Citrus Sinensis ID: 044858

---

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
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHccccccEEEEEccccccHHHHHHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccEEEEEEEccccccccccccccccccccccEEEEEEccHHHHcccccccccEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccccHHHHHHcccccccccHHHHHHccccccccccHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccccEEccccccccccccccccccccccHHHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHccHHHHccccEEEEEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccEEEEEEEccccHccHHHHcccccccccccEEEEEEccHHHHHHHcccccccEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccccccccHHHEEcHcccccHHHHHHEEEEEEcccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQykvddsrikgdgiqqpVEEWLITVDEAINEVETLIADKeksnnrclkglcpnlktRYQLSKKAEREANAIVGlhekgrfdsvsfrtipeetwLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVygmggigkTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDiwgsldleaigipladdnggcKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMtgdciengelkSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
Flexible Loop (DISEMBL)
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARAsvqykvddsrikgdgiqqpveEWLITVDEAINEVETLiadkeksnnrclkglcpnlkTRYQLSKKAEREANAivglhekgrfdsvsfrTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKennlfekvissrvsqtpqikEIQREIAEKlglkidqesesVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIakalknkspYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
Low Complexity Region (SEG)
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTnleklkneleklkIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
Disordered region (IsUnstruct)
**IVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKA*REANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVI****************IAEKLGLKID***ESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYR****
Disordered Region (DISOPRED)
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIV********************************SRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK******************EQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKR***********VAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
Disordered Region (DISEMBL)
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
Disordered Region (DISPRO)
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSF*************DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNxxxxxxxxxxxxxxxxxxxxxVDDSRIKGDGIQQPVEEWLITxxxxxxxxxxxxxxxxxxxxxCLKGLCPNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICNVKDLLYRGMGL
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	426	2.2.26 [Sep-21-2011]
P60838	894	Probable disease resistan	yes	no	0.868	0.413	0.304	3e-36
O64789	925	Probable disease resistan	no	no	0.882	0.406	0.311	1e-34
Q940K0	889	Probable disease resistan	no	no	0.882	0.422	0.306	7e-34
O22727	967	Probable disease resistan	no	no	0.863	0.380	0.309	2e-33
Q9T048	985	Disease resistance protei	no	no	0.899	0.388	0.267	2e-33
P60839	884	Probable disease resistan	no	no	0.875	0.421	0.288	1e-32
O64973	889	Disease resistance protei	no	no	0.870	0.417	0.290	2e-32
Q8L3R3	885	Disease resistance protei	no	no	0.873	0.420	0.287	2e-31
Q8RXS5	888	Probable disease resistan	no	no	0.887	0.425	0.281	2e-31
Q9LMP6	851	Probable disease resistan	no	no	0.845	0.423	0.283	7e-30

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

 Score =  153 bits (386), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 121/397 (30%), Positives = 197/397 (49%), Gaps = 27/397 (6%)

Query: 25  YCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRI--KGDGIQQPVEEWLITVDEAINEV 82
           Y C  + N+  +K ++E LK  R  V+ +VD      + + + Q V+ WL  V    N+ 
Sbjct: 28  YICELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEFTRRRERLSQ-VQGWLTNVSTVENKF 86

Query: 83  ETLIADKEKSNNR-CLKGLCP-NLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIP- 139
             L+   +    R CL G C  N+K  Y   K+       I  L  +G FD+V+  T P 
Sbjct: 87  NELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVLMLKEIESLSSQGDFDTVTLAT-PI 145

Query: 140 ---EETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA 196
              EE  ++ T        +++ L+ +   L+     ++G+YGMGG+GKTTL+  +  + 
Sbjct: 146 ARIEEMPIQPT-----IVGQETMLERVWTRLTEDGDEIVGLYGMGGVGKTTLLTRINNKF 200

Query: 197 KEN-NLFEKVISSRVSQTPQIKEIQREIAEKLGL---KIDQESESVRAWRLLEQLKKETK 252
            E  + F  VI   VS++P I  IQ +I ++L L   + D  +E+ RA  +   L K+ K
Sbjct: 201 SEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEEWDNVNENQRALDIYNVLGKQ-K 259

Query: 253 ILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEA 312
            +++LDDIW  ++LE +G+P      GCKV+ T RS+DV    M       V  L   EA
Sbjct: 260 FVLLLDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCG-RMRVDDPMEVSCLEPNEA 318

Query: 313 WSLFKKMTGDCIENG--ELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY-EWRNALRQL 369
           W LF+   G+    G  ++  +  +V  +C GLP+A+  I + +  K    EWRNA+  L
Sbjct: 319 WELFQMKVGENTLKGHPDIPELARKVAGKCCGLPLALNVIGETMACKRMVQEWRNAIDVL 378

Query: 370 KRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
             ++   F G + +     ++ SY+ L  E+++  FL
Sbjct: 379 S-SYAAEFPGMEQILP--ILKYSYDNLNKEQVKPCFL 412

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 =  147 bits (372), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 122/392 (31%), Positives = 198/392 (50%), Gaps = 16/392 (4%)

Query: 24  TYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVE 83
           +Y  +   NL  L+ E+E L+  +  VQ KV     +     + V+ WL  V+    E +
Sbjct: 27  SYIRTLEKNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVNSIDIECK 86

Query: 84  TLIA-DKEKSNNRCLKGLCPN-LKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEE 141
            L++    +    CL GLC   + + Y+  KK       +  L  +G FD VS      E
Sbjct: 87  DLLSVSPVELQKLCLCGLCTKYVCSSYKYGKKVFLLLEEVKILKSEGNFDEVSQPPPRSE 146

Query: 142 TWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE-NN 200
              + TQ  +    ++  L+   + L      ++G++GMGG+GKTTL K++  +  E   
Sbjct: 147 VEERPTQPTI---GQEEMLEKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEIGG 203

Query: 201 LFEKVISSRVSQTPQIKEIQREIAEKLGLKID---QESESVRAWRLLEQLKKETKILIIL 257
            F+ VI   VSQ  ++ ++Q +IAEKL L  D    ++ES +A  +   LK + + +++L
Sbjct: 204 TFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATDIHRVLKGK-RFVLML 262

Query: 258 DDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFK 317
           DDIW  +DLEAIGIP   +   CKV  T RS++V   EM   +   V+ L  ++AW LFK
Sbjct: 263 DDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCG-EMGDHKPMQVNCLEPEDAWELFK 321

Query: 318 KMTGDCIENGE--LKSVVTEVVKECAGLPIAIVPIAKALKNKSPY-EWRNALRQLKRNFL 374
              GD   + +  +  +  EV ++C GLP+A+  I + + +K+   EW  A+  L R+  
Sbjct: 322 NKVGDNTLSSDPVIVGLAREVAQKCRGLPLALNVIGETMASKTMVQEWEYAIDVLTRS-A 380

Query: 375 RSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
             FSG +       ++ SY+ LG E ++  FL
Sbjct: 381 AEFSGMEN-KILPILKYSYDSLGDEHIKSCFL 411

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  145 bits (365), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 120/392 (30%), Positives = 196/392 (50%), Gaps = 16/392 (4%)

Query: 24  TYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVE 83
           +Y  +   NL  L+ E+E L+  +  VQ KV     +     + V+ WL  V+    E +
Sbjct: 25  SYIRTLEKNLRALQREMEDLRAIQHEVQNKVARDEARHQRRLEAVQVWLDRVNSVDIECK 84

Query: 84  TLIA-DKEKSNNRCLKGLCPN-LKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEE 141
            L++    +    CL GLC   + + Y+  KK       +  L+ +G FD VS      E
Sbjct: 85  DLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVFLLLEEVKKLNSEGNFDEVSQPPPRSE 144

Query: 142 TWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE-NN 200
              + TQ  +    ++  L+   + L      ++G++GMGG+GKTTL K++  +  E   
Sbjct: 145 VEERPTQPTI---GQEDMLEKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEIGG 201

