCCCCChHHHHHHHHHHHHHh---CCCCEEEEECC
Confidence            568899985 9999999999998887732   12346666655

>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=92.26  E-value=0.076  Score=44.79  Aligned_cols=26  Identities=23%  Similarity=0.277  Sum_probs=21.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...-|+|+|.+|+|||||+..+....
T Consensus        27 ~~~ki~v~G~~~~GKSsli~~l~~~~   52 (199)
T 2p5s_A           27 KAYKIVLAGDAAVGKSSFLMRLCKNE   52 (199)
T ss_dssp             -CEEEEEESSTTSSHHHHHHHHHHCC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhCC
Confidence            34578999999999999999987653

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=92.24  E-value=0.16  Score=44.34  Aligned_cols=40  Identities=15%  Similarity=0.172  Sum_probs=27.7

Q ss_pred             CCeEEEEE-ecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          168 PVGIVGLY-GMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       168 ~~~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      ..++|+|+ +-||+||||++..++..+.. . .-..++.+...
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA~~la~-~-~g~~VlliD~D   43 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFAFALSQ-E-PDIHVLAVDIS   43 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHHHHHTT-S-TTCCEEEEECC
T ss_pred             CCeEEEEECCCCCcchHHHHHHHHHHHHh-C-cCCCEEEEECC
Confidence            35678887 46899999999999988832 1 12345556554

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=92.21  E-value=0.073  Score=44.69  Aligned_cols=26  Identities=27%  Similarity=0.367  Sum_probs=22.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|+|.+|+|||||+..+.+..
T Consensus        16 ~~~ki~v~G~~~~GKSsl~~~l~~~~   41 (199)
T 4bas_A           16 TKLQVVMCGLDNSGKTTIINQVKPAQ   41 (199)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHSCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            34679999999999999999987654

>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=92.20  E-value=0.08  Score=45.62  Aligned_cols=22  Identities=32%  Similarity=0.430  Sum_probs=19.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|.|+|.+|+|||+|+..+.+.
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4789999999999999998754

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=92.15  E-value=0.08  Score=45.32  Aligned_cols=23  Identities=43%  Similarity=0.543  Sum_probs=19.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      --|+|+|.+|+|||||+..+.+.
T Consensus        35 ~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           35 VKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHC-
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999998764

>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=92.13  E-value=0.087  Score=51.25  Aligned_cols=26  Identities=15%  Similarity=0.271  Sum_probs=22.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.++|++|+||||+++.+.+..
T Consensus        38 ~~~~IvlvGlpGsGKSTia~~La~~l   63 (469)
T 1bif_A           38 CPTLIVMVGLPARGKTYISKKLTRYL   63 (469)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHH
Confidence            34589999999999999999998775

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=92.08  E-value=0.082  Score=45.32  Aligned_cols=22  Identities=41%  Similarity=0.409  Sum_probs=19.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      --|+|+|.+|+|||||+..+..
T Consensus        38 ~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           38 YRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4589999999999999999874

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.06  E-value=0.088  Score=44.07  Aligned_cols=24  Identities=38%  Similarity=0.354  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        19 ~ki~v~G~~~~GKssli~~l~~~~   42 (194)
T 2atx_A           19 LKCVVVGDGAVGKTCLLMSYANDA   42 (194)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            468999999999999999998653

>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=92.04  E-value=0.083  Score=46.16  Aligned_cols=26  Identities=23%  Similarity=0.135  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|+|.+|+|||||+..+....
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCCC
Confidence            34679999999999999999998754

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=92.04  E-value=0.13  Score=46.78  Aligned_cols=34  Identities=32%  Similarity=0.555  Sum_probs=26.5

Q ss_pred             HHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          157 LDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       157 ~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++++.+.+.   ..+++|.|+.|+|||||.+.+....
T Consensus       160 v~~lf~~l~---geiv~l~G~sG~GKSTll~~l~g~~  193 (301)
T 1u0l_A          160 IEELKEYLK---GKISTMAGLSGVGKSSLLNAINPGL  193 (301)
T ss_dssp             HHHHHHHHS---SSEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             HHHHHHHhc---CCeEEEECCCCCcHHHHHHHhcccc
Confidence            455555553   3589999999999999999997654

>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=92.03  E-value=0.12  Score=41.63  Aligned_cols=24  Identities=38%  Similarity=0.495  Sum_probs=20.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .++.+|+|+.|+||||+...++--
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~~   46 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILVG   46 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999887643

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.02  E-value=0.088  Score=44.71  Aligned_cols=24  Identities=29%  Similarity=0.331  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .-|+|+|.+|+|||||+..+....
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~~   49 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSKDE   49 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             cEEEEECcCCCCHHHHHHHHhcCC
Confidence            468999999999999999988654

>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=92.02  E-value=0.067  Score=49.42  Aligned_cols=105  Identities=15%  Similarity=0.038  Sum_probs=54.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR  249 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~  249 (427)
                      ..++|+|+.|+|||||++.+.....   . -...+.+.-.........    -..++.-    .. ........+...|.
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~---~-~~g~i~i~~~~e~~~~~~----~~~i~~~----~g-gg~~~r~~la~aL~  238 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIP---K-EERIISIEDTEEIVFKHH----KNYTQLF----FG-GNITSADCLKSCLR  238 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSC---T-TSCEEEEESSCCCCCSSC----SSEEEEE----CB-TTBCHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCc---C-CCcEEEECCeeccccccc----hhEEEEE----eC-CChhHHHHHHHHhh
Confidence            4799999999999999999987762   1 223444332211110000    0000000    00 11223344556677


Q ss_pred             CCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChh
Q 042645          250 NRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       250 ~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                      .++=+|+||++-+...++.+ ..+..  .+..+|+||...+
T Consensus       239 ~~p~ilildE~~~~e~~~~l-~~~~~--g~~tvi~t~H~~~  276 (330)
T 2pt7_A          239 MRPDRIILGELRSSEAYDFY-NVLCS--GHKGTLTTLHAGS  276 (330)
T ss_dssp             SCCSEEEECCCCSTHHHHHH-HHHHT--TCCCEEEEEECSS
T ss_pred             hCCCEEEEcCCChHHHHHHH-HHHhc--CCCEEEEEEcccH
Confidence            78889999998764333322 22221  1223666665543

>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=92.00  E-value=0.09  Score=44.48  Aligned_cols=25  Identities=24%  Similarity=0.283  Sum_probs=21.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .--|+|+|.+|+|||||+..+.+..
T Consensus        29 ~~ki~vvG~~~vGKSsli~~l~~~~   53 (201)
T 2hup_A           29 LFKLVLVGDASVGKTCVVQRFKTGA   53 (201)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhhCC
Confidence            3468999999999999999987653

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=91.99  E-value=0.089  Score=44.77  Aligned_cols=24  Identities=29%  Similarity=0.220  Sum_probs=20.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        10 ~ki~i~G~~~~GKTsli~~l~~~~   33 (212)
T 2j0v_A           10 IKCVTVGDGAVGKTCMLICYTSNK   33 (212)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            468899999999999999988653

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=91.96  E-value=0.077  Score=51.35  Aligned_cols=26  Identities=23%  Similarity=0.126  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus       137 ~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          137 EGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            45689999999999999999987654

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=91.92  E-value=0.072  Score=44.67  Aligned_cols=24  Identities=33%  Similarity=0.458  Sum_probs=19.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        27 ~ki~vvG~~~~GKSsLi~~l~~~~   50 (192)
T 2il1_A           27 LQVIIIGSRGVGKTSLMERFTDDT   50 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHCC--
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            358899999999999999987543

>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=91.90  E-value=0.094  Score=44.30  Aligned_cols=24  Identities=29%  Similarity=0.362  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~~   49 (201)
T 2gco_A           26 KKLVIVGDGACGKTCLLIVFSKDQ   49 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCc
Confidence            468899999999999999988654

>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=91.86  E-value=0.097  Score=52.45  Aligned_cols=26  Identities=31%  Similarity=0.381  Sum_probs=23.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|.|++|+||||+|+.+.+.+
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L   76 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYL   76 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            45789999999999999999998876

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.84  E-value=0.091  Score=44.65  Aligned_cols=25  Identities=32%  Similarity=0.410  Sum_probs=21.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~~   44 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVEDK   44 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCC
Confidence            3578999999999999999988653

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=91.84  E-value=0.14  Score=52.04  Aligned_cols=62  Identities=19%  Similarity=0.276  Sum_probs=37.5

Q ss_pred             hhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          155 STLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       155 ~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      ...+.+...|...  .+..|+||||.|||+.+..+...+...    ...+.++...+....+++..+.
T Consensus       193 ~Q~~AV~~al~~~--~~~lI~GPPGTGKT~ti~~~I~~l~~~----~~~ILv~a~TN~AvD~i~erL~  254 (646)
T 4b3f_X          193 SQKEAVLFALSQK--ELAIIHGPPGTGKTTTVVEIILQAVKQ----GLKVLCCAPSNIAVDNLVERLA  254 (646)
T ss_dssp             HHHHHHHHHHHCS--SEEEEECCTTSCHHHHHHHHHHHHHHT----TCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCC--CceEEECCCCCCHHHHHHHHHHHHHhC----CCeEEEEcCchHHHHHHHHHHH
Confidence            3445555555433  468899999999997665554444221    1245666665555666666554

>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=91.82  E-value=0.068  Score=44.62  Aligned_cols=24  Identities=29%  Similarity=0.350  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|+|+|.+|+|||||...+....
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            568999999999999999987654

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=91.76  E-value=0.15  Score=51.15  Aligned_cols=40  Identities=20%  Similarity=0.159  Sum_probs=28.8

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      +..+++.+.|.||+||||+|..++..+.. .  -..++.|...
T Consensus         6 ~~~~i~~~sgkGGvGKTT~a~~lA~~lA~-~--G~rVLlvd~D   45 (589)
T 1ihu_A            6 NIPPYLFFTGKGGVGKTSISCATAIRLAE-Q--GKRVLLVSTD   45 (589)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHH-T--TCCEEEEECC
T ss_pred             CCCEEEEEeCCCcCHHHHHHHHHHHHHHH-C--CCcEEEEECC
Confidence            45678899999999999999998877732 1  2235555544

>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=91.75  E-value=0.11  Score=44.37  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=20.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        28 ~ki~vvG~~~vGKSsL~~~l~~~~   51 (214)
T 3q3j_B           28 CKLVLVGDVQCGKTAMLQVLAKDC   51 (214)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECcCCCCHHHHHHHHhcCC
Confidence            468899999999999999987653

>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=91.74  E-value=0.096  Score=48.73  Aligned_cols=24  Identities=33%  Similarity=0.416  Sum_probs=21.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+++|+|++|+|||||+..+....
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~  239 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQ  239 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCS
T ss_pred             CEEEEECCCCccHHHHHHHHhccc
Confidence            589999999999999999998655

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=91.74  E-value=0.2  Score=42.76  Aligned_cols=41  Identities=20%  Similarity=0.096  Sum_probs=28.8

Q ss_pred             EEEEE-ecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          171 IVGLY-GMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       171 vi~I~-G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      +|+|+ +-||+||||++..++..+. ..  - .++-+......+..
T Consensus         2 vI~v~s~KGGvGKTT~a~~LA~~la-~~--g-~VlliD~D~q~~~~   43 (209)
T 3cwq_A            2 IITVASFKGGVGKTTTAVHLSAYLA-LQ--G-ETLLIDGDPNRSAT   43 (209)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHH-TT--S-CEEEEEECTTCHHH
T ss_pred             EEEEEcCCCCCcHHHHHHHHHHHHH-hc--C-CEEEEECCCCCCHH
Confidence            45664 7899999999999998883 22  2 56667766554443

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=91.72  E-value=0.18  Score=46.34  Aligned_cols=25  Identities=36%  Similarity=0.388  Sum_probs=21.1

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++...|-||+||||+|..++..+
T Consensus        14 ~~i~v~sgKGGvGKTTvA~~LA~~l   38 (324)
T 3zq6_A           14 TTFVFIGGKGGVGKTTISAATALWM   38 (324)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCchHHHHHHHHHHHH
Confidence            3567777999999999999988776

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=91.66  E-value=0.13  Score=44.41  Aligned_cols=26  Identities=12%  Similarity=0.089  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|.|+.|+||||+++.+++.+
T Consensus        13 ~~~iI~i~g~~gsGk~~i~~~la~~l   38 (223)
T 3hdt_A           13 KNLIITIEREYGSGGRIVGKKLAEEL   38 (223)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHc
Confidence            34699999999999999999999887

>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=91.65  E-value=0.056  Score=44.73  Aligned_cols=23  Identities=35%  Similarity=0.401  Sum_probs=9.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      --|+|+|.+|+|||||+..+.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEECCCCC------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999988754

>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=91.62  E-value=0.095  Score=47.85  Aligned_cols=25  Identities=40%  Similarity=0.583  Sum_probs=22.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...|+|+|.+|+|||||...+....
T Consensus        10 ~g~v~ivG~~nvGKSTLin~l~g~~   34 (308)
T 3iev_A           10 VGYVAIVGKPNVGKSTLLNNLLGTK   34 (308)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            4689999999999999999988653

>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=91.58  E-value=0.16  Score=43.02  Aligned_cols=26  Identities=15%  Similarity=0.231  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|+|+|++|+||+|+|..+.+.+
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~~~   35 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQSRL   35 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHHHc
Confidence            45799999999999999999987755

>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=91.42  E-value=0.1  Score=44.61  Aligned_cols=24  Identities=33%  Similarity=0.329  Sum_probs=20.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      --|+|+|.+|+|||||+..+....
T Consensus        26 ~ki~vvG~~~~GKSsLi~~l~~~~   49 (217)
T 2f7s_A           26 IKLLALGDSGVGKTTFLYRYTDNK   49 (217)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHCSC
T ss_pred             EEEEEECcCCCCHHHHHHHHhcCC
Confidence            468999999999999999988653

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=91.40  E-value=0.23  Score=44.83  Aligned_cols=26  Identities=15%  Similarity=0.235  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|+|.+|+|||||...+....
T Consensus        25 ~~~~i~vvG~~~~GKSSLln~l~g~~   50 (299)
T 2aka_B           25 DLPQIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             CCCEEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             CCCeEEEEeCCCCCHHHHHHHHHCCC
Confidence            45689999999999999999998654

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=91.40  E-value=0.12  Score=45.72  Aligned_cols=23  Identities=35%  Similarity=0.410  Sum_probs=20.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +.|+|+|.+|+|||||...+...
T Consensus         2 ~kI~lvG~~n~GKSTL~n~L~g~   24 (256)
T 3iby_A            2 THALLIGNPNCGKTTLFNALTNA   24 (256)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            46899999999999999998765

---

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	427
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-35

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score =  130 bits (328), Expect = 1e-35
 Identities = 42/268 (15%), Positives = 82/268 (30%), Gaps = 28/268 (10%)

Query: 145 PLPPTVVGMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQI-NNSFLHTPNDF 200
           P   T    +  +DRV + L E        + L+G  G GK+ + +Q  + S      ++
Sbjct: 17  PKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINY 76

Query: 201 DFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNK--------SFDEKAQEIFKTMRNRK 252
           D ++W   S               + L +E             S   K       +    
Sbjct: 77  DSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPN 136

Query: 253 IVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVC-GLMDAHKSFKVECLGYEDA 311
            + + DD+ +            ++    + + TTR+ E+        +  +V  L  ++ 
Sbjct: 137 TLFVFDDVVQEET------IRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDEC 190

Query: 312 WRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVL 371
           +   E       +       ++         G P  L+   ++   K    + A     L
Sbjct: 191 YDFLEAYGMPMPVGEKE--EDVLNKTIELSSGNPATLMMFFKSCEPKT-FEKMAQLNNKL 247

Query: 372 RSSASKFSGMEKKALSRLKFSYDFLPSN 399
            S      G+E        +SY  L   
Sbjct: 248 ES--RGLVGVEC----ITPYSYKSLAMA 269

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	427
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.47
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.19
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.13
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.09
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.08
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.0
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.98
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.97
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.92
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.92
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.82
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.81
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.68
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.66
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.65
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.61
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.55
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.55
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.53
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.42
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.27
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.23
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.82
d1okkd2	207	GTPase domain of the signal recognition particle r	97.34
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.28
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.28
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.27
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.25
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.23
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.23
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.18
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.16
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.14
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.11
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.1
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.08
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.08
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.07
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	97.03
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.03
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.98
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.97
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.97
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.96
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.93
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.92
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.92
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.88
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.87
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.83
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.82
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.82
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.8
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.8
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.77
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.71
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.7
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.68
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.67
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.66
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.65
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.65
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.61
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.54
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.51
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.5
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.46
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.45
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.45
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.44
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.37
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.33
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.26
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	96.25
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.24
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.24
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.24
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.22
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.22
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.22
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.21
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.12
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.03
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.01
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.0
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.99
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.98
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.93
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.89
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.77
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.73
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.7
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.65
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.54
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.5
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	95.44
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.36
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.35
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.34
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	95.33
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.25
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.2
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.16
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.08
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.04
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	95.02
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.01
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	95.01
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	94.99
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.93
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.85
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.84
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.83
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.82
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.78
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.74
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.73
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.72
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.67
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.67
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	94.67
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.58
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	94.57
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.53
d1nrjb_	209	Signal recognition particle receptor beta-subunit	94.53
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.51
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.51
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.51
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.47
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.47
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.46
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.43
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.39
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.36
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.32
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.3
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	94.27
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	94.25
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.24
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.24
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.24
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.23
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	94.21
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	94.18
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.14
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.13
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.11
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	94.08
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.07
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.07
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.06
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.04
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.03
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.03
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.03
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.03
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.02
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.0
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.95
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.95
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.93
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.91
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.88
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.88
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.87
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.87
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.86
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	93.82
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	93.8
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.78
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.78
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.76
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.73
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	93.72
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.7
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.67
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.59
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.57
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	93.54
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.54
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.53
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	93.49
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.48
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.45
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	93.44
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.31
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.3
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.24
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	93.18
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	93.16
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.12
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.11
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	93.08
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	93.07
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	93.06
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.05
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	93.04
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	93.01
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.97
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	92.84
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	92.84
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.82
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	92.81
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.68
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	92.68
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.61
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	92.6
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	92.56
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	92.45
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.4
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	92.39
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	92.22
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	92.21
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.15
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	92.09
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	91.64
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	91.56
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	91.53
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	91.49
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	91.13
d1tuea_	205	Replication protein E1 helicase domain {Human papi	90.48
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	90.45
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	90.34
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	90.22
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	90.2
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.01
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	89.66
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	88.67
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	88.17
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	88.13
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	87.03
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	86.96
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	86.92
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	86.84
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	86.67
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.65
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	85.33
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	84.76
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	84.56
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	84.46
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	83.98
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	83.84
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.71
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	82.1
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	81.93
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	81.44
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	80.16

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=4.1e-43  Score=320.37  Aligned_cols=246  Identities=15%  Similarity=0.099  Sum_probs=196.4