Query: 201 LFEKVISSRVSQTPQIKEIQREIAEKLGLKID---QESESVRAWRLLEQLKKETKILIIL 257
            F+ VI   VS+   I ++Q +IAEKL L  D    ++ES +A  +   LK + + +++L
Sbjct: 202 TFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDLWKNKNESDKATDIHRVLKGK-RFVLML 260

Query: 258 DDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFK 317
           DDIW  +DLEAIGIP   +   CKV  T RS++V   EM   +   V+ L  ++AW LFK
Sbjct: 261 DDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCG-EMGDHKPMQVNCLEPEDAWELFK 319

Query: 318 KMTGDCIENGE--LKSVVTEVVKECAGLPIAIVPIAKALKNKSPY-EWRNALRQLKRNFL 374
              GD   + +  +  +  EV ++C GLP+A+  I + + +K+   EW +A+     +  
Sbjct: 320 NKVGDNTLSSDPVIVELAREVAQKCRGLPLALNVIGETMSSKTMVQEWEHAIHVFNTS-A 378

Query: 375 RSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
             FS  Q       ++ SY+ LG E ++  FL
Sbjct: 379 AEFSDMQN-KILPILKYSYDSLGDEHIKSCFL 409

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 =  144 bits (362), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 119/384 (30%), Positives = 191/384 (49%), Gaps = 16/384 (4%)

Query: 32  NLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIA-DKE 90
           NL  L+ E+E L+  +  VQ KV     +     + V+ WL  V+    E + L++    
Sbjct: 34  NLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVNSIDIECKDLLSVSPV 93

Query: 91  KSNNRCLKGLCPN-LKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQD 149
           +    CL GLC   + + Y+  K+       +  L  +G FD VS      E   + TQ 
Sbjct: 94  ELQKLCLCGLCSKYVCSSYKYGKRVFLLLEEVTKLKSEGNFDEVSQPPPRSEVEERPTQP 153

Query: 150 FMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQ-AKENNLFEKVISS 208
            +    ++  LK   + L      ++G++GMGG+GKTTL K++  + A+    F+ VI  
Sbjct: 154 TI---GQEEMLKKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAETGGTFDIVIWI 210

Query: 209 RVSQTPQIKEIQREIAEKLGLKID---QESESVRAWRLLEQLKKETKILIILDDIWGSLD 265
            VSQ  ++ ++Q +IAEKL L  D    ++ES +A  +   LK + + +++LDDIW  +D
Sbjct: 211 VVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATDIHRVLKGK-RFVLMLDDIWEKVD 269

Query: 266 LEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIE 325
           LEAIGIP   +   CKV  T R Q V   +M   +   V  L  ++AW LFK   GD   
Sbjct: 270 LEAIGIPYPSEVNKCKVAFTTRDQKVCG-QMGDHKPMQVKCLEPEDAWELFKNKVGDNTL 328

Query: 326 NGE--LKSVVTEVVKECAGLPIAIVPIAKALKNKSPY-EWRNALRQLKRNFLRSFSGTQA 382
             +  +  +  EV ++C GLP+A+  I + + +K+   EW +A+  L R+    FS  Q 
Sbjct: 329 RSDPVIVGLAREVAQKCRGLPLALSCIGETMASKTMVQEWEHAIDVLTRS-AAEFSDMQN 387

Query: 383 VAAYSTIQLSYNQLGGEELRKTFL 406
                 ++ SY+ L  E ++  FL
Sbjct: 388 -KILPILKYSYDSLEDEHIKSCFL 410

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9T048|DRL27_ARATH Disease resistance protein At4g27190 OS=Arabidopsis thaliana GN=At4g27190 PE=2 SV=1

 Score =  144 bits (362), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 108/403 (26%), Positives = 196/403 (48%), Gaps = 20/403 (4%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           ME    V  ++   +      +      + +N++ L   LE+L   + ++    +    K
Sbjct: 1   MECCAPVIGEILRLMYESTFSRVANAIKFKSNVKALNESLERLTELKGNMSEDHETLLTK 60

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
              ++  +  W    +E I++    + ++          +   +  R ++S+K  +  + 
Sbjct: 61  DKPLRLKLMRWQREAEEVISKARLKLEER----------VSCGMSLRPRMSRKLVKILDE 110

Query: 121 IVGLHEKG--RFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVY 178
           +  L + G    D +S  + PE          +H     + L  I D L++     IGV+
Sbjct: 111 VKMLEKDGIEFVDMLSVESTPERVEHVPGVSVVHQTMASNMLAKIRDGLTSEKAQKIGVW 170

Query: 179 GMGGIGKTTLVKEVGRQAKE---NNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID-QE 234
           GMGG+GKTTLV+ +  + +E      F  VI   VS+    +E+Q++IAE+L +    +E
Sbjct: 171 GMGGVGKTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDPREVQKQIAERLDIDTQMEE 230

Query: 235 SESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSC 294
           SE   A R+   L KE K L+ILDD+W  +DL+ +GIP  ++N G KV+LT+R  +V   
Sbjct: 231 SEEKLARRIYVGLMKERKFLLILDDVWKPIDLDLLGIPRTEENKGSKVILTSRFLEVCR- 289

Query: 295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL 354
            M    +  VD L +++AW LF K  GD + +  ++ +   V +EC GLP+AI+ +  A+
Sbjct: 290 SMKTDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAM 349

Query: 355 KNKSPYE-WRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQL 396
           + K   + W + L +L ++     S  + +  +  ++LSY+ L
Sbjct: 350 RGKKNVKLWNHVLSKLSKSVPWIKSIEEKI--FQPLKLSYDFL 390

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 =  140 bits (354), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 116/402 (28%), Positives = 192/402 (47%), Gaps = 29/402 (7%)

Query: 21  RQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAIN 80
           R+  Y  +   NL  L+  +E LK  R  +  KV  +   G      ++ WL    + + 
Sbjct: 24  RKLYYIQNIKENLTSLEEAMEDLKALRDDLLRKVQTAEEGGLQRLHQIKVWL----KRVK 79

Query: 81  EVETLIADKEKSNNRCLKGLC------PNLKTRYQLSKKAEREANAIVGLHEKGRFDSVS 134
            +E+   D + S    L+ LC       NL+  Y   ++     N +  L  KG F+ V+
Sbjct: 80  TIESQFNDLDSSRTVELQRLCCCGVGSRNLRLSYDYGRRVFLMLNIVEDLKSKGIFEEVA 139

Query: 135 F---RTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKE 191
               R + EE  L+ T        +++ L+   D L +    ++G+YGMGG+GKTTL+ +
Sbjct: 140 HPATRAVGEERPLQPT-----IVGQETILEKAWDHLMDDGTKIMGLYGMGGVGKTTLLTQ 194

Query: 192 VG-RQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGL---KIDQESESVRAWRLLEQL 247
           +  R    ++  E VI   VS   QI +IQ+EI EK+G    + +Q+SE+ +A  +L  L
Sbjct: 195 INNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGEKIGFIGVEWNQKSENQKAVDILNFL 254

Query: 248 KKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVL 307
            K+ + +++LDDIW  ++L  IGIP      GCK+  T R Q V +  M       V  L
Sbjct: 255 SKK-RFVLLLDDIWKRVELTEIGIPNPTSENGCKIAFTTRCQSVCA-SMGVHDPMEVRCL 312

Query: 308 NDKEAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAKALK-NKSPYEWRN 364
              +AW LFKK  GD     + ++  +  +V + C GLP+A+  I + +   K+  EW  
Sbjct: 313 GADDAWDLFKKKVGDITLSSHPDIPEIARKVAQACCGLPLALNVIGETMACKKTTQEWDR 372

Query: 365 ALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
           A+  +   +  +F   +       ++ SY+ L  E ++  FL
Sbjct: 373 AV-DVSTTYAANFGAVKE-RILPILKYSYDNLESESVKTCFL 412

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 =  140 bits (353), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 116/399 (29%), Positives = 205/399 (51%), Gaps = 28/399 (7%)

Query: 24  TYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQ---PVEEWLITVDEAIN 80
           +Y  + + NL  L+  +  LK  +  V  +++     G   QQ    V+ WL +V    N
Sbjct: 27  SYIHNLSKNLASLQKAMRMLKARQYDVIRRLETEEFTGR--QQRLSQVQVWLTSVLIIQN 84

Query: 81  EVETLIADKEKSNNR-CLKGLCP-NLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTI 138
           +   L+   E    R CL G C  +LK  Y+  K+       +  L  +G FD VS  T 
Sbjct: 85  QFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRVIMMLKEVESLSSQGFFDVVSEATP 144

Query: 139 PEETWLKSTQDFMHFESRKSTLKGILDALSNR----NFNMIGVYGMGGIGKTTLVKEVGR 194
             +       D + F+      + +L+   NR       ++G+YGMGG+GKTTL+ ++  
Sbjct: 145 FADV------DEIPFQPTIVGQEIMLEKAWNRLMEDGSGILGLYGMGGVGKTTLLTKINN 198

Query: 195 Q-AKENNLFEKVISSRVSQTPQIKEIQREIAEKLGL---KIDQESESVRAWRLLEQLKKE 250
           + +K ++ F+ VI   VS++  +++IQR+IAEK+GL   +  +++++  A  +   L++ 
Sbjct: 199 KFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWSEKNDNQIAVDIHNVLRRR 258

Query: 251 TKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDK 310
            K +++LDDIW  ++L+A+G+P    + GCKV  T RS+DV    M       V  L  +
Sbjct: 259 -KFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCG-RMGVDDPMEVSCLQPE 316

Query: 311 EAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAKALKNK-SPYEWRNALR 367
           E+W LF+   G      + ++  +  +V ++C GLP+A+  I +A+  K + +EW +A+ 
Sbjct: 317 ESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGEAMACKRTVHEWCHAID 376

Query: 368 QLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
            L  + +  FSG +    +  ++ SY+ L GE ++  FL
Sbjct: 377 VLTSSAI-DFSGMEDEILH-VLKYSYDNLNGELMKSCFL 413

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

 Score =  137 bits (345), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 114/397 (28%), Positives = 192/397 (48%), Gaps = 25/397 (6%)

Query: 24  TYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQ-QPVEEWLITVDEAINEV 82
           +Y  + + NL  L+  +  L   R  VQ +++     G   +   V+ WL  +    N+ 
Sbjct: 27  SYIQNLSENLASLQKAMGVLNAKRDDVQGRINREEFTGHRRRLAQVQVWLTRIQTIENQF 86

Query: 83  ETLIADKEKSNNR-CLKGLCP-NLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIP- 139
             L++       R CL G C  N+K  Y   K+       + GL  +G FD V+    P 
Sbjct: 87  NDLLSTCNAEIQRLCLCGFCSKNVKMSYLYGKRVIVLLREVEGLSSQGVFDIVT-EAAPI 145

Query: 140 ---EETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQ- 195
              EE  ++ST        + S L  + + L      ++G+YGMGG+GKTTL+ ++  + 
Sbjct: 146 AEVEELPIQST-----IVGQDSMLDKVWNCLMEDKVWIVGLYGMGGVGKTTLLTQINNKF 200

Query: 196 AKENNLFEKVISSRVSQTPQIKEIQREIAEKLGL---KIDQESESVRAWRLLEQLKKETK 252
           +K    F+ VI   VS+   + +IQ+ I EKLGL     D+++++ RA  +   L+++ K
Sbjct: 201 SKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVGKNWDEKNKNQRALDIHNVLRRK-K 259

Query: 253 ILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEA 312
            +++LDDIW  ++L+ IG+P      GCKV  T  S++V    M       +  L+   A
Sbjct: 260 FVLLLDDIWEKVELKVIGVPYPSGENGCKVAFTTHSKEVCG-RMGVDNPMEISCLDTGNA 318

Query: 313 WSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAKALKNK-SPYEWRNALRQL 369
           W L KK  G+     + ++  +  +V ++C GLP+A+  I + +  K +  EWR+A   L
Sbjct: 319 WDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPLALNVIGETMSFKRTIQEWRHATEVL 378

Query: 370 KRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
                  FSG +       ++ SY+ L GE+ +  FL
Sbjct: 379 TSA--TDFSGMED-EILPILKYSYDSLNGEDAKSCFL 412

Disease resistance (R) protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  137 bits (344), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 111/394 (28%), Positives = 188/394 (47%), Gaps = 16/394 (4%)

Query: 21  RQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAIN 80
           R   Y      NL  L+  LE+++  R  +  K+     +G      V+ W+  V+  + 
Sbjct: 24  RNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSEERRGLQRLSVVQGWVSKVEAIVP 83

Query: 81  EVETLIADKEKSNNR-CLKGLCP-NLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTI 138
            V  L+  +     R CL G C  NL + Y+  K+  +    +  L  +G F  V+ R  
Sbjct: 84  RVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVMKMIEEVEVLRYQGDFAVVAERVD 143

Query: 139 PEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVG-RQAK 197
                 + T+  +  +     L+   + L      ++G++GMGG+GKTTL+  +  R ++
Sbjct: 144 AARVEERPTRPMVAMDP---MLESAWNRLMEDEIGILGLHGMGGVGKTTLLSHINNRFSR 200

Query: 198 ENNLFEKVISSRVSQTPQIKEIQREIAEKL---GLKIDQESESVRAWRLLEQLKKETKIL 254
               F+ VI   VS+  QI+ IQ EI EKL     K  Q++E ++A  +   LK + + +
Sbjct: 201 VGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDNEKWKQKTEDIKASNIYNVLKHK-RFV 259

Query: 255 IILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWS 314
           ++LDDIW  +DL  +G+P      GCK++ T R +++    M    +  V  L   +AW 
Sbjct: 260 LLLDDIWSKVDLTEVGVPFPSRENGCKIVFTTRLKEICG-RMGVDSDMEVRCLAPDDAWD 318

Query: 315 LFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAKALKNK-SPYEWRNALRQLKR 371
           LF K  G+     + E+ +V   V K+C GLP+A+  I + +  K +  EWR+A+  L  
Sbjct: 319 LFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALNVIGETMAYKRTVQEWRSAIDVLTS 378

Query: 372 NFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTF 405
           +    FSG +       ++ SY+ L  E+L+  F
Sbjct: 379 S-AAEFSGMED-EILPILKYSYDNLKSEQLKLCF 410

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  132 bits (331), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 115/405 (28%), Positives = 191/405 (47%), Gaps = 45/405 (11%)

Query: 25  YCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVET 84
           Y      NLE L+N +++L+  R  +  +V     KG      V+ WL  V +  ++V  
Sbjct: 28  YILKMEANLEALQNTMQELEERRDDLLRRVVIEEDKGLQRLAQVQGWLSRVKDVCSQVND 87

Query: 85  LIADKEKSNNR-CLKGLCP-NLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEET 142
           L+  K     R CL G C  N  +         ++   + GL  KG F+ V+ +    + 
Sbjct: 88  LLKAKSIQTERLCLCGYCSKNFISGRNYGINVLKKLKHVEGLLAKGVFEVVAEKIPAPKV 147

Query: 143 WLKSTQDFMHFESRKSTLKGILDALSNRNFN--------MIGVYGMGGIGKTTLVKEVGR 194
             K  Q          T  G LDA+  R +N         +G+YGMGG+GKTTL+  +  
Sbjct: 148 EKKHIQ----------TTVG-LDAMVGRAWNSLMKDERRTLGLYGMGGVGKTTLLASINN 196

Query: 195 QAKEN-NLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET-- 251
           +  E  N F+ VI   VS+  Q + IQ +I  +LGL         R W+ + + +K +  
Sbjct: 197 KFLEGMNGFDLVIWVVVSKDLQNEGIQEQILGRLGLH--------RGWKQVTEKEKASYI 248