Q ss_pred             CCccccchhhHHHHHHHhcc---CCCeEEEEEecCCCcHHHHHHHHHhhccC-CCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE---EPVGIVGLYGMGGVGKTTLLTQINNSFLH-TPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      .+.++||+.++++|+++|.+   .+.++|+|+||||+||||||+++|++... ...+|++++|++++..++...+...+.
T Consensus        19 ~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~   98 (277)
T d2a5yb3          19 QMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTD   98 (277)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHH
T ss_pred             CCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHH
Confidence            45678999999999999853   46789999999999999999999987522 467899999999999888777776665


Q ss_pred             HHh---CCCCCC-----CCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcccccccccCCCCCCCCcEEEEecCChhHHhh
Q 042645          223 KKI---GLYNES-----WDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLAQVGLPVPSRASASKVVFTTREFEVCGL  294 (427)
Q Consensus       223 ~~l---~~~~~~-----~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~~~~~~l~~~~~gs~IivTtR~~~v~~~  294 (427)
                      ..+   +.....     ............+.+.+.++++|+||||+|+...|..+.      ..||+||||||+.+++..
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~------~~~srilvTTR~~~v~~~  172 (277)
T d2a5yb3          99 ILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQ------ELRLRCLVTTRDVEISNA  172 (277)
T ss_dssp             HHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHH------HTTCEEEEEESBGGGGGG
T ss_pred             HHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhc------ccCceEEEEeehHHHHHh
Confidence            443   221110     011222334456778899999999999999988776542      247999999999999887


Q ss_pred             cCCC-cceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHHHHcCCCChHHHHHHHHHHhh
Q 042645          295 MDAH-KSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGRAMASKKAPREWAHAIEVLRS  373 (427)
Q Consensus       295 ~~~~-~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~~L~~~~~~~~w~~~l~~l~~  373 (427)
                      +... +.|++++|+.+||++||...++...  ..+..++++++|+++|+|+|||++++|+.|+. ++.+.|.+..+.|.+
T Consensus       173 ~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~--~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~-k~~~~~~~~~~~L~~  249 (277)
T d2a5yb3         173 ASQTCEFIEVTSLEIDECYDFLEAYGMPMP--VGEKEEDVLNKTIELSSGNPATLMMFFKSCEP-KTFEKMAQLNNKLES  249 (277)
T ss_dssp             CCSCEEEEECCCCCHHHHHHHHHHTSCCCC----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCS-SSHHHHHHHHHHHHH
T ss_pred             cCCCCceEECCCCCHHHHHHHHHHHhCCcc--CchhhHHHHHHHHHHhCCCHHHHHHHHHHhcc-CCHHHHHHHHHHHhc
Confidence            6554 6799999999999999999887543  34556788999999999999999999999986 578899998888876


Q ss_pred             ccccCCCChHHHHHHHhhhcCCCCCChHhHHHhhh
Q 042645          374 SASKFSGMEKKALSRLKFSYDFLPSNETRFCLLYC  408 (427)
Q Consensus       374 ~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~cf~~~  408 (427)
                      ...      ..+..+|.+||++||+ ++|+||.++
T Consensus       250 ~~~------~~v~~il~~sY~~L~~-~lk~c~~~l  277 (277)
T d2a5yb3         250 RGL------VGVECITPYSYKSLAM-ALQRCVEVL  277 (277)
T ss_dssp             HCS------STTCCCSSSSSSSHHH-HHHHHHHTS
T ss_pred             CcH------HHHHHHHHHHHhcccH-HHHHHHHhC
Confidence            432      2577899999999999 999999864

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.47  E-value=2.2e-13  Score=122.46  Aligned_cols=199  Identities=16%  Similarity=0.163  Sum_probs=117.3

Q ss_pred             CCccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC-----CCCCHHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS-----RDLQLGKIQESI  221 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~-----~~~~~~~l~~~i  221 (427)
                      +..|+||++++++|.+.    ..+.+.|+|++|+|||+|++++.+..   ...   ..|+.+.     .......+...+
T Consensus        11 ~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~---~~~---~~~i~~~~~~~~~~~~~~~~~~~~   80 (283)
T d2fnaa2          11 RKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINEL---NLP---YIYLDLRKFEERNYISYKDFLLEL   80 (283)
T ss_dssp             GGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHH---TCC---EEEEEGGGGTTCSCCCHHHHHHHH
T ss_pred             hhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHC---CCC---eEEEEeccccccccccHHHHHHHH
Confidence            47899999999998764    45689999999999999999998876   222   3344432     112234444444


Q ss_pred             HHHhCC--------------C-------------CCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccccc--ccccC
Q 042645          222 AKKIGL--------------Y-------------NESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFDLA--QVGLP  272 (427)
Q Consensus       222 ~~~l~~--------------~-------------~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~~~--~~~~~  272 (427)
                      ......              .             .......+..+....+. ...++++++++|++.......  .+...
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~i~id~~~~~~~~~~~~~~~~  159 (283)
T d2fnaa2          81 QKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFE-QASKDNVIIVLDEAQELVKLRGVNLLPA  159 (283)
T ss_dssp             HHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHH-HTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHH-hhcccccccccchhhhhcccchHHHHHH
Confidence            332210              0             00001222233333322 245789999999986432211  11101


Q ss_pred             ---CCCCCCCcEEEEecCChhHHhhcC------------CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHH
Q 042645          273 ---VPSRASASKVVFTTREFEVCGLMD------------AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETV  337 (427)
Q Consensus       273 ---l~~~~~gs~IivTtR~~~v~~~~~------------~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i  337 (427)
                         ..........+++++.........            ....+.|++++.+++.+++.+.+....... +.    .++|
T Consensus       160 l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~-~~----~~~i  234 (283)
T d2fnaa2         160 LAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDF-KD----YEVV  234 (283)
T ss_dssp             HHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCC-CC----HHHH
T ss_pred             HHHHHHhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCH-HH----HHHH
Confidence               111223445566655543322111            124578999999999999988764322111 22    5789


Q ss_pred             HHHcCCCchHHHHHHHHHcCCCCh
Q 042645          338 ARECGGLPLALITVGRAMASKKAP  361 (427)
Q Consensus       338 ~~~~~G~Plai~~~~~~L~~~~~~  361 (427)
                      ++.++|+|..+..++..+......
T Consensus       235 ~~~~~G~P~~L~~~~~~~~~~~~~  258 (283)
T d2fnaa2         235 YEKIGGIPGWLTYFGFIYLDNKNL  258 (283)
T ss_dssp             HHHHCSCHHHHHHHHHHHHHHCCH
T ss_pred             HHHhCCCHHHHHHHHHHHHhcccH
Confidence            999999999999998877654443

>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=99.19  E-value=1.1e-09  Score=97.27  Aligned_cols=170  Identities=15%  Similarity=0.145  Sum_probs=113.2

Q ss_pred             CCccccchhhHHHHHHHhcc------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHH
Q 042645          147 PPTVVGMQSTLDRVWRCLTE------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQES  220 (427)
Q Consensus       147 ~~~~vGR~~~~~~l~~~l~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~  220 (427)
                      |..++||+.++++|.++|..      ...+.+.|+|++|+||||+|+.+++.+. ... ....+++..........++..
T Consensus        15 p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~-~~~-~~~~~~~~~~~~~~~~~~~~~   92 (276)
T d1fnna2          15 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYK-DKT-TARFVYINGFIYRNFTAIIGE   92 (276)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHT-TSC-CCEEEEEETTTCCSHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHh-ccc-CCcEEEecchhhhhhhhhhhh
Confidence            45689999999999998853      2457899999999999999999999882 222 224567777777888899999


Q ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc-----ccccccCCC-CCCCCcEEEEecCChhHH
Q 042645          221 IAKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD-----LAQVGLPVP-SRASASKVVFTTREFEVC  292 (427)
Q Consensus       221 i~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~-----~~~~~~~l~-~~~~gs~IivTtR~~~v~  292 (427)
                      +....+..... ...........+...+.  ....++++|++++...     ...+..... .......+|.++......
T Consensus        93 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  171 (276)
T d1fnna2          93 IARSLNIPFPR-RGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVL  171 (276)
T ss_dssp             HHHHTTCCCCS-SCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHH
T ss_pred             hHHhhhhhhhh-hccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhh
Confidence            99888765432 34455666666665543  4677888888876422     111111111 112234455555554332


Q ss_pred             hhc-------CCCcceeccCCChHHHHHHHHHHh
Q 042645          293 GLM-------DAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       293 ~~~-------~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      ..+       .....+.+.+++.++..+++.+++
T Consensus       172 ~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         172 NNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             HTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             hhcchhhhhhhcchhccccchhHHHHHHHHHHHH
Confidence            211       123457899999999999998765

>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=99.13  E-value=9.7e-11  Score=101.48  Aligned_cols=184  Identities=15%  Similarity=0.148  Sum_probs=115.1

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      .+++|.++.+++|.+++.++..+.+.++|++|+||||+|+.+++... ....-..+.-++.+.......+...+......
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~-~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~~~   93 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELL-GRSYADGVLELNASDDRGIDVVRNQIKHFAQK   93 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHH-GGGHHHHEEEECTTSCCSHHHHHTHHHHHHHB
T ss_pred             HHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHh-ccccccccccccccccCCceehhhHHHHHHHh
Confidence            56899999999999999988877789999999999999999988762 11111123334444433333333222222111


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-H-HhhcCCCcceec
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-V-CGLMDAHKSFKV  303 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~~~~~~~l  303 (427)
                      ...                ...++.-++|+|+++....  ...+...+......++++++|.+.. + .........+.+
T Consensus        94 ~~~----------------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~  157 (224)
T d1sxjb2          94 KLH----------------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRY  157 (224)
T ss_dssp             CCC----------------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             hcc----------------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhh
Confidence            100                0023567899999986532  2222222223344566777766543 2 223344567899


Q ss_pred             cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHH
Q 042645          304 ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITV  351 (427)
Q Consensus       304 ~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~  351 (427)
                      ++++.++...++.+.+...+...+   .+..+.|++.|+|.+..+...
T Consensus       158 ~~~~~~~i~~~l~~i~~~e~~~i~---~~~l~~I~~~s~Gd~R~ai~~  202 (224)
T d1sxjb2         158 SKLSDEDVLKRLLQIIKLEDVKYT---NDGLEAIIFTAEGDMRQAINN  202 (224)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCCBC---HHHHHHHHHHHTTCHHHHHHH
T ss_pred             cccchhhhHHHHHHHHHhcccCCC---HHHHHHHHHHcCCcHHHHHHH
Confidence            999999999999887754332222   356889999999988655433

>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=99.09  E-value=2.4e-10  Score=99.19  Aligned_cols=178  Identities=14%  Similarity=0.165  Sum_probs=110.7

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      .+++|.++.++.|.+++..+..+.+.++|++|+||||+|+.+++... .......+.-.+.+...+..............
T Consensus        14 ~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~-~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~   92 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIY-GKNYSNMVLELNASDDRGIDVVRNQIKDFAST   92 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHH-TTSHHHHEEEECTTSCCSHHHHHTHHHHHHHB
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhh-cCCCcceeEEecccccCCeeeeecchhhcccc
Confidence            56899999999999999888777788999999999999999998862 12211222222333322222211111111110


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChh-H-HhhcCCCcceec
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFE-V-CGLMDAHKSFKV  303 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~~~~~~~l  303 (427)
                      .                 ....++.-++|+|+++....  -..+...+......+.++++|.... + .........+.+
T Consensus        93 ~-----------------~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~  155 (227)
T d1sxjc2          93 R-----------------QIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRF  155 (227)
T ss_dssp             C-----------------CSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             c-----------------cccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhcc
Confidence            0                 01123456899999976522  1222223333345677777777643 2 222334467899


Q ss_pred             cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          304 ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       304 ~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      .+++.++...++.+.+...+...+   .+..+.|++.++|...
T Consensus       156 ~~~~~~~i~~~l~~I~~~e~i~i~---~~~l~~i~~~s~Gd~R  195 (227)
T d1sxjc2         156 QPLPQEAIERRIANVLVHEKLKLS---PNAEKALIELSNGDMR  195 (227)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCCBC---HHHHHHHHHHHTTCHH
T ss_pred             ccccccccccccccccccccccCC---HHHHHHHHHHcCCcHH
Confidence            999999999999988755443222   4557889999999754

>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=99.08  E-value=1.5e-10  Score=101.05  Aligned_cols=190  Identities=11%  Similarity=0.090  Sum_probs=114.0

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      .+++|.++.++.|.+++.....+.+.++|++|+||||+++.+++..............++.+...........+-.....
T Consensus        12 ~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (237)
T d1sxjd2          12 DEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARL   91 (237)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHS
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHhhh
Confidence            46899999999999999888777899999999999999999988752111112233444444444444333333222111


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-H-HhhcCCCcceec
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-V-CGLMDAHKSFKV  303 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~~~~~~~l  303 (427)
                      ...   ....    ..+......+.-++|+|+++...  ....+...+......+.+++|+.+.. . .........+.+
T Consensus        92 ~~~---~~~~----~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f  164 (237)
T d1sxjd2          92 TVS---KPSK----HDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRF  164 (237)
T ss_dssp             CCC---CCCT----THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEEC
T ss_pred             hhh---hhhH----HHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhcc
Confidence            110   0000    11222233445589999997652  22222222222334566777665532 1 122222357899


Q ss_pred             cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          304 ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       304 ~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      .+++.++..+++.+.+...+...   ..+..+.|++.++|.+..
T Consensus       165 ~~~~~~~~~~~L~~i~~~e~i~i---~~~~l~~ia~~s~gd~R~  205 (237)
T d1sxjd2         165 KALDASNAIDRLRFISEQENVKC---DDGVLERILDISAGDLRR  205 (237)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCCC---CHHHHHHHHHHTSSCHHH
T ss_pred             ccccccccchhhhhhhhhhcCcC---CHHHHHHHHHHcCCCHHH
Confidence            99999999999998876544322   246689999999887643

>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=99.00  E-value=3.4e-10  Score=98.47  Aligned_cols=180  Identities=13%  Similarity=0.085  Sum_probs=107.5

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGL  227 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~  227 (427)
                      .+++|.+..+++|.+++..+..+.+.|+|++|+||||+|+.+++........++ .+-++.+...+...+...+......
T Consensus        24 ~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~-~~e~n~s~~~~~~~~~~~~~~~~~~  102 (231)
T d1iqpa2          24 DDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHN-FLELNASDERGINVIREKVKEFART  102 (231)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHH-EEEEETTCHHHHHTTHHHHHHHHHS
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCC-eeEEecCcccchhHHHHHHHHHHhh
Confidence            568999999999999999888888999999999999999999887621001111 2223322211111111111111000


Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-H-HhhcCCCcceec
Q 042645          228 YNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-V-CGLMDAHKSFKV  303 (427)
Q Consensus       228 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v-~~~~~~~~~~~l  303 (427)
                      .                 .....++.++++||++...  .+..+...+........+|.||...+ + .........+.+
T Consensus       103 ~-----------------~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~  165 (231)
T d1iqpa2         103 K-----------------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRF  165 (231)
T ss_dssp             C-----------------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEEC
T ss_pred             h-----------------hccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccc
Confidence            0                 0112467899999997542  22233222222233455666665432 2 112223356899


Q ss_pred             cCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHH
Q 042645          304 ECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLAL  348 (427)
Q Consensus       304 ~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai  348 (427)
                      .+.+.++....+.+.+.......   ..+..+.|++.|+|....+
T Consensus       166 ~~~~~~~~~~~l~~~~~~e~i~i---~~~~l~~I~~~~~gdiR~a  207 (231)
T d1iqpa2         166 RPLRDEDIAKRLRYIAENEGLEL---TEEGLQAILYIAEGDMRRA  207 (231)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCEE---CHHHHHHHHHHHTTCHHHH
T ss_pred             cccchhhHHHHHHHHHHHhCCCC---CHHHHHHHHHHcCCCHHHH
Confidence            99999999999998886544221   2456788999999876543

>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=98.98  E-value=3.6e-09  Score=92.25  Aligned_cols=190  Identities=15%  Similarity=0.198  Sum_probs=110.3

Q ss_pred             CccccchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      .+++|.++.++.|.+++..++. +.+.|+|++|+||||+|+.+++.... .....       ............+...-.
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~-~~~~~-------~~~~~~~~~~~~i~~~~~   83 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNC-ETGIT-------ATPCGVCDNCREIEQGRF   83 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHC-TTCSC-------SSCCSCSHHHHHHHHTCC
T ss_pred             HHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcC-ccccc-------cCccccchHHHHHHcCCC
Confidence            4689999999999999987654 45889999999999999998877621 11110       000111111222222110


Q ss_pred             CCC---CCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCccc--ccccccCCCCCCCCcEEEEecCChhH--Hhh
Q 042645          227 LYN---ESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELFD--LAQVGLPVPSRASASKVVFTTREFEV--CGL  294 (427)
Q Consensus       227 ~~~---~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~~--~~~~~~~l~~~~~gs~IivTtR~~~v--~~~  294 (427)
                      ...   ........+... .+.+.+     .++.-++|||+++....  -..+...+......+.+|++|.+.+-  ...
T Consensus        84 ~~~~~~~~~~~~~i~~ir-~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i  162 (239)
T d1njfa_          84 VDLIEIDAASRTKVEDTR-DLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTI  162 (239)
T ss_dssp             TTEEEEETTCSSSHHHHH-HHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHH
T ss_pred             CeEEEecchhcCCHHHHH-HHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhH
Confidence            000   000111122222 222222     24566999999987522  22233333333456778887776432  222


Q ss_pred             cCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          295 MDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       295 ~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      ..-...+.+.+++.++..+.+.+.+......   -..+.+..|++.++|.+--+.
T Consensus       163 ~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~---~~~~~l~~i~~~s~Gd~R~ai  214 (239)
T d1njfa_         163 LSRCLQFHLKALDVEQIRHQLEHILNEEHIA---HEPRALQLLARAAEGSLRDAL  214 (239)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHHTCC---BCHHHHHHHHHHTTTCHHHHH
T ss_pred             hhhhcccccccCcHHHhhhHHHHHHhhhccC---CCHHHHHHHHHHcCCCHHHHH
Confidence            2334678999999999999988877543322   224568889999999886433

>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=98.97  E-value=1.2e-08  Score=91.10  Aligned_cols=199  Identities=13%  Similarity=0.133  Sum_probs=120.2

Q ss_pred             CCCccccchhhHHHHHHHhcc----C----C-CeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEeCCCCC
Q 042645          146 LPPTVVGMQSTLDRVWRCLTE----E----P-VGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVVSRDLQ  213 (427)
Q Consensus       146 ~~~~~vGR~~~~~~l~~~l~~----~----~-~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~~~~~~  213 (427)
                      .|+.++||+.++++|.+++..    +    + ..++.|+|++|+|||++++.+++.+..   .........++.......
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~   93 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPN   93 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccc
Confidence            457899999999999887632    1    1 224567899999999999999987621   112224556777777778