Query: 252 -------KILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVV 304
                  K +++LDD+W  +DLE IG+P      G K++ T RS+DV   +M+      V
Sbjct: 249 CNILNVKKFVLLLDDLWSEVDLEKIGVPPLTRENGSKIVFTTRSKDVCR-DMEVDGEMKV 307

Query: 305 DVLNDKEAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAKALKNK-SPYE 361
           D L   EAW LF+K  G      + ++ ++  +V ++C GLP+A+  I KA+ ++ +  E
Sbjct: 308 DCLPPDEAWELFQKKVGPIPLQSHEDIPTLARKVAEKCCGLPLALSVIGKAMASRETVQE 367

Query: 362 WRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
           W++ +  L  +     S  + +     ++ SY+ L  E+++  FL
Sbjct: 368 WQHVIHVLNSSSHEFPSMEEKI--LPVLKFSYDDLKDEKVKLCFL 410

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	426
147802546	1409	hypothetical protein VITISV_007222 [Viti	0.995	0.300	0.481	1e-106
359488027	1520	PREDICTED: disease resistance protein At	0.995	0.278	0.478	1e-106
224083434	1144	cc-nbs-lrr resistance protein [Populus t	0.997	0.371	0.491	1e-103
147865073	1694	hypothetical protein VITISV_021876 [Viti	0.990	0.249	0.463	1e-102
359488288	1340	PREDICTED: LOW QUALITY PROTEIN: probable	0.997	0.317	0.466	1e-101
224147195	554	cc-nbs resistance protein [Populus trich	0.981	0.754	0.455	1e-100
147833354	1494	hypothetical protein VITISV_041837 [Viti	0.990	0.282	0.451	1e-100
359488103	1530	PREDICTED: disease resistance protein At	0.990	0.275	0.451	1e-99
224111296	1315	cc-nbs-lrr resistance protein [Populus t	0.981	0.317	0.469	3e-98
147777048	1460	hypothetical protein VITISV_009359 [Viti	0.990	0.289	0.447	8e-98

>gi|147802546|emb|CAN77665.1| hypothetical protein VITISV_007222 [Vitis vinifera]

 Score =  392 bits (1007), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 205/426 (48%), Positives = 290/426 (68%), Gaps = 2/426 (0%)

Query: 2   EIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKG 61
           EIV+++ AKVAEYLVAPI R F Y  +Y +N++ L+ ++EKL  ARA ++  VD++   G
Sbjct: 3   EIVVTIAAKVAEYLVAPIGRSFGYLFNYRSNIDDLRQQVEKLGDARARLERSVDEAIRNG 62

Query: 62  DGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAI 121
           D I+  V++WL+ V   + E       ++K+N  C  G CPNLK++YQLS++A++ A  +
Sbjct: 63  DEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKRARVV 122

Query: 122 VGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMG 181
             +   G+F+ VS+R           +     ESR +TL  I++AL + + N+IGV+GM 
Sbjct: 123 AEIQGDGKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIGVWGMA 182

Query: 182 GIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAW 241
           G+GKTTL+K+V +Q +E  LF+KV+ + +S TP++K+IQ E+A+ LGLK ++ESE  RA 
Sbjct: 183 GVGKTTLMKQVAKQVEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESEMGRAA 242

Query: 242 RLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQN 301
           RL E+LKK  KILIILDDIW  LDLE +GIP  DD+ GCK++LT+R++ VLS EM  Q++
Sbjct: 243 RLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHVLSNEMGTQKD 302

Query: 302 FVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYE 361
           F V+ L ++EA  LFKKM GD IE  +L+S+  +V KECAGLPIAIV +AKALKNK    
Sbjct: 303 FPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNKGLSI 362

Query: 362 WRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG-YSYICNVKDLL 420
           W +ALRQLKR+   +  G  A+  YST++LSYN L G+E++  FLL G  S    + DLL
Sbjct: 363 WEDALRQLKRSIPTNIKGMDAM-VYSTLELSYNHLEGDEVKSLFLLCGLMSNKIYIDDLL 421

Query: 421 YRGMGL 426
             GMGL
Sbjct: 422 KYGMGL 427

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488027|ref|XP_002269288.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 204/426 (47%), Positives = 290/426 (68%), Gaps = 2/426 (0%)

Query: 2   EIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKG 61
           EIV+++ AKVAEYLVAPI R F Y  +Y +N++ L+ ++EKL  ARA ++  VD++   G
Sbjct: 3   EIVVTIAAKVAEYLVAPIGRSFGYLFNYRSNIDDLRQQVEKLGDARARLERSVDEAIRNG 62

Query: 62  DGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAI 121
           D I+  V++WL+ V   + E       ++K+N  C  G CPNLK++YQLS++A++ A  +
Sbjct: 63  DEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKRARVV 122

Query: 122 VGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMG 181
             +   G+F+ VS+R           +     ESR +TL  I++AL + + N+IGV+GM 
Sbjct: 123 AEIQGDGKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIGVWGMA 182

Query: 182 GIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAW 241
           G+GKTTL+K+V +QA+E  LF+KV+ + +S TP++K+IQ E+A+ LGLK ++ESE  RA 
Sbjct: 183 GVGKTTLMKQVAKQAEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESEMGRAA 242

Query: 242 RLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQN 301
           RL E+LKK  KILIILDDIW  LDLE +GIP  DD+ GCK++LT+R++ +LS EM  Q++
Sbjct: 243 RLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHILSNEMGTQKD 302

Query: 302 FVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYE 361
           F V+ L ++EA  LFKKM GD IE  +L+S+  +V KECAGLPIAIV +AKALKNK    
Sbjct: 303 FPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNKGLSI 362

Query: 362 WRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG-YSYICNVKDLL 420
           W +ALRQLKR+   +  G  A+  YST++LSY  L G+E++  FLL G  S    + DLL
Sbjct: 363 WEDALRQLKRSIPTNIKGMDAM-VYSTLELSYKHLEGDEVKSLFLLCGLMSNKIYIDDLL 421

Query: 421 YRGMGL 426
             GMGL
Sbjct: 422 KYGMGL 427

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224083434|ref|XP_002307025.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222856474|gb|EEE94021.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  382 bits (980), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 211/429 (49%), Positives = 296/429 (68%), Gaps = 4/429 (0%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           +E +IS    V+++ V PI R+  +C  YN N E LK E++KLK A+  VQ+ VDD+R  
Sbjct: 3   LESIISTIGVVSQHTVVPIAREINHCLKYNHNFENLKREVKKLKSAQLRVQHLVDDARNN 62

Query: 61  GDGIQQPVEEWLITVDEAINEVE-TLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREAN 119
           G+ I + V +WL  V+EA  +VE  ++ D++++  +C  GLCP+LK RYQ SKKA+ E  
Sbjct: 63  GEAILEDVIKWLSLVEEASEKVEREILEDEDRARKKCFIGLCPDLKARYQCSKKAKAETR 122

Query: 120 AIVG-LHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVY 178
            +   L E+  F +VS R  P+     S + +    SR   LK I++AL+  + NM+GVY
Sbjct: 123 FVASLLDERDGFSTVSHRAAPKGMEAISIRSYDAMPSRTPVLKEIMNALTTADVNMVGVY 182

Query: 179 GMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESV 238
           GMGG+GKTTLVKE  RQA +  LF +V+ + ++QT  IK+IQ +IA++L LK D+ESE  
Sbjct: 183 GMGGMGKTTLVKEAARQAIQEKLFNQVVFATITQTQDIKKIQGQIADQLSLKFDEESECG 242

Query: 239 RAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDC 298
           RA RL ++LK+E KILIILDD+W SLDLEA+GIPL D++ GCK+L+T+R  DVLSC MD 
Sbjct: 243 RAGRLRQRLKQEQKILIILDDLWKSLDLEAVGIPLKDEHEGCKMLVTSREFDVLSCGMDI 302

Query: 299 QQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKS 358
           Q+NF ++ L+++E W LFKKM GD +E+ +L+S+  EV K CAGLP+AIV +A+ALKNK+
Sbjct: 303 QKNFPINALSEEETWELFKKMAGDHVEHPDLQSLAIEVAKMCAGLPVAIVTVARALKNKN 362