Q ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhc--CCcEEEEEeccCCccc-----------ccccccCCC---CCC
Q 042645          214 LGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMR--NRKIVLLLDDIWELFD-----------LAQVGLPVP---SRA  277 (427)
Q Consensus       214 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVlDdv~~~~~-----------~~~~~~~l~---~~~  277 (427)
                      ....+..+...++..... ...........+.....  +...++++|.++....           +..+...+.   ...
T Consensus        94 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~  172 (287)
T d1w5sa2          94 LYTILSLIVRQTGYPIQV-RGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVN  172 (287)
T ss_dssp             HHHHHHHHHHHHTCCCCC-TTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCC
T ss_pred             hhhHHHHHhhhccccccc-ccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhccc
Confidence            888888888887765432 34455566666665553  5677888898764311           111111111   112


Q ss_pred             CCcEEEEecCChhHH-------h-hcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHc------CC
Q 042645          278 SASKVVFTTREFEVC-------G-LMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVAREC------GG  343 (427)
Q Consensus       278 ~gs~IivTtR~~~v~-------~-~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~------~G  343 (427)
                      .-..|++++......       . .......+.+++++.++..+++..++.... ....-..+..+.|++++      .|
T Consensus       173 ~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~-~~~~~~~~al~~ia~~~~~~~~~~g  251 (287)
T d1w5sa2         173 RIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGL-RDTVWEPRHLELISDVYGEDKGGDG  251 (287)
T ss_dssp             BEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHB-CTTSCCHHHHHHHHHHHCGGGTSCC
T ss_pred             ceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhh-ccCCCCHHHHHHHHHHHhccccCCC
Confidence            223344444443221       1 111235688999999999999998763211 01111245566666655      56


Q ss_pred             Cch
Q 042645          344 LPL  346 (427)
Q Consensus       344 ~Pl  346 (427)
                      .|-
T Consensus       252 d~R  254 (287)
T d1w5sa2         252 SAR  254 (287)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            664

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.92  E-value=7.3e-10  Score=97.54  Aligned_cols=191  Identities=9%  Similarity=0.107  Sum_probs=100.8

Q ss_pred             CccccchhhHHHHHHHhccC-CCeEEEEEecCCCcHHHHHHHHHhhccCCC---CCCcEEEEEEeCCC------------
Q 042645          148 PTVVGMQSTLDRVWRCLTEE-PVGIVGLYGMGGVGKTTLLTQINNSFLHTP---NDFDFVIWEVVSRD------------  211 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~-~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~~f~~~~wv~~~~~------------  211 (427)
                      .+++|.++..+.|.+++... ..+.+.|+|++|+||||+|+.+++......   ..++...+...+..            
T Consensus        11 ~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (252)
T d1sxje2          11 NALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYH   90 (252)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECSSE
T ss_pred             HHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhhhhhccCCcc
Confidence            46899999999998888654 455688999999999999999998752111   11111111110000            


Q ss_pred             ---------CCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc--cccccccCCCCCCCCc
Q 042645          212 ---------LQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF--DLAQVGLPVPSRASAS  280 (427)
Q Consensus       212 ---------~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs  280 (427)
                               ...................    ..    ...-......+.-++|||+++...  ....+...+......+
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~----~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~  162 (252)
T d1sxje2          91 LEITPSDMGNNDRIVIQELLKEVAQMEQ----VD----FQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNI  162 (252)
T ss_dssp             EEECCC----CCHHHHHHHHHHHTTTTC--------------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTE
T ss_pred             ceeeecccccCCcceeeehhhhhhhhhh----hh----hhhcccccCCCceEEEeccccccccccchhhhcccccccccc
Confidence                     0011111111111110000    00    000001112345589999998652  2223322232234557


Q ss_pred             EEEEecCChh-H-HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHH
Q 042645          281 KVVFTTREFE-V-CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLAL  348 (427)
Q Consensus       281 ~IivTtR~~~-v-~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai  348 (427)
                      ++|+||.+.+ + .....-...+++.+++.++..+++...+...+....  .++..+.|++.+.|.+..+
T Consensus       163 ~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~--~~~~l~~i~~~s~Gd~R~a  230 (252)
T d1sxje2         163 RLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLE--TKDILKRIAQASNGNLRVS  230 (252)
T ss_dssp             EEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEEC--CSHHHHHHHHHHTTCHHHH
T ss_pred             cceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCC--cHHHHHHHHHHcCCcHHHH
Confidence            7777776543 1 111122356889999999999999877643221111  2356788999999987643

>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=98.92  E-value=7.5e-09  Score=90.62  Aligned_cols=153  Identities=16%  Similarity=0.283  Sum_probs=100.4

Q ss_pred             ccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCC--C-CCcEEEEE-EeCCCCCHHHHHHHHHHH
Q 042645          149 TVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTP--N-DFDFVIWE-VVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~-~f~~~~wv-~~~~~~~~~~l~~~i~~~  224 (427)
                      .++||+++++++++.|......-+.++|++|+|||+++..++.......  . .....+|. +.+.      ++      
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~------li------   86 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS------LL------   86 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---------------
T ss_pred             cccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeech------Hh------
Confidence            4699999999999999877767788999999999999999887753211  1 12234442 2221      10      


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHhc-CCcEEEEEeccCCcc----------cccc-cccCCCCCCCCcEEEEecCChhHH
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTMR-NRKIVLLLDDIWELF----------DLAQ-VGLPVPSRASASKVVFTTREFEVC  292 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L~-~k~~LlVlDdv~~~~----------~~~~-~~~~l~~~~~gs~IivTtR~~~v~  292 (427)
                         .... .....++....+...+. .++.++++||++...          +... +.+++.  ...-++|.||..+...
T Consensus        87 ---ag~~-~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~eey~  160 (268)
T d1r6bx2          87 ---AGTK-YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFS  160 (268)
T ss_dssp             ---CCCC-CSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHH
T ss_pred             ---ccCc-cchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCHHHHH
Confidence               0000 23345555555555554 567999999987641          1222 233343  3356889999888775


Q ss_pred             hhcCC-------CcceeccCCChHHHHHHHHHHh
Q 042645          293 GLMDA-------HKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       293 ~~~~~-------~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      .....       .+.+.+++.+.+++..++....
T Consensus       161 ~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         161 NIFEKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             CCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence            54332       2568999999999999997654

>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=98.82  E-value=7.9e-09  Score=90.79  Aligned_cols=185  Identities=11%  Similarity=0.099  Sum_probs=106.1

Q ss_pred             CccccchhhHHHHHHHhcc-----------------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----------------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      .+++|.++.+++|.+++..                 +..+.+.++|++|+||||+|+.+++...      ...++++.+.
T Consensus        14 ~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~------~~~~~~~~~~   87 (253)
T d1sxja2          14 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG------YDILEQNASD   87 (253)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT------CEEEEECTTS
T ss_pred             HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHH------hhhhcccccc
Confidence            5689999999999998842                 2346899999999999999999999871      1244555554


Q ss_pred             CCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc-----ccccccCCCCCCCCcEEEEe
Q 042645          211 DLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD-----LAQVGLPVPSRASASKVVFT  285 (427)
Q Consensus       211 ~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~-----~~~~~~~l~~~~~gs~IivT  285 (427)
                      ..+...+. ..................    ........++..++++|+++....     +..+......  ....+++|
T Consensus        88 ~~~~~~~~-~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~--~~~~ii~i  160 (253)
T d1sxja2          88 VRSKTLLN-AGVKNALDNMSVVGYFKH----NEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLILI  160 (253)
T ss_dssp             CCCHHHHH-HTGGGGTTBCCSTTTTTC--------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEEE
T ss_pred             chhhHHHH-HHHHHHhhcchhhhhhhh----hhhcccccccceEEEeeeccccccchhhhhHHHhhhhcc--cccccccc
Confidence            44433332 222222111100000000    001112345788999999875422     1121111111  12234444


Q ss_pred             cCC--h-hHHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHH
Q 042645          286 TRE--F-EVCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLAL  348 (427)
Q Consensus       286 tR~--~-~v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai  348 (427)
                      +..  . .+.........+.+.+++.++....+...+...+...++.   ....|++.++|....+
T Consensus       161 ~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~---~l~~i~~~s~GDiR~a  223 (253)
T d1sxja2         161 CNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPN---VIDRLIQTTRGDIRQV  223 (253)
T ss_dssp             ESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTT---HHHHHHHHTTTCHHHH
T ss_pred             cccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCHH---HHHHHHHhCCCcHHHH
Confidence            332  2 2233333446789999999999999988764433233333   4788999999977433

>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=98.81  E-value=9e-09  Score=85.11  Aligned_cols=150  Identities=16%  Similarity=0.269  Sum_probs=91.2

Q ss_pred             ccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCC--C-CCCcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          149 TVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHT--P-NDFDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~-~~f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      .++||+++++++++.|......-+.++|.+|+|||+++..++.+....  . ...+..+|.     .+...++.    ..
T Consensus        23 ~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~-----ld~~~LiA----g~   93 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA-----LDMGALVA----GA   93 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEE-----ECHHHHHT----TT
T ss_pred             CCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEE-----eeHHHHhc----cC
Confidence            468999999999999998766778999999999999999988766321  1 122334442     12222221    00


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHh-c-CCcEEEEEeccCCccc---------ccc-cccCCCCCCCCcEEEEecCChhHHh
Q 042645          226 GLYNESWDNKSFDEKAQEIFKTM-R-NRKIVLLLDDIWELFD---------LAQ-VGLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~l~~~L-~-~k~~LlVlDdv~~~~~---------~~~-~~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                      .      .....++....+.+.+ + ..+.+|++||+.....         ... +.+++.  ...-++|.||..++...
T Consensus        94 ~------~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~--rg~l~~IgatT~eey~~  165 (195)
T d1jbka_          94 K------YRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQ  165 (195)
T ss_dssp             C------SHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECHHHHHH
T ss_pred             C------ccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHh--CCCceEEecCCHHHHHH
Confidence            0      0112233343333333 2 4589999999976421         111 122222  23457888888777654


Q ss_pred             hcC-------CCcceeccCCChHHHHHHH
Q 042645          294 LMD-------AHKSFKVECLGYEDAWRLF  315 (427)
Q Consensus       294 ~~~-------~~~~~~l~~L~~~e~~~lf  315 (427)
                      ...       ..+.+.++..+.+++..++
T Consensus       166 ~~e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         166 YIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             HHHcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence            333       2356888888888876643

>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=98.68  E-value=4.5e-07  Score=78.42  Aligned_cols=171  Identities=17%  Similarity=0.153  Sum_probs=101.0

Q ss_pred             CccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      .+++|.++.+++|..++..     ...+.+.++|++|+||||+|+.+++.+   ...|   +.++.+......       
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~---~~~~---~~~~~~~~~~~~-------   75 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL---QTNI---HVTSGPVLVKQG-------   75 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH---TCCE---EEEETTTCCSHH-------
T ss_pred             HHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhcc---CCCc---ccccCcccccHH-------
Confidence            5689999999999888752     345678899999999999999999987   2222   223322222221       


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------ccccccC-----------CCCCCCCcEE
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------LAQVGLP-----------VPSRASASKV  282 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~~~~~~~-----------l~~~~~gs~I  282 (427)
                                      .....+..  .+++..+++|+++....         .+.....           .........+
T Consensus        76 ----------------~~~~~~~~--~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (238)
T d1in4a2          76 ----------------DMAAILTS--LERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTL  137 (238)
T ss_dssp             ----------------HHHHHHHH--CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEE
T ss_pred             ----------------HHHHHHHh--hccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEE
Confidence                            11111111  24556777787764311         0000000           0001223455


Q ss_pred             EEecCChhH---HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHH
Q 042645          283 VFTTREFEV---CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVG  352 (427)
Q Consensus       283 ivTtR~~~v---~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~  352 (427)
                      |.+|.+...   .........+.+++.+.++...++..........   ...+....|++.++|.+-.+..+.
T Consensus       138 I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~l~~i~~~s~gd~R~ai~~l  207 (238)
T d1in4a2         138 VGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVE---IEDAAAEMIAKRSRGTPRIAIRLT  207 (238)
T ss_dssp             EEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCC---BCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             EEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccch---hhHHHHHHHHHhCCCCHHHHHHHH
Confidence            555555432   1111233457899999999999998877544322   234568899999999887665544

>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=98.66  E-value=4.9e-07  Score=78.27  Aligned_cols=173  Identities=16%  Similarity=0.081  Sum_probs=100.3

Q ss_pred             CccccchhhHHHHHHHhcc-----CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          148 PTVVGMQSTLDRVWRCLTE-----EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      .++||.++.+++|..++..     ...+.+.++|++|+||||+|+.+++..   ...   ..+++.+.....        
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~---~~~---~~~~~~~~~~~~--------   74 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL---GVN---LRVTSGPAIEKP--------   74 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHH---TCC---EEEEETTTCCSH--------
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh---CCC---eEeccCCccccc--------
Confidence            4689999999888887742     245678899999999999999999887   222   223332222111        


Q ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------ccc----cccCC-------CCCCCCcEE
Q 042645          223 KKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------LAQ----VGLPV-------PSRASASKV  282 (427)
Q Consensus       223 ~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~~~----~~~~l-------~~~~~gs~I  282 (427)
                                     ......+...+ +.+.++++|+++....         .+.    .....       ....+...+
T Consensus        75 ---------------~~~~~~~~~~~-~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (239)
T d1ixsb2          75 ---------------GDLAAILANSL-EEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTL  138 (239)
T ss_dssp             ---------------HHHHHHHHTTC-CTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEE
T ss_pred             ---------------hhhHHHHHhhc-cCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEE
Confidence                           11111222222 2344667788764311         000    00000       001123344


Q ss_pred             EEecCC-hhH--HhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHHHHHH
Q 042645          283 VFTTRE-FEV--CGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALITVGR  353 (427)
Q Consensus       283 ivTtR~-~~v--~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~~~~~  353 (427)
                      +.+|.+ ...  .........+.+...+.++...++.+.+...+..   ...+....|++.+.|.+-.+..+..
T Consensus       139 i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~---~~~~~l~~ia~~s~gd~R~a~~~l~  209 (239)
T d1ixsb2         139 IGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVR---ITEEAALEIGRRSRGTMRVAKRLFR  209 (239)
T ss_dssp             EEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCCC---BCHHHHHHHHHHTTSSHHHHHHHHH
T ss_pred             EeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCCc---cchHHHHHHHHHcCCCHHHHHHHHH
Confidence            444433 221  2222345667899999999999888777544322   2356789999999998876655443

>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=98.65  E-value=4.5e-07  Score=76.59  Aligned_cols=181  Identities=11%  Similarity=0.059  Sum_probs=103.9

Q ss_pred             cchhhHHHHHHHhccCCC-eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCC--
Q 042645          152 GMQSTLDRVWRCLTEEPV-GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLY--  228 (427)
Q Consensus       152 GR~~~~~~l~~~l~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~--  228 (427)
                      +-+...+++.+.+..+.. +.+.++|++|+||||+|+.+++.+.........    .+...    .-...+.......  
T Consensus         6 w~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~----~~~~~----~~~~~i~~~~~~~~~   77 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHK----SCGHC----RGCQLMQAGTHPDYY   77 (207)
T ss_dssp             GGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTB----CCSCS----HHHHHHHHTCCTTEE
T ss_pred             ccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccc----ccccc----chhhhhhhccccccc
Confidence            445667888888877654 458999999999999999998865211100000    00000    0111111111000  


Q ss_pred             ----CCCCCCCCHHHHHHHHHHHh-----cCCcEEEEEeccCCcc--cccccccCCCCCCCCcEEEEecCChh-HHh-hc
Q 042645          229 ----NESWDNKSFDEKAQEIFKTM-----RNRKIVLLLDDIWELF--DLAQVGLPVPSRASASKVVFTTREFE-VCG-LM  295 (427)
Q Consensus       229 ----~~~~~~~~~~~~~~~l~~~L-----~~k~~LlVlDdv~~~~--~~~~~~~~l~~~~~gs~IivTtR~~~-v~~-~~  295 (427)
                          .........++ ++.+.+.+     .+++-++|+||++...  ....+...+.....++.+|+||++.+ +.. ..
T Consensus        78 ~~~~~~~~~~i~~~~-ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~  156 (207)
T d1a5ta2          78 TLAPEKGKNTLGVDA-VREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLR  156 (207)
T ss_dssp             EECCCTTCSSBCHHH-HHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHH
T ss_pred             hhhhhhcccccccch-hhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhc
Confidence                00001112222 22333333     2466799999998653  23334333444456788888887754 322 22


Q ss_pred             CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchHHH
Q 042645          296 DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLALI  349 (427)
Q Consensus       296 ~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Plai~  349 (427)
                      .-...+.+.+++.++....+.+....        .++.+..|++.++|.|..+.
T Consensus       157 SRc~~i~~~~~~~~~~~~~L~~~~~~--------~~~~~~~i~~~s~Gs~r~al  202 (207)
T d1a5ta2         157 SRCRLHYLAPPPEQYAVTWLSREVTM--------SQDALLAALRLSAGSPGAAL  202 (207)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHCCC--------CHHHHHHHHHHTTTCHHHHH
T ss_pred             ceeEEEecCCCCHHHHHHHHHHcCCC--------CHHHHHHHHHHcCCCHHHHH
Confidence            33467899999999999999776421        13558889999999986543

>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=98.61  E-value=3.1e-07  Score=80.05  Aligned_cols=173  Identities=17%  Similarity=0.115  Sum_probs=101.2

Q ss_pred             CccccchhhHHHHHHHh---cc---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCL---TE---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l---~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|.++.+++|.+.+   ..         ...+.+.++|++|+|||++|+.+++..   ..+   .+.+..+.-.+  
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~---~~~---~~~i~~~~l~~--   83 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA---KVP---FFTISGSDFVE--   83 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH---TCC---EEEECSCSSTT--
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc---CCC---EEEEEhHHhhh--
Confidence            46899998887775543   21         235678999999999999999999887   211   22233222111  


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCcc------------c----ccccccCCC--CCC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELF------------D----LAQVGLPVP--SRA  277 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~------------~----~~~~~~~l~--~~~  277 (427)
                                     ...+.....+...+...-+..+++|++||++...            .    ...+...+.  ...
T Consensus        84 ---------------~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~  148 (256)
T d1lv7a_          84 ---------------MFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGN  148 (256)
T ss_dssp             ---------------SCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSS
T ss_pred             ---------------cchhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCC
Confidence                           0122333333344444445788999999996420            0    011111111  123


Q ss_pred             CCcEEEEecCChhH-Hhh-cC---CCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          278 SASKVVFTTREFEV-CGL-MD---AHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       278 ~gs~IivTtR~~~v-~~~-~~---~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      .+.-||.||..... ... ..   -...+.+++.+.++-.++|+............+    ...+++.+.|..-+
T Consensus       149 ~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~----~~~la~~t~G~s~a  219 (256)
T d1lv7a_         149 EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDID----AAIIARGTPGFSGA  219 (256)
T ss_dssp             SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCCHH
T ss_pred             CCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccC----HHHHHHhCCCCCHH
Confidence            34445557765432 121 21   346789999999999999998875544332233    46677888887543

>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=98.55  E-value=5.3e-07  Score=78.20  Aligned_cols=171  Identities=16%  Similarity=0.152  Sum_probs=96.5

Q ss_pred             CccccchhhHHHHHHHh---cc---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          148 PTVVGMQSTLDRVWRCL---TE---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l---~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      .+++|-++.+++|.+.+   ..         ...+-|.++|++|+|||+||+.+++..   ..+   .+.++.      .
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~---~~~---~~~i~~------~   76 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA---RVP---FITASG------S   76 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT---TCC---EEEEEH------H
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHc---CCC---EEEEEh------H
Confidence            46789988777665533   21         234569999999999999999999886   221   222222      2


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH-hcCCcEEEEEeccCCccc----------------ccccccCCC--CC
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKT-MRNRKIVLLLDDIWELFD----------------LAQVGLPVP--SR  276 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~-L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~--~~  276 (427)
                      ++..    .    .   .+. ....+..+.+. -...+++|+|||++....                ...+...+.  ..
T Consensus        77 ~l~~----~----~---~g~-~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~  144 (247)
T d1ixza_          77 DFVE----M----F---VGV-GAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK  144 (247)
T ss_dssp             HHHH----S----C---TTH-HHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCT
T ss_pred             Hhhh----c----c---ccH-HHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCC
Confidence            2221    0    0   111 12223333333 346889999999864210                111111111  11


Q ss_pred             CCCcEEEEecCChh-HHhhc----CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCch
Q 042645          277 ASASKVVFTTREFE-VCGLM----DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPL  346 (427)
Q Consensus       277 ~~gs~IivTtR~~~-v~~~~----~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pl  346 (427)
                      ..+.-||.||.... +...+    .-...+.+++.+.++-.++|+............+    ...+++.|.|..-
T Consensus       145 ~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~----~~~la~~t~g~s~  215 (247)
T d1ixza_         145 DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVD----LALLAKRTPGFVG  215 (247)
T ss_dssp             TCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCCH
T ss_pred             CCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccC----HHHHHHHCCCCCH
Confidence            22333334665433 22211    1235789999999999999998886544333333    4667788888644

>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=98.55  E-value=6.4e-07  Score=78.39  Aligned_cols=172  Identities=16%  Similarity=0.121  Sum_probs=101.1

Q ss_pred             ccccchhhHHHHHHHhc----c---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHH
Q 042645          149 TVVGMQSTLDRVWRCLT----E---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~  215 (427)
                      ++.|-+..+++|.+.+.    .         ...+-+.++|++|+|||++|+.+++..   ..+   .+.++.+      
T Consensus         5 dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~---~~~---~~~i~~~------   72 (258)
T d1e32a2           5 DVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET---GAF---FFLINGP------   72 (258)
T ss_dssp             GCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHT---TCE---EEEECHH------
T ss_pred             hhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHh---CCe---EEEEEch------
Confidence            57899988888877642    1         235679999999999999999999876   222   2222211      


Q ss_pred             HHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc---------c----cccccCC--CCCCCCc
Q 042645          216 KIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD---------L----AQVGLPV--PSRASAS  280 (427)
Q Consensus       216 ~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~---------~----~~~~~~l--~~~~~gs  280 (427)
                      .+.        ...   .+.....+...+...-..++++|++||++....         .    ..+...+  .....+.
T Consensus        73 ~l~--------~~~---~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~v  141 (258)
T d1e32a2          73 EIM--------SKL---AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  141 (258)
T ss_dssp             HHT--------TSC---TTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCE
T ss_pred             hhc--------ccc---cccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCc
Confidence            110        000   111122222333333457899999999986411         0    1111111  1223344


Q ss_pred             EEEEecCChhHHh-hc----CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          281 KVVFTTREFEVCG-LM----DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       281 ~IivTtR~~~v~~-~~----~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      -||.||....-.. .+    .-...+.++..+.++-..+|+..........+.+    ...|++.+.|+-.+
T Consensus       142 lvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~----~~~la~~t~G~s~a  209 (258)
T d1e32a2         142 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVD----LEQVANETHGHVGA  209 (258)
T ss_dssp             EEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCC----HHHHHHHCTTCCHH
T ss_pred             cEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccc----hhhhhhcccCCCHH
Confidence            5566777654311 11    1346789999999999999998875443222222    56788999996543

>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=98.53  E-value=3.8e-07  Score=84.12  Aligned_cols=153  Identities=14%  Similarity=0.202  Sum_probs=89.8

Q ss_pred             ccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccC--C-CCCCcEEEEE-EeCCCCCHHHHHHHHHHH
Q 042645          149 TVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLH--T-PNDFDFVIWE-VVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~--~-~~~f~~~~wv-~~~~~~~~~~l~~~i~~~  224 (427)
                      .++||+.+++++++.|...+..-+.++|.+|+|||+++..++.+...  + ....+..+|. .++      .++.    .
T Consensus        23 ~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~------~l~a----g   92 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMG------SLLA----G   92 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC----------------
T ss_pred             CCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHh------hhhc----c
Confidence            36899999999999998765566788899999999998777765421  1 2233344443 222      1111    0


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHh-cC-CcEEEEEeccCCccc---------ccc-cccCCCCCCCCcEEEEecCChhHH
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTM-RN-RKIVLLLDDIWELFD---------LAQ-VGLPVPSRASASKVVFTTREFEVC  292 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L-~~-k~~LlVlDdv~~~~~---------~~~-~~~~l~~~~~gs~IivTtR~~~v~  292 (427)
                      ..      .....++....+...+ .. .+++|++|+++....         ... +.+++.  ...-++|-+|......
T Consensus        93 ~~------~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~--rg~~~~I~~tT~~ey~  164 (387)
T d1qvra2          93 AK------YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEYR  164 (387)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHH--TTCCCEEEEECHHHHH
T ss_pred             cC------cchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHh--CCCcceeeecCHHHHH
Confidence            00      1123444554444444 33 479999999986521         111 222232  2235678777776663


Q ss_pred             hh------cCCCcceeccCCChHHHHHHHHHHh
Q 042645          293 GL------MDAHKSFKVECLGYEDAWRLFEEKV  319 (427)
Q Consensus       293 ~~------~~~~~~~~l~~L~~~e~~~lf~~~~  319 (427)
                      ..      ....+.+.+++.+.+++..++....
T Consensus       165 ~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         165 EIEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             HHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             HhcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence            32      1123678999999999999988654

>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=98.42  E-value=1.2e-06  Score=74.14  Aligned_cols=168  Identities=17%  Similarity=0.200  Sum_probs=93.3

Q ss_pred             ccccchhhH--HHHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          149 TVVGMQSTL--DRVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       149 ~~vGR~~~~--~~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      .++|.....  ..+.++....  ....+.|+|++|+|||.|++.+++...   .....+++++      ..++...+...
T Consensus        12 F~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~---~~~~~~~~~~------~~~~~~~~~~~   82 (213)
T d1l8qa2          12 FIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAK---KRGYRVIYSS------ADDFAQAMVEH   82 (213)
T ss_dssp             CCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHH---HTTCCEEEEE------HHHHHHHHHHH
T ss_pred             ccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhc---cCccceEEec------hHHHHHHHHHH
Confidence            346654432  2333333332  223488999999999999999999883   2233455543      34455555544


Q ss_pred             hCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCc---ccccc-cccCCCC-CCCCcEEEEecCChh---------
Q 042645          225 IGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWEL---FDLAQ-VGLPVPS-RASASKVVFTTREFE---------  290 (427)
Q Consensus       225 l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~---~~~~~-~~~~l~~-~~~gs~IivTtR~~~---------  290 (427)
                      +...       ...    .+.+.++ .--+|+|||++..   ..|+. +...+.. ...|..||+||+...         
T Consensus        83 ~~~~-------~~~----~~~~~~~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~d  150 (213)
T d1l8qa2          83 LKKG-------TIN----EFRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDR  150 (213)
T ss_dssp             HHHT-------CHH----HHHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHH
T ss_pred             HHcc-------chh----hHHHHHh-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchH
Confidence            4211       111    2222222 3458999999754   23433 2222211 235678999998643         


Q ss_pred             HHhhcCCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHc
Q 042645          291 VCGLMDAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVAREC  341 (427)
Q Consensus       291 v~~~~~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~  341 (427)
                      +...+.....+.++ ++.++-.+++++.+...+...+   .++.+-|++.+
T Consensus       151 L~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~---~~v~~yl~~~~  197 (213)
T d1l8qa2         151 LVSRFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELR---KEVIDYLLENT  197 (213)
T ss_dssp             HHHHHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCC---HHHHHHHHHHC
T ss_pred             HHHHhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhc
Confidence            23334455677785 4777777888877743332222   34556566554

>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=98.27  E-value=1.7e-06  Score=75.89  Aligned_cols=173  Identities=15%  Similarity=0.185  Sum_probs=96.7

Q ss_pred             CccccchhhHHHHHHHhc----c---------CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH
Q 042645          148 PTVVGMQSTLDRVWRCLT----E---------EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~  214 (427)
                      .+++|-++.+++|.+.+.    .         ...+.|.++|++|+|||+||+.+++..   ..+|     +.++    .
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~---~~~~-----~~~~----~   74 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC---QANF-----ISIK----G   74 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHT---TCEE-----EEEC----H
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHh---CCcE-----EEEE----H
Confidence            346788777666665542    1         234579999999999999999999987   2221     2221    1


Q ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHhcCCcEEEEEeccCCccc----------------ccccccCCCC--C
Q 042645          215 GKIQESIAKKIGLYNESWDNKSFDEKAQEIFKTMRNRKIVLLLDDIWELFD----------------LAQVGLPVPS--R  276 (427)
Q Consensus       215 ~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~~~----------------~~~~~~~l~~--~  276 (427)
                      ..+.       +.    ........+...+...-...+++|+|||++....                ...+...+..  .
T Consensus        75 ~~l~-------~~----~~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~  143 (265)
T d1r7ra3          75 PELL-------TM----WFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST  143 (265)
T ss_dssp             HHHH-------TS----CTTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC----
T ss_pred             HHhh-------hc----cccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCC
Confidence            1111       10    0122222333333334456899999999974311                0112222221  1


Q ss_pred             CCCcEEEEecCChh-HHhhc----CCCcceeccCCChHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHcCCCchH
Q 042645          277 ASASKVVFTTREFE-VCGLM----DAHKSFKVECLGYEDAWRLFEEKVGRDILDSHPDIPELAETVARECGGLPLA  347 (427)
Q Consensus       277 ~~gs~IivTtR~~~-v~~~~----~~~~~~~l~~L~~~e~~~lf~~~~~~~~~~~~~~~~~~~~~i~~~~~G~Pla  347 (427)
                      ..+--||.||.... +...+    .-...+++++.+.++-.++|+..........+.+    ...|++++.|...+
T Consensus       144 ~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~----l~~la~~t~g~s~~  215 (265)
T d1r7ra3         144 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVD----LEFLAKMTNGFSGA  215 (265)
T ss_dssp             --CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCC----CHHHHHHHCSSCCH
T ss_pred             CCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhh----HHHHHhcCCCCCHH
Confidence            23345566666543 22211    1235789999999999999988765432222222    46778888886654

>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=98.23  E-value=2.9e-05  Score=66.87  Aligned_cols=46  Identities=24%  Similarity=0.207  Sum_probs=35.5

Q ss_pred             CccccchhhHHHHHHHhc-------c---CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLT-------E---EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~-------~---~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|..+.++.+++-..       .   ...+.|.++|++|+|||++|+.+++..
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~   64 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEES   64 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhcc
Confidence            457888777776665543       1   235678999999999999999999887

>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=97.82  E-value=4.4e-05  Score=63.33  Aligned_cols=115  Identities=10%  Similarity=0.070  Sum_probs=68.3

Q ss_pred             hHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccC-CCCCCcEEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCC
Q 042645          156 TLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLH-TPNDFDFVIWEVVS-RDLQLGKIQESIAKKIGLYNESWD  233 (427)
Q Consensus       156 ~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~~f~~~~wv~~~-~~~~~~~l~~~i~~~l~~~~~~~~  233 (427)
                      .++.+.+++..+..+.+.++|++|+|||++|..+.+.... ...|.|. +++... .....+++ +++...+....    
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~-~~i~~~~~~I~Id~I-R~i~~~~~~~~----   75 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDDI-RTIKDFLNYSP----   75 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHHH-HHHHHHHTSCC----
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCE-EEEeCCcCCCCHHHH-HHHHHHHhhCc----
Confidence            3556666777778899999999999999999998876522 2234443 333321 12223332 23433333221    


Q ss_pred             CCCHHHHHHHHHHHhcCCcEEEEEeccCCc--ccccccccCCCCCCCCcEEEEecCChh
Q 042645          234 NKSFDEKAQEIFKTMRNRKIVLLLDDIWEL--FDLAQVGLPVPSRASASKVVFTTREFE  290 (427)
Q Consensus       234 ~~~~~~~~~~l~~~L~~k~~LlVlDdv~~~--~~~~~~~~~l~~~~~gs~IivTtR~~~  290 (427)
                                    ..+++=++|+|+++..  .....+...+-....++.+|++|.+.+
T Consensus        76 --------------~~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~  120 (198)
T d2gnoa2          76 --------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWH  120 (198)
T ss_dssp             --------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGG
T ss_pred             --------------ccCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChh
Confidence                          1245569999999865  334444444433355677777777643

>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=97.34  E-value=0.00038  Score=57.66  Aligned_cols=60  Identities=18%  Similarity=0.233  Sum_probs=43.2

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCC
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~  229 (427)
                      ++.++|.++|+.|+||||.+.+++..+. ..+  ..+..++... .....+-++..++.++.+.
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~-~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   64 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQ-NLG--KKVMFCAGDTFRAAGGTQLSEWGKRLSIPV   64 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHH-TTT--CCEEEECCCCSSTTHHHHHHHHHHHHTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH-HCC--CcEEEEEeccccccchhhHhhcccccCceE
Confidence            3567999999999999999888888772 222  3566676543 3456677777788777653

>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=97.28  E-value=0.0005  Score=56.93  Aligned_cols=91  Identities=14%  Similarity=0.171  Sum_probs=52.2

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCH--HHHHHHHHHHhCCCCCC-CCCCCHHHHHHH
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQL--GKIQESIAKKIGLYNES-WDNKSFDEKAQE  243 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~--~~l~~~i~~~l~~~~~~-~~~~~~~~~~~~  243 (427)
                      ....+|.++|+.|+||||.+.+++..+ ...+  ..+..++. +.+.+  .+-++...+.++++... ....+....+..
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~~~-~~~g--~kV~lit~-Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~   82 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLARQF-EQQG--KSVMLAAG-DTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFD   82 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHHHH-HTTT--CCEEEECC-CTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH-HHCC--CcEEEEec-ccccccchhhhhhhhhhcCCcccccccCCCHHHHHHH
Confidence            346799999999999999988888877 2222  23333333 44443  55666777777765421 123344444443


Q ss_pred             HHHHhcCCc-EEEEEeccC
Q 042645          244 IFKTMRNRK-IVLLLDDIW  261 (427)
Q Consensus       244 l~~~L~~k~-~LlVlDdv~  261 (427)
                      ..+..+.+. =++++|=.-
T Consensus        83 ~~~~a~~~~~d~ilIDTaG  101 (211)
T d2qy9a2          83 AIQAAKARNIDVLIADTAG  101 (211)
T ss_dssp             HHHHHHHTTCSEEEECCCC
T ss_pred             HHHHHHHcCCCEEEeccCC
Confidence            333322222 366667553

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.28  E-value=0.00049  Score=59.48  Aligned_cols=87  Identities=17%  Similarity=0.144  Sum_probs=63.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..+++-|+|++|+|||+||.+++.....   .-..++|+.....+++.     +++.++++.+..   ...+.++..+.+
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk---~g~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~  127 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQK---AGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIM  127 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH---TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHh---CCCEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHH
Confidence            5579999999999999999998877632   22457899988888874     677888765431   344666766666


Q ss_pred             HHHhcC-CcEEEEEeccCC
Q 042645          245 FKTMRN-RKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~~-k~~LlVlDdv~~  262 (427)
                      ....+. ..-|||+|-+-.
T Consensus       128 ~~l~~~~~~~liIiDSi~a  146 (268)
T d1xp8a1         128 ELLVRSGAIDVVVVDSVAA  146 (268)
T ss_dssp             HHHHTTTCCSEEEEECTTT
T ss_pred             HHHHhcCCCcEEEEecccc
Confidence            666654 466999999854

>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=97.27  E-value=6.7e-05  Score=61.22  Aligned_cols=25  Identities=24%  Similarity=0.456  Sum_probs=23.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|+|.|++|+||||||+.+.+.+
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999999886

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.25  E-value=0.00068  Score=58.50  Aligned_cols=88  Identities=17%  Similarity=0.181  Sum_probs=62.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..+++-|+|++|+||||+|.+++....   ..-..++|+.....+++..     +++++++.+..   ...+.++..+.+
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q---~~g~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~  130 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQ---AAGGVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIA  130 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHH---HTTCEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHH
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHh---cCCCEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHH
Confidence            567999999999999999988877662   2234689999888887654     56667664321   234566666666


Q ss_pred             HHHhc-CCcEEEEEeccCCc
Q 042645          245 FKTMR-NRKIVLLLDDIWEL  263 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~~  263 (427)
                      ....+ ++.-|||+|.+-..
T Consensus       131 ~~l~~~~~~~liIiDSi~al  150 (269)
T d1mo6a1         131 DMLIRSGALDIVVIDSVAAL  150 (269)
T ss_dssp             HHHHHTTCEEEEEEECSTTC
T ss_pred             HHHHhcCCCCEEEEeccccc
Confidence            65555 45679999998543

>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=97.23  E-value=7.4e-05  Score=59.97  Aligned_cols=25  Identities=28%  Similarity=0.527  Sum_probs=23.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++++|+|.+|+|||||+..+.+.+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l   26 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPAL   26 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4799999999999999999999876

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.23  E-value=7.1e-05  Score=59.62  Aligned_cols=24  Identities=29%  Similarity=0.342  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.|.|++|+||||+|+.+++.+
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            468889999999999999999987

>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=97.18  E-value=0.0001  Score=58.08  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=21.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|.|+|++|+||||+|+.+....
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            578999999999999999987654

>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=97.16  E-value=0.0001  Score=59.21  Aligned_cols=24  Identities=25%  Similarity=0.400  Sum_probs=22.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|.|.|++|+||||+|+.+...+
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            579999999999999999998876

>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=97.14  E-value=0.00022  Score=63.46  Aligned_cols=45  Identities=29%  Similarity=0.485  Sum_probs=35.9