Query: 359 PYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG-YSYICNVK 417
             +W+NALR+LKR   R+F+G Q    Y+ I+LSYN L  +EL+ TFLL     Y  + +
Sbjct: 363 LSQWKNALRELKRPSPRNFAGVQE-DVYAAIELSYNHLESKELKSTFLLCSRMGYNASTR 421

Query: 418 DLLYRGMGL 426
           DLL  GMGL
Sbjct: 422 DLLKYGMGL 430

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865073|emb|CAN83232.1| hypothetical protein VITISV_021876 [Vitis vinifera]

 Score =  379 bits (973), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/427 (46%), Positives = 283/427 (66%), Gaps = 5/427 (1%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           +EIV+SV AKV+EYLV P IRQ  Y  +Y  N+E L  ++EKL+ ARA +Q+ VD++   
Sbjct: 2   VEIVLSVAAKVSEYLVDPAIRQLGYLFNYRANIEDLSQQVEKLRDARARLQHSVDEAIGN 61

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
           G  I+  V +W+   D  I      + D++++   C  GLCPNLK+RYQLS++A ++A  
Sbjct: 62  GHIIEDDVRKWMKRADGFIQNACKFLEDEKEARKSCFNGLCPNLKSRYQLSREARKKAGV 121

Query: 121 IVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGM 180
            V +H  G+F+ VS+R   +E     ++     ESR  TL  +++AL + N N IGV+GM
Sbjct: 122 AVEIHGAGQFERVSYRAPLQEIRTAPSEAL---ESRMLTLNEVMEALRDANINRIGVWGM 178

Query: 181 GGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRA 240
           GG+GK+TLVK+V  QA++  LF KV+   V QTP  K IQ++IA+KLG+K ++ SE  RA
Sbjct: 179 GGVGKSTLVKQVAEQAEQEKLFRKVVMVPVIQTPDFKGIQQQIADKLGMKFEEVSEQGRA 238

Query: 241 WRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQ 300
            RL +++K+E  ILIILDD+W  L+LE +GIP  DD+ GCK++LT+R++ VLS EM  Q+
Sbjct: 239 DRLHQRIKQENTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQK 298

Query: 301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY 360
           +F V  L + E W LFK   GD IEN EL+ +  +V KECAGLPIAIV +AKALKNK+  
Sbjct: 299 DFRVQHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPIAIVTVAKALKNKNVS 358

Query: 361 EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG-YSYICNVKDL 419
            W++AL+QL      + +G +    YS+++LSY  L G+E++  FLL G +S    ++DL
Sbjct: 359 IWKDALQQLNSQTSTNITGMET-KVYSSLKLSYEHLEGDEVKSLFLLCGLFSNYIYIRDL 417

Query: 420 LYRGMGL 426
           L  GMGL
Sbjct: 418 LKYGMGL 424

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488288|ref|XP_003633735.1| PREDICTED: LOW QUALITY PROTEIN: probable disease resistance protein At1g61310-like [Vitis vinifera]

 Score =  376 bits (965), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 199/427 (46%), Positives = 279/427 (65%), Gaps = 2/427 (0%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           +EIV+SV AKV+EYLVAP+ RQ  +  +Y TN+E L  ++ KL+ ARA  Q+ VD++  K
Sbjct: 2   VEIVVSVAAKVSEYLVAPVGRQLGHLFNYRTNVEDLSQQVAKLRDARARQQHSVDEAIRK 61

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
           G  I+  V +W    D  I      + +++++   C  GLCPNLK+RYQLSK+A ++A  
Sbjct: 62  GHKIEDDVCKWFTRADGFIQVACKFLEEEKEAQKTCFNGLCPNLKSRYQLSKEARKKAGV 121

Query: 121 IVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGM 180
            V +H  G+F+ VS+R    E      +     ESR  TL  ++ AL + + N IG++GM
Sbjct: 122 AVEIHGDGQFERVSYRPPLLEIGSAPPKASKVLESRMLTLNEVMKALRDADINTIGIWGM 181

Query: 181 GGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRA 240
           GG+GK TLVK+V  QA +  LF+KV+ + V QTP  + IQ EIA+ LG+K ++ESE  RA
Sbjct: 182 GGVGKNTLVKQVAEQAAQEKLFDKVVMTSVFQTPDFRRIQGEIADMLGMKFEEESEQGRA 241

Query: 241 WRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQ 300
            RL  ++ +E  ILIILDDIW  L+LE IGIP  D++ GCK++LT+R++ VLS EM  Q+
Sbjct: 242 ARLHRKINEEKTILIILDDIWAELELEKIGIPSPDNHKGCKLVLTSRNKHVLSNEMSTQK 301

Query: 301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY 360
           +F V+ L   EAW LFK M GD IEN +L  + T+V KEC GLPIAIV +AKALKNK+  
Sbjct: 302 DFGVEHLQGDEAWILFKNMVGDSIENPDLLLIATDVAKECTGLPIAIVTVAKALKNKNVS 361

Query: 361 EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG-YSYICNVKDL 419
            W++AL+QLK     + +G      YST++LSY  L G+E++  FLL G +S   +++DL
Sbjct: 362 IWKDALKQLKTQTSTNITG-MGTKVYSTLKLSYKHLEGDEVKSLFLLCGLFSNYIDIRDL 420

Query: 420 LYRGMGL 426
           L  GMGL
Sbjct: 421 LKYGMGL 427

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224147195|ref|XP_002336426.1| cc-nbs resistance protein [Populus trichocarpa] gi|222834979|gb|EEE73428.1| cc-nbs resistance protein [Populus trichocarpa]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 195/428 (45%), Positives = 279/428 (65%), Gaps = 10/428 (2%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           MEIVIS+ AKVAE LV PI RQ  Y    N+N++ LKNE+EKL  A+  V + +++++  
Sbjct: 1   MEIVISIVAKVAELLVVPIKRQIGYVLDCNSNIQNLKNEVEKLTDAKTRVIHSIEEAQWN 60

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
           G+ I+  V  WL +VD  I     ++AD+  S+ +C  GLCP+LK RY+L K A++E   
Sbjct: 61  GEEIEVEVLNWLGSVDGVIEGAGGVVADE--SSKKCFMGLCPDLKIRYRLGKAAKKELTV 118

Query: 121 IVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGM 180
           +V L  KG+FD VS+R  P  + +   +D+  FESR S L  I+ AL + + NM+GV+GM
Sbjct: 119 VVDLQGKGKFDRVSYRAAP--SGIGPVKDYEAFESRNSVLNDIVGALKDGDENMVGVFGM 176

Query: 181 GGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRA 240
            G+GKTTLVK+V  Q KE  LF +V+ + VSQTP I+ IQ EIA+ LGLK+D E++  RA
Sbjct: 177 AGVGKTTLVKKVAEQVKEGRLFNEVVLAVVSQTPDIRRIQGEIADGLGLKLDAETDKGRA 236

Query: 241 WRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQ 300
            +L + LKK T++L+ILDDIW  L LE +GIP   D+ GCK+L+T+R ++VLSCEM   +
Sbjct: 237 SQLCKGLKKVTRVLVILDDIWKELKLEDVGIPSGSDHDGCKILMTSRDKNVLSCEMGANK 296

Query: 301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY 360
           NF + VL + EAW LF+K  G  ++N  ++ V  +V K CAGLPI +  +A+AL+N+  Y
Sbjct: 297 NFQIQVLPESEAWDLFEKTVGVTVKNPSVQPVAAKVAKRCAGLPILLAAVARALRNEEVY 356

Query: 361 EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG--YSYICNVKD 418
            W +AL+QL R F +     Q    Y  ++LSY  L G+E++  FLL G   +Y  ++ D
Sbjct: 357 AWNDALKQLNR-FDKDEIDNQ---VYLGLELSYKALRGDEIKSLFLLCGQFLTYDSSISD 412