Q ss_pred             ccccchhhHHHHHHHhcc-------C--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLTE-------E--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.++.++.+.+.+..       +  ...++.++|+.|+|||.||+.+++.+
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l   77 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL   77 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHh
Confidence            578999888888776631       2  23478899999999999999999876

>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=97.11  E-value=0.00013  Score=59.06  Aligned_cols=26  Identities=15%  Similarity=0.123  Sum_probs=23.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.|+|++|+||||+|+.++..+
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L   30 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTL   30 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999999887

>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=97.10  E-value=0.00015  Score=59.86  Aligned_cols=27  Identities=30%  Similarity=0.340  Sum_probs=24.5

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+.+|.|.|++|+||||+|+.+++++
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            456799999999999999999999887

>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=97.08  E-value=0.00011  Score=59.07  Aligned_cols=24  Identities=38%  Similarity=0.386  Sum_probs=21.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.|.|++|+||||+|+.+.+.+
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            458899999999999999999887

>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=97.08  E-value=0.00082  Score=57.89  Aligned_cols=87  Identities=20%  Similarity=0.163  Sum_probs=60.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCCCHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESW---DNKSFDEKAQEI  244 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~~~l  244 (427)
                      ..+++-|+|++|+|||||+.+++.....   .-..++|+.....++..     .++.+++..+..   ...+.++..+.+
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~---~g~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i  124 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEIC  124 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH---TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHc---CCCEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHH
Confidence            4569999999999999999999887732   23457899888877764     356777654321   234456666666


Q ss_pred             HHHhc-CCcEEEEEeccCC
Q 042645          245 FKTMR-NRKIVLLLDDIWE  262 (427)
Q Consensus       245 ~~~L~-~k~~LlVlDdv~~  262 (427)
                      ....+ +..-|+|+|.+-.
T Consensus       125 ~~l~~~~~~~liViDSi~a  143 (263)
T d1u94a1         125 DALARSGAVDVIVVDSVAA  143 (263)
T ss_dssp             HHHHHHTCCSEEEEECGGG
T ss_pred             HHHHhcCCCCEEEEECccc
Confidence            65554 4456899998853

>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=97.07  E-value=0.00011  Score=59.79  Aligned_cols=25  Identities=40%  Similarity=0.433  Sum_probs=22.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      +.|.|+|++|+|||||++.++..+.
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH
Confidence            5699999999999999999998873

>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=97.03  E-value=0.00028  Score=62.80  Aligned_cols=46  Identities=20%  Similarity=0.235  Sum_probs=36.6

Q ss_pred             CccccchhhHHHHHHHhcc--------------CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--------------EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--------------~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.++.++.+..++..              ...+.+.++||+|+|||.||+.+++..
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~   73 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   73 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcc
Confidence            3578999888888765510              134678899999999999999999886

>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=97.03  E-value=0.00034  Score=60.72  Aligned_cols=26  Identities=31%  Similarity=0.241  Sum_probs=23.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++.|.++|++|+||||||+.+++..
T Consensus        31 ~P~~ilL~GpPGtGKT~la~~la~~~   56 (273)
T d1gvnb_          31 SPTAFLLGGQPGSGKTSLRSAIFEET   56 (273)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45679999999999999999999987

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.98  E-value=0.00022  Score=58.86  Aligned_cols=27  Identities=22%  Similarity=0.418  Sum_probs=24.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..++|.|.|++|+||||+|+.+++++
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            357899999999999999999999887

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.97  E-value=0.00023  Score=57.05  Aligned_cols=26  Identities=23%  Similarity=0.455  Sum_probs=24.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+++.|.|++|+||||+|+.+.+.+
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            56899999999999999999999887

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.97  E-value=0.00021  Score=57.52  Aligned_cols=25  Identities=16%  Similarity=0.325  Sum_probs=23.2

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.|.|++|+||||+|+.+++.+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999999987

>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=96.96  E-value=0.0023  Score=54.23  Aligned_cols=88  Identities=15%  Similarity=0.143  Sum_probs=55.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCC-------------CCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYN-------------ESWDN  234 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~-------------~~~~~  234 (427)
                      ...++.|+|.+|+|||+++.+++.+.   ......++|++....  ...+.+. +..++...             .....
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~---~~~~~~~~~is~e~~--~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENA---CANKERAILFAYEES--RAQLLRN-AYSWGMDFEEMERQNLLKIVCAYPES   98 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHH---HTTTCCEEEEESSSC--HHHHHHH-HHTTSCCHHHHHHTTSEEECCCCGGG
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH---HHhccccceeeccCC--HHHHHHH-HHHcCCChHHHhhcCceEEEEeecch
Confidence            56799999999999999999998886   345556778776543  3333322 22232211             00123


Q ss_pred             CCHHHHHHHHHHHhc-CCcEEEEEeccC
Q 042645          235 KSFDEKAQEIFKTMR-NRKIVLLLDDIW  261 (427)
Q Consensus       235 ~~~~~~~~~l~~~L~-~k~~LlVlDdv~  261 (427)
                      .........+...+. .+.-++|+|.+.
T Consensus        99 ~~~~~~~~~i~~~i~~~~~~~vviDs~~  126 (242)
T d1tf7a2          99 AGLEDHLQIIKSEINDFKPARIAIDSLS  126 (242)
T ss_dssp             SCHHHHHHHHHHHHHTTCCSEEEEECHH
T ss_pred             hhHHHHHHHHHHHHHhcCCceeeeecch
Confidence            345555666665554 466788999874

>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=96.93  E-value=0.00033  Score=57.51  Aligned_cols=27  Identities=30%  Similarity=0.495  Sum_probs=24.0

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.-+|+|.|++|+||||||+.+.+.+
T Consensus        20 ~~~~iIgI~G~~GSGKSTla~~L~~~l   46 (198)
T d1rz3a_          20 AGRLVLGIDGLSRSGKTTLANQLSQTL   46 (198)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            455689999999999999999998877

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.92  E-value=0.00026  Score=56.85  Aligned_cols=27  Identities=22%  Similarity=0.234  Sum_probs=23.5

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +....|.|.|++|+||||+|+.+++.+
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            344579999999999999999999886

>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=96.92  E-value=0.0012  Score=54.57  Aligned_cols=59  Identities=15%  Similarity=0.104  Sum_probs=38.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~  229 (427)
                      +.+++.++|+.|+||||.+.+++..+. ..  -..+..+++.. .....+-++...+.++.+.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~-~~--g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~   68 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYK-GK--GRRPLLVAADTQRPAAREQLRLLGEKVGVPV   68 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHH-HT--TCCEEEEECCSSCHHHHHHHHHHHHHHTCCE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH-HC--CCcEEEEecccccchHHHHHHHHHHhcCCcc
Confidence            457899999999999999888887773 22  22355555432 2234456666777777653

>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=96.88  E-value=0.00017  Score=59.25  Aligned_cols=25  Identities=32%  Similarity=0.408  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+|.++|++|+||||+|+.+...+
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l   43 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYL   43 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4688999999999999999999877

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.87  E-value=0.00031  Score=56.51  Aligned_cols=25  Identities=32%  Similarity=0.340  Sum_probs=22.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++|.|.|++|+||||+|+.+.+.+
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLP   28 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4789999999999999999998765

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.83  E-value=0.00032  Score=56.55  Aligned_cols=26  Identities=27%  Similarity=0.303  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+|.++|++|+||||+|+.+....
T Consensus        13 ~p~liil~G~pGsGKST~a~~l~~~~   38 (172)
T d1yj5a2          13 NPEVVVAVGFPGAGKSTFIQEHLVSA   38 (172)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHTGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            45789999999999999999987654

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.82  E-value=0.00028  Score=57.35  Aligned_cols=24  Identities=29%  Similarity=0.371  Sum_probs=22.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|+|.|++|+||||+++.+.+.+
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l   25 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNL   25 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            689999999999999999999887

>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=96.82  E-value=0.00097  Score=55.23  Aligned_cols=58  Identities=16%  Similarity=0.080  Sum_probs=34.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLY  228 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~  228 (427)
                      .+.+|.++|+.|+||||.+.+++..+. ..+  ..+..++... .....+-++..++.++.+
T Consensus        11 ~p~vi~lvGptGvGKTTTiAKLA~~~~-~~g--~kV~lit~Dt~R~ga~eQL~~~a~~l~v~   69 (211)
T d1j8yf2          11 IPYVIMLVGVQGTGKATTAGKLAYFYK-KKG--FKVGLVGADVYRPAALEQLQQLGQQIGVP   69 (211)
T ss_dssp             SSEEEEEECSCCC----HHHHHHHHHH-HTT--CCEEEEECCCSSHHHHHHHHHHHHHHTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHH-HCC--CceEEEEeeccccchhHHHHHhccccCcc
Confidence            567999999999999999888887762 222  2456666532 223344555666666654

>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=96.80  E-value=0.002  Score=53.37  Aligned_cols=59  Identities=17%  Similarity=0.240  Sum_probs=40.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC-CCCHHHHHHHHHHHhCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR-DLQLGKIQESIAKKIGLYN  229 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~-~~~~~~l~~~i~~~l~~~~  229 (427)
                      .+.+|.++|+.|+||||.+.+++.++. ..+  ..+..++... .....+-++..++.++.+.
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~~~-~~~--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   69 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKMFV-DEG--KSVVLAAADTFRAAAIEQLKIWGERVGATV   69 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHH-HTT--CCEEEEEECTTCHHHHHHHHHHHHHHTCEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHH-HCC--CceEEEeecccccchhHHHHHHhhhcCccc
Confidence            456899999999999999888887772 222  3466666543 2234456667777777643

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.80  E-value=0.00028  Score=56.48  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=19.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.+.|++|+||||+++.+++.+
T Consensus         4 IvliG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5566999999999999999988

>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=96.77  E-value=0.00035  Score=55.81  Aligned_cols=24  Identities=25%  Similarity=0.293  Sum_probs=22.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++++|+|..|+|||||+..+...+
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L   25 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAA   25 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHH
Confidence            589999999999999999999887

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.71  E-value=0.00037  Score=55.51  Aligned_cols=22  Identities=27%  Similarity=0.507  Sum_probs=20.6

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|.|++|+||||+++.+++.+
T Consensus         3 I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7788999999999999999987

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.70  E-value=0.0004  Score=58.33  Aligned_cols=42  Identities=24%  Similarity=0.418  Sum_probs=32.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      .++|+|-|++|+||||+|+.+.+++.     |.+         .+..++++.++..
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~g-----l~~---------iStGdLlR~~a~~   44 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQ-----WHL---------LDSGAIYRVLALA   44 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHT-----CEE---------EEHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC-----CcE---------ECHHHHHHHHHHH
Confidence            47999999999999999999999981     221         2466788877653

>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=96.68  E-value=0.00037  Score=56.02  Aligned_cols=24  Identities=21%  Similarity=0.317  Sum_probs=21.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.+.|++|+||||+|+.+++.+
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHh
Confidence            346788999999999999999987

>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=96.67  E-value=0.00083  Score=58.53  Aligned_cols=39  Identities=31%  Similarity=0.486  Sum_probs=32.9

Q ss_pred             hHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhcc
Q 042645          156 TLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFL  194 (427)
Q Consensus       156 ~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  194 (427)
                      ++..+.+.+..+..++|.+.|-||+||||++..++..+.
T Consensus         7 ~~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA   45 (279)
T d1ihua2           7 SLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLA   45 (279)
T ss_dssp             CHHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             cHHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            466777778888899999999999999999888877663

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.66  E-value=0.00047  Score=57.31  Aligned_cols=24  Identities=17%  Similarity=0.361  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -+|.++|.+|+||||+|+++++..
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l   26 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYL   26 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999999999876

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.65  E-value=0.00048  Score=56.53  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=22.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.+|.|.|++|+||||+|+.+++.+
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999999887

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.65  E-value=0.0032  Score=54.05  Aligned_cols=102  Identities=18%  Similarity=0.305  Sum_probs=62.2

Q ss_pred             HHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC------
Q 042645          159 RVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE------  230 (427)
Q Consensus       159 ~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~------  230 (427)
                      +.++.+.. .....++|.|.+|+|||+|+..+.++..  +.+-+.++++-+.+.. ...++.+++.+.--....      
T Consensus        57 raID~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~~--~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~t  134 (276)
T d2jdid3          57 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVA--KAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKV  134 (276)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHHT--TTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCE
T ss_pred             eeeeeeccccCCCEEEeeCCCCCCHHHHHHHHHHHHH--hhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceE
Confidence            44555543 3445699999999999999999988752  3445677888887654 456677777664211100      


Q ss_pred             ----CCCCCCHHHH------HHHHHHHh---cCCcEEEEEeccCC
Q 042645          231 ----SWDNKSFDEK------AQEIFKTM---RNRKIVLLLDDIWE  262 (427)
Q Consensus       231 ----~~~~~~~~~~------~~~l~~~L---~~k~~LlVlDdv~~  262 (427)
                          .....+....      .-.+-+++   +++.+|+++||+-.
T Consensus       135 vvv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr  179 (276)
T d2jdid3         135 ALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFR  179 (276)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhH
Confidence                0011222221      11233444   37899999999843

>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=96.61  E-value=0.00045  Score=55.68  Aligned_cols=22  Identities=41%  Similarity=0.594  Sum_probs=20.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+|+|++|+|||||++.+...+
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l   24 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhcC
Confidence            8899999999999999999876

>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=96.54  E-value=0.0015  Score=57.59  Aligned_cols=25  Identities=32%  Similarity=0.574  Sum_probs=21.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++.++|++|+|||.||+.++...
T Consensus       123 ~g~~l~~G~pG~GKT~la~ala~~~  147 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVHALGEAL  147 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHHHHHHHH
T ss_pred             CceEEEECCCCccHHHHHHHHHHHh
Confidence            3466679999999999999999886

>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=96.51  E-value=0.0011  Score=55.00  Aligned_cols=30  Identities=23%  Similarity=0.369  Sum_probs=25.6

Q ss_pred             hccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          164 LTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       164 l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .......+|.+.|++|+||||+|+.+.+.+
T Consensus        19 ~~~~kg~vIwltGlsGsGKTTia~~L~~~l   48 (208)
T d1m7ga_          19 LRNQRGLTIWLTGLSASGKSTLAVELEHQL   48 (208)
T ss_dssp             HHTSSCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HhCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            344567899999999999999999998765

>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=96.50  E-value=0.0007  Score=55.08  Aligned_cols=24  Identities=33%  Similarity=0.545  Sum_probs=22.5

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|.|.|++|+||||+++.+.+.+
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L   25 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEIL   25 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999999887

>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=96.46  E-value=0.01  Score=51.84  Aligned_cols=82  Identities=11%  Similarity=0.016  Sum_probs=46.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSFDEKAQEIFKT  247 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~l~~~  247 (427)
                      .+-+|+|.|..|+||||+|+.+...+.+.... ..+.-++...-+-....+..  ..+..........+.+.+.+.+...
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~-~~v~~Is~D~F~~~~~~l~~--~~~~~~~g~Pes~D~~~L~~~L~~l  155 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALLSRWPEH-RRVELITTDGFLHPNQVLKE--RGLMKKKGFPESYDMHRLVKFVSDL  155 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHTTSTTC-CCEEEEEGGGGBCCHHHHHH--HTCTTCTTSGGGBCHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHHhhhcCC-CceEEEeeeeeECCchHHHH--hcCCccCCchHhhhHHHHHHHHHHH
Confidence            45699999999999999999998877211112 22333443332222222211  1111111112456777788877777


Q ss_pred             hcCCc
Q 042645          248 MRNRK  252 (427)
Q Consensus       248 L~~k~  252 (427)
                      ..++.
T Consensus       156 k~g~~  160 (308)
T d1sq5a_         156 KSGVP  160 (308)
T ss_dssp             TTTCS
T ss_pred             HcCCC
Confidence            76654

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=96.45  E-value=0.00071  Score=55.27  Aligned_cols=24  Identities=25%  Similarity=0.210  Sum_probs=21.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|.|.|++|+||||+|+.+++.+
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            458899999999999999999887

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.45  E-value=0.0019  Score=57.49  Aligned_cols=64  Identities=19%  Similarity=0.105  Sum_probs=34.0

Q ss_pred             HHHHHHhc--cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHH
Q 042645          158 DRVWRCLT--EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIA  222 (427)
Q Consensus       158 ~~l~~~l~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~  222 (427)
                      .++++.+.  .++..+|+|.|++|+|||||...+...+ ...++--.++-+..+.+.+-..++.+-.
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~-~~~g~~vavlavDpss~~~ggailgdr~  106 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLL-IREGLKVAVIAVDPSSPVTGGSILGDKT  106 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHH-HHTTCCEEEEEECCC-------------
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHH-HhcCCceeeecCCCceeeeccccccchh
Confidence            44554443  3578899999999999999999998776 2223222334344444444444554433

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=96.44  E-value=0.00087  Score=54.98  Aligned_cols=26  Identities=27%  Similarity=0.312  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.|.|++|+||||+|+.+++.+
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999999876

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=96.37  E-value=0.002  Score=57.16  Aligned_cols=56  Identities=18%  Similarity=0.176  Sum_probs=36.5

Q ss_pred             hHHHHHHHhc--cCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC
Q 042645          156 TLDRVWRCLT--EEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL  212 (427)
Q Consensus       156 ~~~~l~~~l~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~  212 (427)
                      ...++++.+.  .++..+|+|.|+||+|||||...+...+ ...++--.++-+..+.++
T Consensus        36 ~~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~-~~~g~~vaViavDpss~~   93 (323)
T d2qm8a1          36 AVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL-TAAGHKVAVLAVDPSSTR   93 (323)
T ss_dssp             HHHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH-HHTTCCEEEEEECGGGGS
T ss_pred             HHHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHH-hhcCCceeeeecccccHH
Confidence            3445555553  3578899999999999999999998776 222333344444444443

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.33  E-value=0.00085  Score=54.26  Aligned_cols=22  Identities=32%  Similarity=0.520  Sum_probs=20.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|.|++|+||||+|+.+++.+
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7799999999999999999887

>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=96.26  E-value=0.0011  Score=53.99  Aligned_cols=24  Identities=29%  Similarity=0.506  Sum_probs=21.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.|+|++|+|||||++.+.+..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhC
Confidence            457899999999999999998886

>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=96.25  E-value=0.00076  Score=60.55  Aligned_cols=44  Identities=20%  Similarity=0.322  Sum_probs=33.8

Q ss_pred             CccccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHh
Q 042645          148 PTVVGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      +.++|.+..+..|.-.+...+..-|.|.|.+|+||||||+.+..
T Consensus         7 ~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_           7 SAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             GGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHH
Confidence            46799998877665444433334689999999999999999875

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=96.24  E-value=0.0011  Score=54.13  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.1

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|.|.|++|+||||+|+.+++++
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHH
Confidence            356678999999999999999887

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.24  E-value=0.001  Score=53.81  Aligned_cols=23  Identities=30%  Similarity=0.368  Sum_probs=21.0

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+|+.+++.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37888999999999999999887

>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=96.24  E-value=0.0013  Score=54.66  Aligned_cols=25  Identities=20%  Similarity=0.328  Sum_probs=22.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +-+|+|.|..|+||||+|+.+.+.+
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l   26 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLL   26 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3489999999999999999998876

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=96.22  E-value=0.0033  Score=54.34  Aligned_cols=35  Identities=26%  Similarity=0.140  Sum_probs=28.5

Q ss_pred             HHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          159 RVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       159 ~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++++.+.. .....++|.|..|+|||+|+..+.+..
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHH
Confidence            56777654 455679999999999999999998865

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=96.22  E-value=0.0011  Score=53.77  Aligned_cols=23  Identities=30%  Similarity=0.481  Sum_probs=21.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+|+.+++.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37789999999999999999987

>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=96.22  E-value=0.002  Score=56.47  Aligned_cols=43  Identities=19%  Similarity=0.187  Sum_probs=30.3

Q ss_pred             ccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          165 TEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       165 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      .+...++|.+.|-||+||||++..++..+.+ .+  ..+.-|....
T Consensus         4 ~~~~p~~i~~sGKGGVGKTTvaa~lA~~lA~-~G--~rVLlvD~Dp   46 (296)
T d1ihua1           4 LQNIPPYLFFTGKGGVGKTSISCATAIRLAE-QG--KRVLLVSTDP   46 (296)
T ss_dssp             GSSCCSEEEEECSTTSSHHHHHHHHHHHHHH-TT--CCEEEEECCT
T ss_pred             CCCCCeEEEEECCCcChHHHHHHHHHHHHHH-CC--CCEEEEeCCC
Confidence            3445789999999999999999888877732 22  2355555443

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.21  E-value=0.0011  Score=55.46  Aligned_cols=41  Identities=22%  Similarity=0.373  Sum_probs=31.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      +|+|-|++|+||||+|+.++.++.     |.+         .+..++++.++...
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg-----~~~---------istGdl~R~~a~~~   45 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFG-----FTY---------LDTGAMYRAATYMA   45 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHC-----CEE---------EEHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC-----CcE---------ECHHHHHHHHHHHH
Confidence            688999999999999999999881     111         25677888776543

>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=96.12  E-value=0.0032  Score=55.74  Aligned_cols=46  Identities=28%  Similarity=0.475  Sum_probs=37.8

Q ss_pred             CccccchhhHHHHHHHhc-------cC--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLT-------EE--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~-------~~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++|.++.++.+...+.       ++  ...++.++|++|+|||.||+.++...
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l   76 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL   76 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhc
Confidence            467999999999988773       11  34578899999999999999999876

>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=96.03  E-value=0.0019  Score=52.65  Aligned_cols=24  Identities=38%  Similarity=0.549  Sum_probs=20.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .++| |.|++|+||||+|+.+++.+
T Consensus         4 ~rii-l~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           4 VRAV-LLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHHHH
T ss_pred             cEEE-EECCCCCCHHHHHHHHHHHh
Confidence            3455 78999999999999999876

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.01  E-value=0.0016  Score=52.67  Aligned_cols=22  Identities=32%  Similarity=0.475  Sum_probs=19.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|.|++|+||||+|+.+++.+
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5577999999999999999887

>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=96.00  E-value=0.0015  Score=53.31  Aligned_cols=23  Identities=39%  Similarity=0.505  Sum_probs=20.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|.|++|+|||||++.+.+.+
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            37799999999999999998876

>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=95.99  E-value=0.0017  Score=52.38  Aligned_cols=23  Identities=26%  Similarity=0.219  Sum_probs=20.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|++|+||||+|+.+++++
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            36789999999999999999887

>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=95.98  E-value=0.0019  Score=52.27  Aligned_cols=24  Identities=29%  Similarity=0.451  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++|.|+|++|+|||||++.+.++.
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            578999999999999999998876

>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=95.93  E-value=0.0036  Score=54.03  Aligned_cols=37  Identities=22%  Similarity=0.372  Sum_probs=27.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      +.|+|+|-||+||||+|..++..+. ..+ + .++-+.+.
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA-~~G-~-rVllID~D   38 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLH-AMG-K-TIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHH-TTT-C-CEEEEEEC
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHH-hCC-C-cEEEEecC
Confidence            6799999999999999999988883 222 2 34445543

>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=95.89  E-value=0.0063  Score=52.61  Aligned_cols=82  Identities=11%  Similarity=0.007  Sum_probs=44.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC-----CCCCCCCCCCHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG-----LYNESWDNKSFDEKAQE  243 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~-----~~~~~~~~~~~~~~~~~  243 (427)
                      +-+|+|.|..|+|||||+..+...+.........+..++...-+-..+-...+.+...     .........+.+.+.+.
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~ll~~~  106 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLLQEV  106 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHHHHHH
T ss_pred             CEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhHHHHHHH
Confidence            4489999999999999999887665211111223455554443332232334444431     11112245566666777


Q ss_pred             HHHHhcC
Q 042645          244 IFKTMRN  250 (427)
Q Consensus       244 l~~~L~~  250 (427)
                      +....++
T Consensus       107 l~~l~~~  113 (286)
T d1odfa_         107 LNTIFNN  113 (286)
T ss_dssp             HHHHTC-
T ss_pred             HHHHHhh
Confidence            7666654

>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=95.77  E-value=0.0028  Score=51.08  Aligned_cols=24  Identities=21%  Similarity=0.360  Sum_probs=21.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|.|+|+.|+|||||++.+..+.
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            578999999999999999998775

>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=95.73  E-value=0.012  Score=49.42  Aligned_cols=48  Identities=13%  Similarity=0.064  Sum_probs=34.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCCCCHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRDLQLG  215 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~~~~~  215 (427)
                      ..+++.|+|++|+|||||+.+++......   ...-..++|+.........
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   83 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPV   83 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGG
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHH
Confidence            55799999999999999999987654211   1223467888876665533

>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=95.70  E-value=0.023  Score=47.89  Aligned_cols=50  Identities=22%  Similarity=0.250  Sum_probs=35.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCCCCHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRDLQLGKI  217 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~~~~~~l  217 (427)
                      ..+++.|.|++|+||||++.+++.+....   .......+|+......+...+
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            56799999999999999999998765211   123456778877666665433

>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=95.65  E-value=0.0034  Score=51.06  Aligned_cols=22  Identities=32%  Similarity=0.460  Sum_probs=19.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~  190 (427)
                      +-+|+|+|..|+||||+|..+-
T Consensus         3 p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4689999999999999999874

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=95.54  E-value=0.014  Score=50.02  Aligned_cols=90  Identities=10%  Similarity=0.124  Sum_probs=49.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCCCCH------
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDL-QLGKIQESIAKKIGLYNE----SWDNKSF------  237 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~------  237 (427)
                      ..-++|.|.+|+|||+|+.......   ..+...++++.+.... ...++..++...=.....    .....+.      
T Consensus        67 GQr~~Ifg~~g~GKt~l~~~~~~~~---~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a  143 (276)
T d1fx0a3          67 GQRELIIGDRQTGKTAVATDTILNQ---QGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLA  143 (276)
T ss_dssp             TCBCBEEESSSSSHHHHHHHHHHTC---CTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHH
T ss_pred             CceEeeccCCCCChHHHHHHHHhhh---cccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHH
Confidence            3458899999999999998765544   3444566777776653 233333333322101000    0001111      


Q ss_pred             HHHHHHHHHHh--cCCcEEEEEeccC
Q 042645          238 DEKAQEIFKTM--RNRKIVLLLDDIW  261 (427)
Q Consensus       238 ~~~~~~l~~~L--~~k~~LlVlDdv~  261 (427)
                      ....-.+-+++  +++++|+++||+-
T Consensus       144 ~~~a~tiAEyfrd~G~~Vlll~Dslt  169 (276)
T d1fx0a3         144 PYTGAALAEYFMYRERHTLIIYDDLS  169 (276)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHcCCceeEEeeccH
Confidence            12222333443  4799999999984

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.50  E-value=0.0034  Score=53.05  Aligned_cols=23  Identities=39%  Similarity=0.537  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ||+|.|+.|+|||||...+.++.
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Confidence            78999999999999999998766

>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=95.44  E-value=0.011  Score=50.10  Aligned_cols=45  Identities=18%  Similarity=0.141  Sum_probs=35.3

Q ss_pred             ccccchhhHHHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          149 TVVGMQSTLDRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       149 ~~vGR~~~~~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|||....++++.+.+..  ....-|.|.|..|+|||++|+.+.+..
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s   47 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLS   47 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            378888888888887754  222347899999999999999997654

>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=95.36  E-value=0.0036  Score=51.11  Aligned_cols=26  Identities=31%  Similarity=0.192  Sum_probs=22.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+-+|+|-|.-|+||||+++.+.+.+
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHh
Confidence            34589999999999999999998776

>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=95.35  E-value=0.009  Score=49.29  Aligned_cols=24  Identities=21%  Similarity=0.387  Sum_probs=22.2

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..|+|.|+.|+||||+++.+.+.+
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L   27 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEAL   27 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999999887

>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=95.34  E-value=0.0062  Score=53.06  Aligned_cols=38  Identities=21%  Similarity=0.334  Sum_probs=27.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR  210 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~  210 (427)
                      +.|+|.|-||+||||+|..++..+.. .+  ..++-|.+..
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA~-~G--~rVLlID~Dp   40 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALAE-MG--KKVMIVGCDP   40 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHH-TT--CCEEEEEECS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHH-CC--CCEEEEecCC
Confidence            57889999999999999998877732 22  2355566543

>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=95.33  E-value=0.057  Score=46.03  Aligned_cols=24  Identities=29%  Similarity=0.441  Sum_probs=21.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+..|+|.+|+|||||+..++-..
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHH
Confidence            578899999999999998887664

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=95.25  E-value=0.0087  Score=53.89  Aligned_cols=46  Identities=20%  Similarity=0.211  Sum_probs=35.8

Q ss_pred             CccccchhhHHHHHHHhc------------------------------cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLT------------------------------EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~------------------------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+||.++.++.+..++.                              +.....+...|+.|+|||.||+.++...
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhc
Confidence            467999998887765551                              1245568899999999999999998765

>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=95.20  E-value=0.0059  Score=50.27  Aligned_cols=24  Identities=17%  Similarity=0.281  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|.|+|++|+|||||.+.+....
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            578999999999999999998876

>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=95.16  E-value=0.0064  Score=51.29  Aligned_cols=26  Identities=19%  Similarity=0.336  Sum_probs=23.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +++.|+|-|+-|+||||+++.+.+.+
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~l   26 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            35789999999999999999999887

>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=95.08  E-value=0.0082  Score=53.97  Aligned_cols=27  Identities=22%  Similarity=0.039  Sum_probs=24.7

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +..+.+.++|++|+|||++|..+++..
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~  178 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELC  178 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHc
Confidence            456789999999999999999999988

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=95.04  E-value=0.006  Score=47.54  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=19.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|.+|+|||||...+..+.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            6799999999999999987654

>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=95.02  E-value=0.0053  Score=50.33  Aligned_cols=26  Identities=38%  Similarity=0.589  Sum_probs=22.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||.+.++.-.
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            44689999999999999999998755

>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=95.01  E-value=0.038  Score=46.43  Aligned_cols=56  Identities=16%  Similarity=0.101  Sum_probs=38.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccC---CCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLH---TPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ...++.|+|++|+|||++|.+++.....   ....+..+.|+......... ....+...
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~   94 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD-RLRDIADR   94 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH-HHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH-HHHHHHhh
Confidence            5679999999999999999999865422   12345677788776665533 33334433

>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=95.01  E-value=0.015  Score=45.23  Aligned_cols=26  Identities=35%  Similarity=0.300  Sum_probs=23.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..-+|.+.|.=|+||||+++.+++.+
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhc
Confidence            44589999999999999999999887

>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=94.99  E-value=0.016  Score=47.68  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=22.0

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|+|-|+.|+||||+++.+.+.+
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            568999999999999999998877

>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=94.93  E-value=0.0084  Score=48.72  Aligned_cols=25  Identities=24%  Similarity=0.432  Sum_probs=22.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +.+.|+|+|.+|+|||||...+.+.
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcCC
Confidence            4567999999999999999999853

>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=94.85  E-value=0.0076  Score=50.33  Aligned_cols=26  Identities=31%  Similarity=0.363  Sum_probs=21.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.+..-.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCcchhhHhccCCC
Confidence            44689999999999999999876543

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=94.84  E-value=0.0071  Score=47.46  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=20.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||...+.+..
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            37899999999999999987664

>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=94.83  E-value=0.0065  Score=50.70  Aligned_cols=26  Identities=46%  Similarity=0.625  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..++..|.|+-|+|||||.+.+.+..
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhcC
Confidence            46899999999999999999998753

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.82  E-value=0.0087  Score=49.99  Aligned_cols=26  Identities=35%  Similarity=0.351  Sum_probs=22.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            44689999999999999999987543

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.78  E-value=0.013  Score=48.19  Aligned_cols=47  Identities=11%  Similarity=0.080  Sum_probs=30.9

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC---CCCCcEEEEEEeCCCCCH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT---PNDFDFVIWEVVSRDLQL  214 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~~f~~~~wv~~~~~~~~  214 (427)
                      ...++.|.|++|+|||+||.+++.+....   ...+....++........
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRP   71 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHH
Confidence            45699999999999999999988765221   122334445554444443

>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=94.74  E-value=0.0086  Score=50.28  Aligned_cols=26  Identities=35%  Similarity=0.456  Sum_probs=22.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.++--.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCc
Confidence            44689999999999999999987644

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=94.73  E-value=0.0082  Score=50.42  Aligned_cols=26  Identities=35%  Similarity=0.295  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.++.-.
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            34689999999999999999997654

>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=94.72  E-value=0.0057  Score=51.53  Aligned_cols=25  Identities=16%  Similarity=0.290  Sum_probs=22.8

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+.|+|-|+-|+||||+++.+.+.+
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998876

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=94.67  E-value=0.016  Score=45.91  Aligned_cols=34  Identities=32%  Similarity=0.577  Sum_probs=25.1

Q ss_pred             HHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          158 DRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       158 ~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..+..++..... -|.|+|.+|+|||||+..+...
T Consensus         5 ~~~~~~~~~k~~-kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           5 TRIWRLFNHQEH-KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHHTTSCE-EEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHHhCCCeE-EEEEECCCCCCHHHHHHHHhcC
Confidence            345555554444 5779999999999999988654

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.67  E-value=0.0099  Score=49.83  Aligned_cols=26  Identities=35%  Similarity=0.313  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.+..-.
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            44689999999999999999987644

>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=94.67  E-value=0.0039  Score=53.88  Aligned_cols=81  Identities=11%  Similarity=0.207  Sum_probs=41.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCC--CCCHHHHHHHHHHH--hC---CCCCCCCCCCHHHH
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSR--DLQLGKIQESIAKK--IG---LYNESWDNKSFDEK  240 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~--~~~~~~l~~~i~~~--l~---~~~~~~~~~~~~~~  240 (427)
                      +.++|+|.|.+|+||||+++.+.+.+..  .... .+.++...  .++-.+.-..+...  ..   .........+.+.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~--~~v~-~~iI~~Dsfyr~~R~~~~~~~~~~~~~~~~~~~~~~P~A~d~dlL   79 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRR--EGVK-AVSIEGDAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKEL   79 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH--HTCC-EEEEEGGGGBSCCHHHHHHHHHHHHHHTCTTCSTTSGGGBCHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhh--cCCC-eEEEeCCCCCccchhhhhhhhhhhhhhhccCCCCCCcccccHHHH
Confidence            4579999999999999999998776621  1111 22333222  12333322222221  11   11112244566777


Q ss_pred             HHHHHHHhcCC
Q 042645          241 AQEIFKTMRNR  251 (427)
Q Consensus       241 ~~~l~~~L~~k  251 (427)
                      .+.+..+.+++
T Consensus        80 ~~~l~~L~~g~   90 (288)
T d1a7ja_          80 ERVFREYGETG   90 (288)
T ss_dssp             HHHHHHHHHHS
T ss_pred             HHHHHHHHCCC
Confidence            77777766553

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.58  E-value=0.0096  Score=50.60  Aligned_cols=26  Identities=31%  Similarity=0.455  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....++|+|+.|+|||||++.+..-.
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            44689999999999999999997644

>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=94.57  E-value=0.031  Score=46.10  Aligned_cols=26  Identities=19%  Similarity=0.250  Sum_probs=23.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....|+|-|+-|+||||+++.+.+.+
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHH
Confidence            34689999999999999999999887

>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=94.53  E-value=0.0095  Score=48.85  Aligned_cols=23  Identities=30%  Similarity=0.768  Sum_probs=21.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|-|.-|+||||+++.+.+.+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l   24 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAF   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            58899999999999999998877

>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=94.53  E-value=0.0099  Score=48.70  Aligned_cols=24  Identities=29%  Similarity=0.315  Sum_probs=21.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|+|+|.+|+|||||...+.+.-
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~~   27 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTDS   27 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            579999999999999999998653

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.51  E-value=0.0088  Score=50.41  Aligned_cols=26  Identities=31%  Similarity=0.557  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....++|+|+.|+|||||++.+..-.
T Consensus        28 ~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          28 QGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            34689999999999999999997755

>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=94.51  E-value=0.011  Score=49.97  Aligned_cols=26  Identities=27%  Similarity=0.589  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....++|+|+.|+|||||++.+..-.
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            45789999999999999999987644

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.51  E-value=0.01  Score=49.78  Aligned_cols=24  Identities=29%  Similarity=0.389  Sum_probs=21.3

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+++|.|+.|+|||||++.++.-.
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCChHHHHHHHHHcCC
Confidence            478899999999999999998754

>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=94.47  E-value=0.012  Score=50.91  Aligned_cols=26  Identities=31%  Similarity=0.436  Sum_probs=23.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-+
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCC
Confidence            45689999999999999999998765

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.47  E-value=0.0097  Score=47.31  Aligned_cols=21  Identities=38%  Similarity=0.525  Sum_probs=18.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.|+|.+|+|||||+..+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999998765

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.46  E-value=0.01  Score=46.84  Aligned_cols=21  Identities=38%  Similarity=0.482  Sum_probs=18.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+|+|.+|+|||||+..+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778999999999999988764

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.43  E-value=0.01  Score=46.69  Aligned_cols=21  Identities=24%  Similarity=0.517  Sum_probs=18.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999988754

>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=94.39  E-value=0.011  Score=50.16  Aligned_cols=26  Identities=31%  Similarity=0.563  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....++|+|+.|+|||||++.+..-+
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhccc
Confidence            45689999999999999999987654

>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=94.36  E-value=0.011  Score=46.50  Aligned_cols=21  Identities=29%  Similarity=0.333  Sum_probs=19.1

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>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=94.32  E-value=0.01  Score=50.57  Aligned_cols=26  Identities=31%  Similarity=0.423  Sum_probs=22.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            45689999999999999999997643