Query: 419 LLYRGMGL 426
           LL   +GL
Sbjct: 413 LLKYAIGL 420

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147833354|emb|CAN66237.1| hypothetical protein VITISV_041837 [Vitis vinifera]

 Score =  370 bits (949), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 193/427 (45%), Positives = 286/427 (66%), Gaps = 5/427 (1%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           ++IV SV AKV+EYLV P++RQ  Y  +Y TN+E L  E+EKL+ AR   Q+ V+++   
Sbjct: 2   VDIVFSVAAKVSEYLVVPVVRQLGYLFNYRTNIEDLSQEVEKLRDARDRHQHSVNEAIGN 61

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
           G  I+  V +WL   D  I +    + D++++   C  GLCPNLK+R+QLS++A ++A  
Sbjct: 62  GHKIEDYVCKWLTRADGFIQDACKFLEDEKEAQKSCFNGLCPNLKSRHQLSREARKKAGV 121

Query: 121 IVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGM 180
            V + E G+F+ VS+RT P +    +  + +  ESR  TL  +++AL + N N IG++GM
Sbjct: 122 SVQILENGQFEKVSYRT-PLQGIRTAPSEAL--ESRMLTLNEVMEALRDANINRIGLWGM 178

Query: 181 GGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRA 240
           GG+GK+TLVK +  QA +  LF+KV+   V QTP ++ IQRE+A+ LG+K ++ESE  RA
Sbjct: 179 GGVGKSTLVKHLAEQANQEKLFDKVVKVSVLQTPDLERIQRELADGLGMKFEEESEQGRA 238

Query: 241 WRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQ 300
            RLL++++ E  ILIILDD+W  L+LE +GIP  DD+ GCK++LT+R++ VLS EM  Q+
Sbjct: 239 ARLLQRMEAEKTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQK 298

Query: 301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY 360
           +F V  L + E W LFK   GD IEN EL+ +  +V KECAGLP+AIV +AKALKNK+  
Sbjct: 299 DFRVRHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPLAIVTVAKALKNKNVS 358

Query: 361 EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG-YSYICNVKDL 419
            W++AL+QLK     + +G +    YS+++LSY  L G+E++   LL G +S   +++DL
Sbjct: 359 IWKDALQQLKSQTSTNITGIET-KVYSSLKLSYEHLEGDEVKSLCLLCGLFSSYIHIRDL 417

Query: 420 LYRGMGL 426
           L  G+GL
Sbjct: 418 LKYGVGL 424

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488103|ref|XP_002263579.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  369 bits (947), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 193/427 (45%), Positives = 285/427 (66%), Gaps = 5/427 (1%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           +EIV+SV AKV+EYLV P +RQ  Y  +Y  N+E+L  +++KL+ ARA +Q+ VD++   
Sbjct: 2   VEIVLSVAAKVSEYLVDPAVRQLGYLFNYRANIEELSQQVQKLRDARARLQHSVDEAIGN 61

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
           G  I+  V +W+   D  I      + D++++   C  GLCPNLK+RYQLS++A ++A  
Sbjct: 62  GLIIEDDVCKWMKRADGFIQNACKFLEDEKEARKSCFNGLCPNLKSRYQLSREASKKAGV 121

Query: 121 IVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGM 180
            V +   G+F+ V++R   +    + ++     ESR  TL  +++AL + N N IGV+GM
Sbjct: 122 SVQILGDGQFEKVAYRAPLQGIRCRPSEAL---ESRMLTLNEVMEALRDANINRIGVWGM 178

Query: 181 GGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRA 240
           GG+GK+TLVK+V  QA +  LFEKV++  V QTP ++ IQRE+A+ LG+K ++ESE  RA
Sbjct: 179 GGVGKSTLVKQVAEQANQEKLFEKVVNVSVLQTPDLERIQRELADWLGMKFEEESEQGRA 238

Query: 241 WRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQ 300
            RL +++K E  ILIILDD+W  L+LE +GIP  DD+ GCK++LT+R++ VLS EM  Q+
Sbjct: 239 ARLHQRMKAEKTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQK 298

Query: 301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY 360
           +F V  L + E W LFK   GD IEN EL+ +  +V KECAGLPIAIV +AKALKNK+  
Sbjct: 299 DFRVRHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPIAIVTVAKALKNKNVS 358

Query: 361 EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG-YSYICNVKDL 419
            W++AL+QLK     + +G +    YS+++LSY  L G+E++   LL G +S   +++DL
Sbjct: 359 IWKDALQQLKSQTSTNITGMET-KVYSSLKLSYEHLEGDEVKSLCLLCGLFSRYIHIRDL 417

Query: 420 LYRGMGL 426
           L  G+GL
Sbjct: 418 LKYGVGL 424

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111296|ref|XP_002332952.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222834264|gb|EEE72741.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  364 bits (935), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 201/428 (46%), Positives = 277/428 (64%), Gaps = 10/428 (2%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           MEIVIS+ AKVAE LV PI RQ  Y  + NTN++ LKNE+EKL  AR  V + ++++R  
Sbjct: 1   MEIVISIVAKVAELLVVPIKRQIGYVLNCNTNIQNLKNEVEKLTDARTRVNHSIEEARRN 60

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
           G+ I+  V  WL +VD  I+         ++S+ +C  GLCP+LK RY+L K A++E   
Sbjct: 61  GEEIEVEVFNWLGSVDGVIDGGGG--GVADESSKKCFMGLCPDLKIRYRLGKAAKKELTV 118

Query: 121 IVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGM 180
           +V L EKGRFD VS+R  P  + +   +D+  FESR S L  I+DAL +   NM+GVYGM
Sbjct: 119 VVDLQEKGRFDRVSYRAAP--SGIGPVKDYEAFESRDSVLNAIVDALKDGGVNMVGVYGM 176

Query: 181 GGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRA 240
            G+GKTTLVK+V  Q KE  LF+K + + VS TP I+ IQ EIA+ LGLK+D E++  RA
Sbjct: 177 PGVGKTTLVKKVAEQVKEGRLFDKEVLAVVSHTPDIRRIQGEIADGLGLKLDAETDKGRA 236

Query: 241 WRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQ 300
            +L E+LKK T++L+ILDDIW  L LE +GIP   D+ GCK+L+++R++ VLS EM   +
Sbjct: 237 SQLYERLKKVTRVLVILDDIWKELKLEDVGIPSGSDHEGCKILMSSRNEYVLSREMGSNR 296

Query: 301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY 360
           NF + VL   EAW+LF+KM G  ++   ++ V  EV + CAGLPI +  +A+ALKNK  Y
Sbjct: 297 NFPIQVLPASEAWNLFEKMVGVAVKKHSVRLVAAEVARRCAGLPILLATVARALKNKDLY 356

Query: 361 EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYICN--VKD 418
            W+ AL+QL R F +     Q    Y  ++LSY  L G+E++  FLL G     N  + D
Sbjct: 357 AWKKALKQLTR-FDKDDIDDQ---VYLGLELSYKSLRGDEIKSLFLLCGQLRSNNILISD 412

Query: 419 LLYRGMGL 426
           LL  G+GL
Sbjct: 413 LLRYGIGL 420

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147777048|emb|CAN65562.1| hypothetical protein VITISV_009359 [Vitis vinifera]

 Score =  363 bits (932), Expect = 8e-98,   Method: Compositional matrix adjust.
 Identities = 191/427 (44%), Positives = 281/427 (65%), Gaps = 5/427 (1%)

Query: 1   MEIVISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIK 60
           +EIV+SV AKV+EYLV P +RQ  +  +Y  N+E L  ++EKL+ ARA +Q+ VD++   
Sbjct: 2   VEIVVSVAAKVSEYLVDPAVRQLGHLFNYRANIEHLSLQVEKLRDARARLQHSVDEAIGN 61

Query: 61  GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANA 120
           G  I+  V +W+   DE        + D++++   C  GLCPNLK+RYQLS++A ++A  
Sbjct: 62  GHIIEDDVCKWMKRADEFTQNACKFLEDEKEARKSCFNGLCPNLKSRYQLSREARKKAGV 121