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.30  E-value=0.018  Score=47.88  Aligned_cols=37  Identities=22%  Similarity=0.214  Sum_probs=28.2

Q ss_pred             eEEEEE-ecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          170 GIVGLY-GMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       170 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      ++|+|. |-||+||||+|..++..+.+   .-..++.+...
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~la~---~g~~VlliD~D   39 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVALAQ---LGHDVTIVDAD   39 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHHHH---TTCCEEEEECC
T ss_pred             EEEEEECCCCCChHHHHHHHHHHHHHh---CCCCEEEEeCC
Confidence            678887 88999999999999888732   23356777654

>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=94.27  E-value=0.083  Score=45.08  Aligned_cols=52  Identities=13%  Similarity=0.068  Sum_probs=33.0

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKK  224 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~  224 (427)
                      ..++.|.|.+|+|||+++.+++.+...  .+-..+++++..  .+..++...++..
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~--~~g~~v~~~s~E--~~~~~~~~r~~~~   86 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGT--AMGKKVGLAMLE--ESVEETAEDLIGL   86 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHH--TSCCCEEEEESS--SCHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhh--hcccceeEeeec--cchhhHHhHHHHH
Confidence            458899999999999999998765411  112245555543  3455555555443

>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=94.25  E-value=0.012  Score=46.57  Aligned_cols=23  Identities=35%  Similarity=0.572  Sum_probs=19.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|.|+|.+|+|||||+..+.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~~   29 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQGL   29 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            37899999999999999988653

>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=94.24  E-value=0.0095  Score=49.60  Aligned_cols=26  Identities=27%  Similarity=0.277  Sum_probs=22.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.+..-.
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            44689999999999999999997654

>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=94.24  E-value=0.012  Score=46.62  Aligned_cols=21  Identities=38%  Similarity=0.827  Sum_probs=18.6

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+|+|.+|+|||||+..+.+.
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999988764

>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=94.24  E-value=0.012  Score=48.51  Aligned_cols=20  Identities=40%  Similarity=0.494  Sum_probs=18.1

Q ss_pred             EEEEEecCCCcHHHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~  190 (427)
                      +|+|+|+.|+||||.++.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998663

>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=94.23  E-value=0.011  Score=46.56  Aligned_cols=23  Identities=30%  Similarity=0.463  Sum_probs=19.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||...+.+..
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~~   26 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGED   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCC
Confidence            37799999999999999987653

>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=94.21  E-value=0.012  Score=46.34  Aligned_cols=23  Identities=39%  Similarity=0.528  Sum_probs=19.8

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|.|+|.+|+|||||+..+.++.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~~   27 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            37889999999999999987653

>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=94.18  E-value=0.012  Score=46.43  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=18.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.++|.+|+|||||+..+.+.
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999988754

>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=94.14  E-value=0.013  Score=46.24  Aligned_cols=21  Identities=43%  Similarity=0.569  Sum_probs=18.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.|+|.+|+|||+|+..+.+.
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988754

>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=94.13  E-value=0.013  Score=48.14  Aligned_cols=21  Identities=48%  Similarity=0.526  Sum_probs=18.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHH
Q 042645          170 GIVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~  190 (427)
                      -+|+|+|..|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            479999999999999998763

>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=94.11  E-value=0.014  Score=45.85  Aligned_cols=21  Identities=33%  Similarity=0.484  Sum_probs=18.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+|+|.+|+|||||+..+.+.
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778999999999999998754

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.08  E-value=0.099  Score=44.72  Aligned_cols=104  Identities=9%  Similarity=0.082  Sum_probs=53.6

Q ss_pred             HHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhccC----CC-CCCcEEEEEEeCCCCC-HHHHHHHHHHHhCCCCC-
Q 042645          159 RVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSFLH----TP-NDFDFVIWEVVSRDLQ-LGKIQESIAKKIGLYNE-  230 (427)
Q Consensus       159 ~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~----~~-~~f~~~~wv~~~~~~~-~~~l~~~i~~~l~~~~~-  230 (427)
                      +.++.|.. .....++|.|.+|+|||+|+..+......    .. ..-..++++-+++... ..++...+...-..... 
T Consensus        57 raID~l~pig~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tv  136 (285)
T d2jdia3          57 KAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTI  136 (285)
T ss_dssp             HHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEE
T ss_pred             eEEecccCccCCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceE
Confidence            34555543 34456899999999999998877654311    11 1122456666665543 34444444432111100 


Q ss_pred             ---CCCCCCHHHHH------HHHHHHh--cCCcEEEEEeccCC
Q 042645          231 ---SWDNKSFDEKA------QEIFKTM--RNRKIVLLLDDIWE  262 (427)
Q Consensus       231 ---~~~~~~~~~~~------~~l~~~L--~~k~~LlVlDdv~~  262 (427)
                         .....+.....      -.+-+++  ++|.+|+++||+-.
T Consensus       137 vv~~ts~~~~~~r~~~~~~a~tiAEyfrd~G~~VLll~Dsltr  179 (285)
T d2jdia3         137 VVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSK  179 (285)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEEEETHHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcChHH
Confidence               00111221111      1122333  58999999999843

>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=94.07  E-value=0.013  Score=46.19  Aligned_cols=22  Identities=27%  Similarity=0.610  Sum_probs=19.4

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.++|.+|+|||+|...+.+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999988754

>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=94.07  E-value=0.014  Score=46.35  Aligned_cols=22  Identities=41%  Similarity=0.525  Sum_probs=19.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>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=94.06  E-value=0.014  Score=46.15  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=19.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .|+|.|.+|+|||||+..+...
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            5899999999999999998754

>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=94.04  E-value=0.014  Score=46.03  Aligned_cols=22  Identities=32%  Similarity=0.481  Sum_probs=19.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+|+|.+|+|||||+..+.+..
T Consensus         7 i~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6788999999999999987653

>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=94.03  E-value=0.014  Score=45.85  Aligned_cols=22  Identities=36%  Similarity=0.504  Sum_probs=19.4

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.++|.+|+|||||+..+.+..
T Consensus         5 i~vvG~~~vGKTSli~~l~~~~   26 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVEDK   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7799999999999999987653

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=94.03  E-value=0.012  Score=46.88  Aligned_cols=25  Identities=32%  Similarity=0.563  Sum_probs=20.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +..-|+|+|.+|+|||||...+...
T Consensus        12 k~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          12 KTGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3456889999999999999988654

>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=94.03  E-value=0.014  Score=46.12  Aligned_cols=22  Identities=41%  Similarity=0.520  Sum_probs=19.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|.|+|.+|+|||||...+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999988764

>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=94.03  E-value=0.015  Score=47.70  Aligned_cols=24  Identities=25%  Similarity=0.296  Sum_probs=20.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|+|+|.+|+|||||...+....
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~~   24 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTGQ   24 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999987653

>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=94.02  E-value=0.014  Score=46.14  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=19.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|.|+|.+|+|||||+..+.+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            37899999999999999988543

>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=94.00  E-value=0.013  Score=47.08  Aligned_cols=21  Identities=38%  Similarity=0.532  Sum_probs=18.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.|+|.+|+|||||+..+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            778999999999999998764

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.95  E-value=0.015  Score=46.21  Aligned_cols=21  Identities=43%  Similarity=0.618  Sum_probs=18.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+|+|.+|+|||||+..+.+.
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999998754

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=93.95  E-value=0.028  Score=47.08  Aligned_cols=58  Identities=14%  Similarity=0.158  Sum_probs=37.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCC-------------CCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHT-------------PNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      ...++.|.|.+|+|||+++.+++.+....             ......+.|++....... .....+...+.
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~-~~~~~~~~~~~  103 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRP-ERIMQMAEHAG  103 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCH-HHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCH-HHHHHHHhhcc
Confidence            45799999999999999999998665211             111234677776554443 33444444443

>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=93.93  E-value=0.015  Score=45.95  Aligned_cols=22  Identities=36%  Similarity=0.407  Sum_probs=18.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+|+|.+|+|||||+..+.+..
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~~   25 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGVE   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC-
T ss_pred             EEEECCCCcCHHHHHHHHhCCc
Confidence            7789999999999999987653

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.91  E-value=0.016  Score=45.65  Aligned_cols=23  Identities=26%  Similarity=0.439  Sum_probs=19.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .-|+|+|.+|+|||||+..+.+.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            35788999999999999998754

>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=93.88  E-value=0.016  Score=45.98  Aligned_cols=21  Identities=33%  Similarity=0.457  Sum_probs=18.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.++|.+|+|||||+..+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999987654

>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=93.88  E-value=0.018  Score=45.91  Aligned_cols=24  Identities=38%  Similarity=0.581  Sum_probs=21.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .+.|+|+|.+|+|||||+..+.+.
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            357999999999999999999865

>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=93.87  E-value=0.016  Score=45.98  Aligned_cols=24  Identities=33%  Similarity=0.614  Sum_probs=21.3

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +..|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999999864

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.87  E-value=0.016  Score=45.57  Aligned_cols=22  Identities=36%  Similarity=0.605  Sum_probs=19.4

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|.+|+|||||+..+.+..
T Consensus         6 i~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            7889999999999999987653

>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=93.86  E-value=0.024  Score=52.28  Aligned_cols=46  Identities=22%  Similarity=0.275  Sum_probs=36.3

Q ss_pred             CccccchhhHHHHHHHhcc--------C------CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          148 PTVVGMQSTLDRVWRCLTE--------E------PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       148 ~~~vGR~~~~~~l~~~l~~--------~------~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+||.++.++.|--++.+        .      ..+-|.++||.|+|||.||+.++...
T Consensus        14 ~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l   73 (443)
T d1g41a_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   73 (443)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHh
Confidence            4678998888887665521        1      24579999999999999999999866

>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=93.82  E-value=0.017  Score=48.52  Aligned_cols=26  Identities=42%  Similarity=0.519  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|+|+.|+|||||.+.+..-.
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            44689999999999999999987655

>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=93.80  E-value=0.016  Score=44.92  Aligned_cols=23  Identities=35%  Similarity=0.486  Sum_probs=20.0

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.+|+|||||+..+.+..
T Consensus         2 KI~liG~~nvGKSSLln~l~~~~   24 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKNDR   24 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999987653

>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=93.78  E-value=0.015  Score=48.90  Aligned_cols=26  Identities=42%  Similarity=0.492  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||.+.+..-.
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            44689999999999999999997654

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.78  E-value=0.016  Score=45.56  Aligned_cols=22  Identities=36%  Similarity=0.611  Sum_probs=19.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|.+|+|||+|+..+....
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            7799999999999999987653

>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=93.76  E-value=0.012  Score=49.29  Aligned_cols=26  Identities=31%  Similarity=0.365  Sum_probs=22.5

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.+..-.
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            44689999999999999999997643

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.73  E-value=0.017  Score=45.94  Aligned_cols=21  Identities=43%  Similarity=0.681  Sum_probs=18.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+|+|.+|+|||||+..+.+.
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988664

>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=93.72  E-value=0.018  Score=45.87  Aligned_cols=23  Identities=30%  Similarity=0.339  Sum_probs=19.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|.|+|.+|+|||+|+..+.+..
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            46788999999999999887653

>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=93.70  E-value=0.023  Score=50.90  Aligned_cols=64  Identities=19%  Similarity=0.150  Sum_probs=35.7

Q ss_pred             hhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHH
Q 042645          155 STLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESI  221 (427)
Q Consensus       155 ~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i  221 (427)
                      .....+...+.   .++..|.|++|.||||++..+...+......-...+.++....-....+...+
T Consensus       152 ~Q~~A~~~al~---~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         152 WQKVAAAVALT---RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             HHHHHHHHHHT---BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            34445555553   36899999999999999866544332212222334555554433333333333

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.67  E-value=0.027  Score=46.86  Aligned_cols=37  Identities=24%  Similarity=0.269  Sum_probs=27.5

Q ss_pred             eEEEEE-ecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          170 GIVGLY-GMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       170 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      ++|+|+ +-||+||||+|..++..+..   .-..++-+...
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~---~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGD---RGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHH---TTCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHh---CCCCEEEEeCC
Confidence            689898 77999999999999888732   22346666543

>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=93.59  E-value=0.019  Score=45.34  Aligned_cols=22  Identities=23%  Similarity=0.383  Sum_probs=19.0

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+|+|.+|+|||+|+..+.+..
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999887653

>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=93.57  E-value=0.015  Score=46.10  Aligned_cols=23  Identities=39%  Similarity=0.525  Sum_probs=19.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      --|+|+|.+|+|||||...+...
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35889999999999999988553

>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=93.54  E-value=0.019  Score=45.98  Aligned_cols=23  Identities=35%  Similarity=0.403  Sum_probs=19.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|.|+|.+|+|||+|+..+.+..
T Consensus         7 KivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48899999999999999887653

>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=93.54  E-value=0.021  Score=47.94  Aligned_cols=24  Identities=25%  Similarity=0.317  Sum_probs=21.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .+|+|+|..|+||||+|..+.+.+
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            589999999999999999997764

>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=93.53  E-value=0.018  Score=48.98  Aligned_cols=26  Identities=27%  Similarity=0.397  Sum_probs=22.7

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ...+++|.|+.|+|||||++.+..-.
T Consensus        29 ~Gei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            34689999999999999999998765

>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=93.49  E-value=0.02  Score=46.38  Aligned_cols=22  Identities=36%  Similarity=0.560  Sum_probs=19.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+|+|.+|+|||||+..+.+..
T Consensus         9 ivvvG~~~vGKTsli~~l~~~~   30 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDDT   30 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHhhCC
Confidence            7899999999999999987643

>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=93.48  E-value=0.02  Score=45.19  Aligned_cols=22  Identities=45%  Similarity=0.613  Sum_probs=19.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999988664

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.45  E-value=0.02  Score=45.73  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=20.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|+|+|.+|+|||||...+.+..
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~~   24 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGKK   24 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48999999999999999998653

>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=93.44  E-value=0.021  Score=45.86  Aligned_cols=22  Identities=41%  Similarity=0.484  Sum_probs=19.4

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.|+|.+|+|||+|+..+.+..
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            7899999999999999987653

>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=93.31  E-value=0.022  Score=44.60  Aligned_cols=22  Identities=32%  Similarity=0.410  Sum_probs=18.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |++.|.+|+|||||...+....
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~~   26 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASGQ   26 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6788999999999999886543

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.30  E-value=0.022  Score=45.62  Aligned_cols=21  Identities=48%  Similarity=0.643  Sum_probs=18.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+++|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999988764

>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=93.24  E-value=0.029  Score=44.33  Aligned_cols=23  Identities=26%  Similarity=0.419  Sum_probs=19.4

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|.|+|.+|+|||||...+.+..
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            46789999999999999986543

>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=93.18  E-value=0.024  Score=44.68  Aligned_cols=22  Identities=41%  Similarity=0.519  Sum_probs=19.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999997654

>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=93.16  E-value=0.024  Score=44.91  Aligned_cols=21  Identities=43%  Similarity=0.686  Sum_probs=18.7

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.|+|.+|+|||||+..+.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999887654

>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=93.12  E-value=0.024  Score=45.01  Aligned_cols=21  Identities=33%  Similarity=0.651  Sum_probs=18.8

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.++|.+|+|||||+..+.+.
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988754

>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=93.11  E-value=0.026  Score=43.89  Aligned_cols=22  Identities=27%  Similarity=0.398  Sum_probs=19.2

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.+|+|||||...+...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3779999999999999998754

>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=93.08  E-value=0.026  Score=45.03  Aligned_cols=22  Identities=27%  Similarity=0.362  Sum_probs=19.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.++|..|+|||+|+..+.+..
T Consensus         5 ivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999887753

>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=93.07  E-value=0.039  Score=45.56  Aligned_cols=34  Identities=32%  Similarity=0.579  Sum_probs=26.7

Q ss_pred             HHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          157 LDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       157 ~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++.|.++|.+   +..++.|.+|+|||||...+..+.
T Consensus        86 ~~~L~~~l~~---kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          86 IEELKEYLKG---KISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             HHHHHHHHSS---SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             HhhHHHHhcC---CeEEEECCCCCCHHHHHHhhcchh
Confidence            5666666633   567899999999999999987654

>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=93.06  E-value=0.019  Score=48.03  Aligned_cols=24  Identities=38%  Similarity=0.574  Sum_probs=21.3

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      ...+++|.|+.|+|||||.+.+..
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            346899999999999999999876

>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=93.05  E-value=0.015  Score=49.30  Aligned_cols=26  Identities=35%  Similarity=0.505  Sum_probs=22.0

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ....++|+|+.|+|||||++.+..-.
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~gl~   68 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPRFY   68 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhcC
Confidence            45689999999999999999886544

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.04  E-value=0.025  Score=45.39  Aligned_cols=23  Identities=30%  Similarity=0.433  Sum_probs=19.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|.++|.+|+|||+|+..+....
T Consensus         4 KivllG~~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKIIH   26 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            36799999999999999986554

>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=93.01  E-value=0.025  Score=44.76  Aligned_cols=22  Identities=41%  Similarity=0.454  Sum_probs=19.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|.++|.+|+|||+|+..+...
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988754

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.97  E-value=0.027  Score=44.43  Aligned_cols=22  Identities=36%  Similarity=0.543  Sum_probs=19.1

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.++|.+|+|||||+..+.+..
T Consensus         7 i~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6688999999999999988653

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.84  E-value=0.02  Score=45.62  Aligned_cols=21  Identities=38%  Similarity=0.695  Sum_probs=19.0

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+|+|.+|+|||||...+.+.
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999998654

>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=92.84  E-value=0.029  Score=45.21  Aligned_cols=22  Identities=36%  Similarity=0.437  Sum_probs=18.9

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |+++|.+|+|||+|+..+.+..
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999998887653

>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=92.82  E-value=0.026  Score=45.63  Aligned_cols=19  Identities=42%  Similarity=0.639  Sum_probs=17.3

Q ss_pred             EEEEEecCCCcHHHHHHHH
Q 042645          171 IVGLYGMGGVGKTTLLTQI  189 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v  189 (427)
                      -|.|.|.+|+|||||+..+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3779999999999999988

>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=92.81  E-value=0.016  Score=45.77  Aligned_cols=21  Identities=38%  Similarity=0.542  Sum_probs=17.1

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.|+|.+|+|||||+..+.+.
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999887554

>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=92.68  E-value=0.031  Score=45.01  Aligned_cols=22  Identities=32%  Similarity=0.481  Sum_probs=19.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhhc
Q 042645          172 VGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      |.+.|.+|+|||+|...+....
T Consensus         5 iv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7799999999999999986654

>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=92.68  E-value=0.047  Score=45.20  Aligned_cols=40  Identities=15%  Similarity=-0.012  Sum_probs=26.6

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVS  209 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~  209 (427)
                      ...++.|+|.+|+|||+||.+++.....  ..-..++|++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~--~~~~~~~~~s~e   64 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGII--EFDEPGVFVTFE   64 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH--HHCCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHH--hcCCCccccccc
Confidence            5578999999999999999876543211  112235666544