Query: 121 IVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGM 180
            V +    +F+ VS+R   +E     ++     +SR  TL  +++AL + + N IGV+G+
Sbjct: 122 AVQILGDRQFEKVSYRAPLQEIRSAPSEAL---QSRMLTLNEVMEALRDADINRIGVWGL 178

Query: 181 GGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRA 240
           GG+GK+TLVK V  QA++  LF KV+++ V QTP  KEIQ++IAEKLG+K ++ SE  RA
Sbjct: 179 GGVGKSTLVKRVAEQAEQEELFHKVVTASVFQTPDYKEIQQQIAEKLGMKFEEVSEQGRA 238

Query: 241 WRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQ 300
            RL +++K+E  ILIILDD+W  L+LE +GIP  DD+ GCK++LT+R++ VLS EM  Q+
Sbjct: 239 GRLHQRIKQENTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQK 298

Query: 301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPY 360
           +F V  L + E W LFK   GD IEN EL+ +  +V KECAGLPIAIV +AKALKNK+  
Sbjct: 299 DFRVQHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPIAIVTVAKALKNKNVA 358

Query: 361 EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGYSYI-CNVKDL 419
            W++AL+QL+     + +G +    YS+++LSY  L G+E++   LL G  Y    + DL
Sbjct: 359 IWKDALQQLESQTSTNITGMET-KVYSSLKLSYEHLEGDEMKSLCLLCGLCYSQIYISDL 417

Query: 420 LYRGMGL 426
           L  G+GL
Sbjct: 418 LKYGVGL 424

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	426
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.816	0.389	0.304	1.1e-35
TAIR|locus:2136447	985	AT4G27190 [Arabidopsis thalian	0.704	0.304	0.321	3.7e-35
TAIR|locus:2008440	899	AT1G61180 [Arabidopsis thalian	0.821	0.389	0.308	2.2e-34
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.772	0.370	0.301	3.5e-34
TAIR|locus:2008510	967	AT1G61190 "AT1G61190" [Arabido	0.821	0.361	0.308	8.8e-34
TAIR|locus:2131689	919	AT4G27220 [Arabidopsis thalian	0.833	0.386	0.311	1e-33
TAIR|locus:2201986	885	RFL1 "AT1G12210" [Arabidopsis	0.819	0.394	0.291	2e-33
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.788	0.378	0.290	8.7e-33
TAIR|locus:2034765	884	AT1G12290 [Arabidopsis thalian	0.776	0.374	0.295	8e-32
TAIR|locus:2153474	874	AT5G05400 [Arabidopsis thalian	0.833	0.406	0.282	9.9e-32

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

 Score = 395 (144.1 bits), Expect = 1.1e-35, P = 1.1e-35
 Identities = 114/375 (30%), Positives = 185/375 (49%)

Query:    47 RASVQYKVDDSRI--KGDGIQQPVEEWLITVDEAINEVETLIADKEKSNNR-CLKGLCP- 102
             R  V+ +VD      + + + Q V+ WL  V    N+   L+   +    R CL G C  
Sbjct:    50 RDDVKRRVDIEEFTRRRERLSQ-VQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSK 108

Query:   103 NLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIP----EETWLKSTQDFMHFESRKS 158
             N+K  Y   K+       I  L  +G FD+V+  T P    EE  ++ T        +++
Sbjct:   109 NVKMSYLYGKRVVLMLKEIESLSSQGDFDTVTLAT-PIARIEEMPIQPT-----IVGQET 162

Query:   159 TLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQTPQIK 217
              L+ +   L+     ++G+YGMGG+GKTTL+  +  +  E  + F  VI   VS++P I 
Sbjct:   163 MLERVWTRLTEDGDEIVGLYGMGGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIH 222

Query:   218 EIQREIAEKLGL---KIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLA 274
              IQ +I ++L L   + D  +E+ RA  +   L K+ K +++LDDIW  ++LE +G+P  
Sbjct:   223 RIQGDIGKRLDLGGEEWDNVNENQRALDIYNVLGKQ-KFVLLLDDIWEKVNLEVLGVPYP 281

Query:   275 DDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENG--ELKSV 332
                 GCKV+ T RS+DV    M       V  L   EAW LF+   G+    G  ++  +
Sbjct:   282 SRQNGCKVVFTTRSRDVCG-RMRVDDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPEL 340

Query:   333 VTEVVKECAGLPIAIVPIAKALKNKSPY-EWRNALRQLKRNFLRSFSGTQAVAAYSTIQL 391
               +V  +C GLP+A+  I + +  K    EWRNA+  L  ++   F G + +     ++ 
Sbjct:   341 ARKVAGKCCGLPLALNVIGETMACKRMVQEWRNAIDVLS-SYAAEFPGMEQILPI--LKY 397

Query:   392 SYNQLGGEELRKTFL 406
             SY+ L  E+++  FL
Sbjct:   398 SYDNLNKEQVKPCFL 412

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2136447 AT4G27190 [Arabidopsis thaliana (taxid:3702)]

 Score = 391 (142.7 bits), Expect = 3.7e-35, P = 3.7e-35
 Identities = 100/311 (32%), Positives = 168/311 (54%)

Query:   104 LKTRYQLSKKAEREANAIVGLHEKG-RF-DSVSFRTIPEETWLKSTQDFMHFESRKSTLK 161
             +  R ++S+K  +  + +  L + G  F D +S  + PE          +H     + L 
Sbjct:    94 MSLRPRMSRKLVKILDEVKMLEKDGIEFVDMLSVESTPERVEHVPGVSVVHQTMASNMLA 153

Query:   162 GILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL---FEKVISSRVSQTPQIKE 218
              I D L++     IGV+GMGG+GKTTLV+ +  + +E      F  VI   VS+    +E
Sbjct:   154 KIRDGLTSEKAQKIGVWGMGGVGKTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDPRE 213

Query:   219 IQREIAEKLGLKID-QESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDN 277
             +Q++IAE+L +    +ESE   A R+   L KE K L+ILDD+W  +DL+ +GIP  ++N
Sbjct:   214 VQKQIAERLDIDTQMEESEEKLARRIYVGLMKERKFLLILDDVWKPIDLDLLGIPRTEEN 273

Query:   278 GGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVV 337
              G KV+LT+R  +V    M    +  VD L +++AW LF K  GD + +  ++ +   V 
Sbjct:   274 KGSKVILTSRFLEVCR-SMKTDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIAKAVS 332

Query:   338 KECAGLPIAIVPIAKALKNKSPYE-WRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQL 396
             +EC GLP+AI+ +  A++ K   + W + L +L ++     S  + +  +  ++LSY+ L
Sbjct:   333 QECGGLPLAIITVGTAMRGKKNVKLWNHVLSKLSKSVPWIKSIEEKI--FQPLKLSYDFL 390

Query:   397 GGEELRKTFLL 407
               ++ +  FLL
Sbjct:   391 E-DKAKFCFLL 400

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

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

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 383 (139.9 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 113/366 (30%), Positives = 183/366 (50%)

Query:    50 VQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIA-DKEKSNNRCLKGLCPN-LKTR 107
             VQ KV     +     + V+ WL  V+    E + L++    +    CL GLC   + + 
Sbjct:    51 VQNKVARDEARHQRRLEAVQVWLDRVNSVDIECKDLLSVTPVELQKLCLCGLCSKYVCSS 110

Query:   108 YQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDAL 167
             Y+  KK       +  L+ +G FD VS      E   + TQ  +    ++  L+   + L
Sbjct:   111 YKYGKKVFLLLEEVKKLNSEGNFDEVSQPPPRSEVEERPTQPTI---GQEDMLEKAWNRL 167

Query:   168 SNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE-NNLFEKVISSRVSQTPQIKEIQREIAEK 226
                   ++G++GMGG+GKTTL K++  +  E    F+ VI   VS+   I ++Q +IAEK
Sbjct:   168 MEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEK 227