>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=92.61  E-value=0.022  Score=45.56  Aligned_cols=22  Identities=45%  Similarity=0.717  Sum_probs=19.3

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.+++|||||...+.+.
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             eEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999988653

>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=92.60  E-value=0.043  Score=43.39  Aligned_cols=24  Identities=25%  Similarity=0.167  Sum_probs=20.6

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..-|.|.|.+|+||||+|..+..+
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc
Confidence            356889999999999999987754

>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=92.56  E-value=0.032  Score=44.28  Aligned_cols=23  Identities=22%  Similarity=0.390  Sum_probs=19.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+++|.+|+|||||+..+.+..
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            47899999999999999887654

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=92.45  E-value=0.048  Score=43.13  Aligned_cols=24  Identities=29%  Similarity=0.238  Sum_probs=20.4

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..-|.|.|.+|+||||||..+..+
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc
Confidence            356889999999999999888654

>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=92.40  E-value=0.035  Score=44.34  Aligned_cols=22  Identities=41%  Similarity=0.540  Sum_probs=19.5

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.+|+|||||...+.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4889999999999999988764

>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=92.39  E-value=0.026  Score=45.07  Aligned_cols=25  Identities=28%  Similarity=0.410  Sum_probs=20.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..--|.++|.+|+|||||...+...
T Consensus        16 k~~KI~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          16 KELRILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHhcC
Confidence            3345779999999999999987543

>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=92.22  E-value=0.021  Score=45.56  Aligned_cols=25  Identities=24%  Similarity=0.302  Sum_probs=21.1

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhh
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      +...|+|+|.+++|||||...+...
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4577999999999999999887543

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=92.21  E-value=0.042  Score=43.16  Aligned_cols=24  Identities=21%  Similarity=0.171  Sum_probs=20.5

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      ..-|.|.|.+|+||||+|..+..+
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc
Confidence            356899999999999999887665

>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=92.15  E-value=0.045  Score=44.81  Aligned_cols=25  Identities=20%  Similarity=0.060  Sum_probs=22.0

Q ss_pred             eEEEEEecC-CCcHHHHHHHHHhhcc
Q 042645          170 GIVGLYGMG-GVGKTTLLTQINNSFL  194 (427)
Q Consensus       170 ~vi~I~G~g-GiGKTtLa~~v~~~~~  194 (427)
                      +.+.|.|-| |+||||++..++..+.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa   27 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAK   27 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHH
Confidence            568899998 9999999999988873

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.09  E-value=0.022  Score=45.08  Aligned_cols=21  Identities=38%  Similarity=0.555  Sum_probs=8.3

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |.|+|.+|+|||||+..+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778999999999999877653

>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=91.64  E-value=0.07  Score=46.82  Aligned_cols=23  Identities=35%  Similarity=0.346  Sum_probs=20.7

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|.|..|+||||++..++...
T Consensus       168 nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             CEEEEeeccccchHHHHHHhhhc
Confidence            48899999999999999998765

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=91.56  E-value=0.091  Score=44.43  Aligned_cols=39  Identities=26%  Similarity=0.322  Sum_probs=28.9

Q ss_pred             hhHHHHHHHhccC--CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          155 STLDRVWRCLTEE--PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       155 ~~~~~l~~~l~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+.++...+.+.  ..-.|+|+|.+|+|||||...++.+.
T Consensus        16 ~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          16 TKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCCC
Confidence            4455566666543  34578899999999999999998653

>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=91.53  E-value=0.045  Score=45.22  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=19.4

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .-|.|.|.+|+|||||+..+...
T Consensus         7 ~KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            45789999999999999987544

>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=91.49  E-value=0.11  Score=47.06  Aligned_cols=43  Identities=30%  Similarity=0.410  Sum_probs=32.8

Q ss_pred             ccchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          151 VGMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       151 vGR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.....-+.++.+.....++|.|.|+.|+||||.+..+.+..
T Consensus       140 LG~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~~~l~~~  182 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQEL  182 (401)
T ss_dssp             SCCCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             hcccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHHHHhhhh
Confidence            4555444444555566667899999999999999999988876

>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=91.13  E-value=0.059  Score=46.05  Aligned_cols=26  Identities=23%  Similarity=0.148  Sum_probs=22.2

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +.|-|+|+|.+|.|||||+..+....
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~~~   30 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILYYT   30 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            45789999999999999999886543

>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=90.48  E-value=0.12  Score=41.57  Aligned_cols=38  Identities=13%  Similarity=0.070  Sum_probs=29.0

Q ss_pred             hHHHHHHHhcc-CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          156 TLDRVWRCLTE-EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       156 ~~~~l~~~l~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -+..+..+|.. +....+.|+|+++.|||++|..+.+-+
T Consensus        39 Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l   77 (205)
T d1tuea_          39 FLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFI   77 (205)
T ss_dssp             HHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHh
Confidence            34455555543 466789999999999999999887766

>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=90.45  E-value=0.33  Score=40.12  Aligned_cols=108  Identities=18%  Similarity=0.127  Sum_probs=55.4

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhcc--CC----------CCCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFL--HT----------PNDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNK  235 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~----------~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~  235 (427)
                      +.+++.|+|+...||||+.+.+.--..  +.          -..|+. ++..+....++..-                ..
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~-I~~~~~~~d~~~~~----------------~S  102 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDR-IFTRVGAADDLASG----------------RS  102 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCE-EEEEEC--------------------------
T ss_pred             CceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchh-heeEEccCcccccc----------------hh
Confidence            457899999999999999988754321  00          112322 23333332222111                11


Q ss_pred             CHHHHHHHHHHHh--cCCcEEEEEeccCCcccc-------cccccCCCCCCCCcEEEEecCChhHHh
Q 042645          236 SFDEKAQEIFKTM--RNRKIVLLLDDIWELFDL-------AQVGLPVPSRASASKVVFTTREFEVCG  293 (427)
Q Consensus       236 ~~~~~~~~l~~~L--~~k~~LlVlDdv~~~~~~-------~~~~~~l~~~~~gs~IivTtR~~~v~~  293 (427)
                      ....-...+...+  .+++.|+++|++-.-.+-       ..+...+. ...++.+++||....+..
T Consensus       103 ~F~~E~~~~~~il~~~~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l~-~~~~~~~i~tTH~~~l~~  168 (234)
T d1wb9a2         103 TFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLA-NKIKALTLFATHYFELTQ  168 (234)
T ss_dssp             -CHHHHHHHHHHHHHCCTTEEEEEESCCCCSSSSHHHHHHHHHHHHHH-HTTCCEEEEECSCGGGGG
T ss_pred             HHHHHHHHHHHHHHhcccccEEeecccccCCChhhhhHHHHHhhhhhh-ccccceEEEecchHHHhh
Confidence            2222233344443  357889999999643211       11111221 134578999999876644

>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=90.34  E-value=0.08  Score=43.84  Aligned_cols=24  Identities=46%  Similarity=0.529  Sum_probs=20.9

Q ss_pred             CeEEEEEecCCCcHHHHHHHHHhh
Q 042645          169 VGIVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .++|+|.|.+++|||||+..+...
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~~   28 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRGS   28 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHhh
Confidence            367999999999999999888654

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.22  E-value=0.023  Score=44.11  Aligned_cols=21  Identities=38%  Similarity=0.556  Sum_probs=19.2

Q ss_pred             EEEEecCCCcHHHHHHHHHhh
Q 042645          172 VGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       172 i~I~G~gGiGKTtLa~~v~~~  192 (427)
                      |+++|.+|+|||||+..+...
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            789999999999999998765

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=90.20  E-value=0.13  Score=45.17  Aligned_cols=24  Identities=25%  Similarity=0.235  Sum_probs=21.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|.|-|.-|+||||+++.+.+.+
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHSGG
T ss_pred             EEEEEECCccCCHHHHHHHHHHHh
Confidence            467888999999999999999987

>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=89.66  E-value=0.11  Score=44.18  Aligned_cols=22  Identities=41%  Similarity=0.557  Sum_probs=19.7

Q ss_pred             CeEEEEEecCCCcHHHHHHHHH
Q 042645          169 VGIVGLYGMGGVGKTTLLTQIN  190 (427)
Q Consensus       169 ~~vi~I~G~gGiGKTtLa~~v~  190 (427)
                      .|.|+|.|..|.|||||+..+.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            3679999999999999999884

>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=88.67  E-value=0.17  Score=43.91  Aligned_cols=54  Identities=15%  Similarity=0.122  Sum_probs=27.7

Q ss_pred             EEEEEecCCCcHHHHHHH-HHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHh
Q 042645          171 IVGLYGMGGVGKTTLLTQ-INNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKI  225 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~-v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l  225 (427)
                      .+.|.|.+|+||||.+.+ +..-..........++.++.+.. ....+...+....
T Consensus        26 ~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~-aa~~~~~~~~~~~   80 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNK-AAREMRERVQSLL   80 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHH-HHHHHHHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHH-HHHHHHHHHHhhc
Confidence            377889999999976543 33222111122344555554432 2333444444433

>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=88.17  E-value=0.14  Score=40.41  Aligned_cols=22  Identities=32%  Similarity=0.457  Sum_probs=19.6

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      .|+|+|.+++|||||...+...
T Consensus         7 nIaiiG~~naGKSTL~n~L~~~   28 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTEI   28 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTT
T ss_pred             EEEEEeCCCCcHHHHHHHHHHh
Confidence            5899999999999999998753

>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=88.13  E-value=0.15  Score=44.77  Aligned_cols=23  Identities=35%  Similarity=0.429  Sum_probs=21.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      .|.|-|.-|+||||+++.+.+.+
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l   29 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHF   29 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48889999999999999999887

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=87.03  E-value=0.13  Score=45.00  Aligned_cols=24  Identities=29%  Similarity=0.102  Sum_probs=19.8

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -.|.|-|.-|+||||+++.+.+..
T Consensus         5 lrI~IEG~iGsGKTTl~~~La~~l   28 (329)
T d1e2ka_           5 LRVYIDGPHGMGKTTTTQLLVALG   28 (329)
T ss_dssp             EEEEECSCTTSSHHHHHHHHTC--
T ss_pred             eEEEEECCcCCCHHHHHHHHHHHh
Confidence            358899999999999999997765

>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=86.96  E-value=0.14  Score=43.99  Aligned_cols=18  Identities=33%  Similarity=0.440  Sum_probs=14.3

Q ss_pred             eEEEEEecCCCcHHHHHH
Q 042645          170 GIVGLYGMGGVGKTTLLT  187 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~  187 (427)
                      ..+.|.|.+|+||||.+.
T Consensus        15 ~~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             SEEEECCCTTSCHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHH
Confidence            346788999999997643

>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=86.92  E-value=0.96  Score=36.86  Aligned_cols=106  Identities=22%  Similarity=0.264  Sum_probs=56.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhcc--CCC----------CCCcEEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCCCH
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSFL--HTP----------NDFDFVIWEVVSRDLQLGKIQESIAKKIGLYNESWDNKSF  237 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~~--~~~----------~~f~~~~wv~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~  237 (427)
                      +++.|.|+...||||+.+.+.--..  +..          ..|+. ++..+....++..                .....
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~-I~~~~~~~d~~~~----------------~~StF   98 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDG-IYTRIGASDDLAG----------------GKSTF   98 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSE-EEEECCC----------------------CCSHH
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecce-EEEEECCCccccC----------------CccHH
Confidence            4789999999999999988753221  100          12332 2333332222111                12222


Q ss_pred             HHHHHHHHHHhc--CCcEEEEEeccCCcccc-------cccccCCCCCCCCcEEEEecCChhHHhh
Q 042645          238 DEKAQEIFKTMR--NRKIVLLLDDIWELFDL-------AQVGLPVPSRASASKVVFTTREFEVCGL  294 (427)
Q Consensus       238 ~~~~~~l~~~L~--~k~~LlVlDdv~~~~~~-------~~~~~~l~~~~~gs~IivTtR~~~v~~~  294 (427)
                      ..-...+...+.  +++.|+++|++-.-.+-       ..+...|.  ..++.+++||...++...
T Consensus        99 ~~el~~~~~il~~~~~~sLvliDE~~~gT~~~eg~ala~aile~L~--~~~~~~i~tTH~~eL~~l  162 (224)
T d1ewqa2          99 MVEMEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALH--ERRAYTLFATHYFELTAL  162 (224)
T ss_dssp             HHHHHHHHHHHHHCCTTEEEEEESTTTTSCHHHHHHHHHHHHHHHH--HHTCEEEEECCCHHHHTC
T ss_pred             HHhHHHHHHHhccCCCCcEEeecccccCcchhhhcchHHHHHHHHh--hcCcceEEeeechhhhhh
Confidence            333344444443  68899999999653221       11112222  236789999998777553

>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=86.84  E-value=0.088  Score=43.49  Aligned_cols=24  Identities=33%  Similarity=0.530  Sum_probs=18.9

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +...+.|.+|+|||||...+..+.
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~~  121 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPEL  121 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC--
T ss_pred             ceEEEECCCCccHHHHHHhhccHh
Confidence            455688999999999999887654

>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=86.67  E-value=2.1  Score=34.86  Aligned_cols=42  Identities=14%  Similarity=0.037  Sum_probs=34.8

Q ss_pred             cchhhHHHHHHHhccCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          152 GMQSTLDRVWRCLTEEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       152 GR~~~~~~l~~~l~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ......+++.+.+..+......|+|..|+|||-++-......
T Consensus        59 ~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~  100 (233)
T d2eyqa3          59 DQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLA  100 (233)
T ss_dssp             HHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHH
Confidence            456677888888888888889999999999999987776554

>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=85.33  E-value=0.47  Score=40.01  Aligned_cols=36  Identities=19%  Similarity=0.253  Sum_probs=27.4

Q ss_pred             HHHHHHhcc--CCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          158 DRVWRCLTE--EPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       158 ~~l~~~l~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ..+..+|..  +....+.++|+|+.|||+++..+.+-+
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            344455532  456789999999999999999988765

>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=84.76  E-value=0.45  Score=35.25  Aligned_cols=52  Identities=13%  Similarity=0.109  Sum_probs=31.8

Q ss_pred             CCeEEEEEecCCCcHHHHHHHHHhhccCCCCCCcEEEEEEeCCCCCHHHHHHHHHHHhC
Q 042645          168 PVGIVGLYGMGGVGKTTLLTQINNSFLHTPNDFDFVIWEVVSRDLQLGKIQESIAKKIG  226 (427)
Q Consensus       168 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~~f~~~~wv~~~~~~~~~~l~~~i~~~l~  226 (427)
                      +.++..|+++.|.|||+++-.++...       ..++.+.+....-..+....+.+.+.
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~~-------~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAAQ-------GYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHTT-------TCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHc-------CCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            45788999999999999987766443       11344444443334444444444443

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=84.56  E-value=0.25  Score=39.91  Aligned_cols=22  Identities=36%  Similarity=0.366  Sum_probs=18.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|.|.++.|||||+.++...
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~~   26 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTYV   26 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHH
Confidence            3889999999999999888543

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.98  E-value=0.37  Score=40.97  Aligned_cols=28  Identities=21%  Similarity=0.459  Sum_probs=24.4

Q ss_pred             cCCCeEEEEEecCCCcHHHHHHHHHhhc
Q 042645          166 EEPVGIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       166 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      +++..||+|+|+-+.|||+|+..+++..
T Consensus        29 ~~~v~vvsi~G~~~sGKS~llN~l~~~~   56 (277)
T d1f5na2          29 TQPMVVVAIVGLYRTGKSYLMNKLAGKK   56 (277)
T ss_dssp             CSBEEEEEEEEBTTSSHHHHHHHHTTCS
T ss_pred             CCCEEEEEEECCCCCCHHHHHHHHcCCC
Confidence            3468899999999999999999998754

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) 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: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.84  E-value=0.34  Score=42.51  Aligned_cols=25  Identities=20%  Similarity=0.185  Sum_probs=21.9

Q ss_pred             CCCeEEEEEecCCCcHHHHHHHHHh
Q 042645          167 EPVGIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       167 ~~~~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      ++.|-|+|.|..|.|||||+..+..
T Consensus        15 ~~IRNI~iiGhvd~GKTTL~d~Ll~   39 (341)
T d1n0ua2          15 TNVRNMSVIAHVDHGKSTLTDSLVQ   39 (341)
T ss_dssp             GGEEEEEEECCGGGTHHHHHHHHHH
T ss_pred             ccCcEEEEEeCCCCcHHHHHHHHHH
Confidence            4678899999999999999988763

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=83.71  E-value=0.1  Score=41.78  Aligned_cols=24  Identities=25%  Similarity=0.390  Sum_probs=19.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      ++.+|+|+.|+||||+...+.--+
T Consensus        25 ~~tvi~G~NGsGKStil~Ai~~~L   48 (222)
T d1qhla_          25 LVTTLSGGNGAGKSTTMAAFVTAL   48 (222)
T ss_dssp             HHHHHHSCCSHHHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            356789999999999999887544

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.10  E-value=0.56  Score=42.11  Aligned_cols=22  Identities=23%  Similarity=0.415  Sum_probs=19.7

Q ss_pred             eEEEEEecCCCcHHHHHHHHHh
Q 042645          170 GIVGLYGMGGVGKTTLLTQINN  191 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~  191 (427)
                      --|+|+|.+|+|||||...+..
T Consensus        57 l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          57 LNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4589999999999999999874

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.93  E-value=1.5  Score=31.55  Aligned_cols=24  Identities=17%  Similarity=0.044  Sum_probs=21.6

Q ss_pred             eEEEEEecCCCcHHHHHHHHHhhc
Q 042645          170 GIVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       170 ~vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      =+|.+.|..|+||+|||..+...+
T Consensus         7 f~i~~tg~~~~gk~~ia~al~~~l   30 (122)
T d1g8fa3           7 FSIVLGNSLTVSREQLSIALLSTF   30 (122)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHH
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHH
Confidence            378899999999999999998777

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=81.44  E-value=0.38  Score=40.91  Aligned_cols=23  Identities=30%  Similarity=0.550  Sum_probs=20.1

Q ss_pred             EEEEEecCCCcHHHHHHHHHhhc
Q 042645          171 IVGLYGMGGVGKTTLLTQINNSF  193 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~~  193 (427)
                      -|+|+|.|.+|||||-..+-+.-
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~~   26 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKAG   26 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTC
T ss_pred             eEEEECCCCCCHHHHHHHHHCCC
Confidence            58999999999999999887654

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=80.16  E-value=0.45  Score=40.81  Aligned_cols=22  Identities=41%  Similarity=0.670  Sum_probs=19.9

Q ss_pred             EEEEEecCCCcHHHHHHHHHhh
Q 042645          171 IVGLYGMGGVGKTTLLTQINNS  192 (427)
Q Consensus       171 vi~I~G~gGiGKTtLa~~v~~~  192 (427)
                      -|+|+|.|.+|||||-..+-+.
T Consensus        12 kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          12 KTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            5999999999999999998864