Query:   227 LGLKID---QESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVL 283
             L L  D    ++ES +A  +   LK + + +++LDDIW  +DLEAIGIP   +   CKV 
Sbjct:   228 LHLCDDLWKNKNESDKATDIHRVLKGK-RFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVA 286

Query:   284 LTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGE--LKSVVTEVVKECA 341
              T RS++V   EM   +   V+ L  ++AW LFK   GD   + +  +  +  EV ++C 
Sbjct:   287 FTTRSREVCG-EMGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVELAREVAQKCR 345

Query:   342 GLPIAIVPIAKALKNKSPY-EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEE 400
             GLP+A+  I + + +K+   EW +A+     +    FS  Q       ++ SY+ LG E 
Sbjct:   346 GLPLALNVIGETMSSKTMVQEWEHAIHVFNTS-AAEFSDMQN-KILPILKYSYDSLGDEH 403

Query:   401 LRKTFL 406
             ++  FL
Sbjct:   404 IKSCFL 409

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

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 381 (139.2 bits), Expect = 3.5e-34, P = 3.5e-34
 Identities = 106/352 (30%), Positives = 186/352 (52%)

Query:    68 VEEWLITVDEAINEVETLIADKEKSNNR-CLKGLCP-NLKTRYQLSKKAEREANAIVGLH 125
             V+ WL +V    N+   L+   E    R CL G C  +LK  Y+  K+       +  L 
Sbjct:    72 VQVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRVIMMLKEVESLS 131

Query:   126 EKGRFDSVSFRTIPEETWLKSTQDFMHFE----SRKSTLKGILDALSNRNFNMIGVYGMG 181
              +G FD VS     E T      D + F+     ++  L+   + L      ++G+YGMG
Sbjct:   132 SQGFFDVVS-----EATPFADV-DEIPFQPTIVGQEIMLEKAWNRLMEDGSGILGLYGMG 185

Query:   182 GIGKTTLVKEVGRQ-AKENNLFEKVISSRVSQTPQIKEIQREIAEKLGL---KIDQESES 237
             G+GKTTL+ ++  + +K ++ F+ VI   VS++  +++IQR+IAEK+GL   +  +++++
Sbjct:   186 GVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWSEKNDN 245

Query:   238 VRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMD 297
               A  +   L++  K +++LDDIW  ++L+A+G+P    + GCKV  T RS+DV    M 
Sbjct:   246 QIAVDIHNVLRRR-KFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCG-RMG 303

Query:   298 CQQNFVVDVLNDKEAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAKALK 355
                   V  L  +E+W LF+   G      + ++  +  +V ++C GLP+A+  I +A+ 
Sbjct:   304 VDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGEAMA 363

Query:   356 NK-SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL 406
              K + +EW +A+  L  + +  FSG +    +  ++ SY+ L GE ++  FL
Sbjct:   364 CKRTVHEWCHAIDVLTSSAI-DFSGMEDEILH-VLKYSYDNLNGELMKSCFL 413

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 = 378 (138.1 bits), Expect = 8.8e-34, P = 8.8e-34
 Identities = 113/366 (30%), Positives = 181/366 (49%)

Query:    50 VQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIA-DKEKSNNRCLKGLCPN-LKTR 107
             VQ KV     +     + V+ WL  V+    E + L++    +    CL GLC   + + 
Sbjct:    52 VQNKVAREESRHQQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCSKYVCSS 111

Query:   108 YQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDAL 167
             Y+  K+       +  L  +G FD VS      E   + TQ  +    ++  LK   + L
Sbjct:   112 YKYGKRVFLLLEEVTKLKSEGNFDEVSQPPPRSEVEERPTQPTI---GQEEMLKKAWNRL 168

Query:   168 SNRNFNMIGVYGMGGIGKTTLVKEVGRQ-AKENNLFEKVISSRVSQTPQIKEIQREIAEK 226
                   ++G++GMGG+GKTTL K++  + A+    F+ VI   VSQ  ++ ++Q +IAEK
Sbjct:   169 MEDGVGIMGLHGMGGVGKTTLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEK 228

Query:   227 LGLKID---QESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVL 283
             L L  D    ++ES +A  +   LK + + +++LDDIW  +DLEAIGIP   +   CKV 
Sbjct:   229 LHLCDDLWKNKNESDKATDIHRVLKGK-RFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVA 287

Query:   284 LTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGE--LKSVVTEVVKECA 341
              T R Q V   +M   +   V  L  ++AW LFK   GD     +  +  +  EV ++C 
Sbjct:   288 FTTRDQKVCG-QMGDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCR 346

Query:   342 GLPIAIVPIAKALKNKSPY-EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEE 400
             GLP+A+  I + + +K+   EW +A+  L R+    FS  Q       ++ SY+ L  E 
Sbjct:   347 GLPLALSCIGETMASKTMVQEWEHAIDVLTRS-AAEFSDMQN-KILPILKYSYDSLEDEH 404

Query:   401 LRKTFL 406
             ++  FL
Sbjct:   405 IKSCFL 410

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2131689 AT4G27220 [Arabidopsis thaliana (taxid:3702)]

 Score = 377 (137.8 bits), Expect = 1.0e-33, P = 1.0e-33
 Identities = 120/385 (31%), Positives = 191/385 (49%)

Query:    49 SVQYKVDDSRIKGDGIQQPVEE-----WLITVDEAINEVETLIADKEKSNNRCLKGLCPN 103
             +VQ KV+++ +K  GIQ+   E     WL  V+E +   E LI +K  S   C   L   
Sbjct:    18 NVQTKVNEA-LKRSGIQEKSLERKLRIWLRKVEENVPLGE-LILEKRSS---CAIWLSDK 72

Query:   104 LKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGI 163
                  +  K+ E +   ++    K    + S R I E     S   F   ++    L  +
Sbjct:    73 DVEILEKVKRLEEQGQDLI----KKISVNKSSREIVERVLGPS---FHPQKTALEMLDKL 125

Query:   164 LDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE---NNLFEKVISSRVSQTPQIKEIQ 220
              D L  +N   IGV+GMGG+GKTTLV+ +     +      F  VI   VS+   +K +Q
Sbjct:   126 KDCLKKKNVQKIGVWGMGGVGKTTLVRTLNNDLLKYAATQQFALVIWVTVSKDFDLKRVQ 185

Query:   221 REIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLA-DDNGG 279
              +IA++LG +  +E  +     + E+L      L+ILDD+W  +DL+ +GIPLA + +  
Sbjct:   186 MDIAKRLGKRFTREQMNQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLALERSKD 245

Query:   280 CKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKE 339
              KV+LT+R  +V   +M   +N  V  L +KEAW LF    G+   +  +K +  +V  E
Sbjct:   246 SKVVLTSRRLEVCQ-QMMTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVSHE 304

Query:   340 CAGLPIAIVPIAKALKNKSPYE-WRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGG 398
             C GLP+AI+ I + L+ K   E W++ L  LKR+   S    + +  + T++LSY+ L  
Sbjct:   305 CCGLPLAIITIGRTLRGKPQVEVWKHTLNLLKRS-APSIDTEEKI--FGTLKLSYDFLQ- 360

Query:   399 EELRKTFL---LIGYSYICNVKDLL 420
             + ++  FL   L    Y   V +L+
Sbjct:   361 DNMKSCFLFCALFPEDYSIKVSELI 385

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 374 (136.7 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 109/374 (29%), Positives = 181/374 (48%)

Query:    47 RASVQYKVDDSRIKGDGIQ-QPVEEWLITVDEAINEVETLIADKEKSNNR-CLKGLCP-N 103
             R  VQ +++     G   +   V+ WL  +    N+   L++       R CL G C  N
Sbjct:    50 RDDVQGRINREEFTGHRRRLAQVQVWLTRIQTIENQFNDLLSTCNAEIQRLCLCGFCSKN 109

Query:   104 LKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIP----EETWLKSTQDFMHFESRKST 159
             +K  Y   K+       + GL  +G FD V+    P    EE  ++ST        + S 
Sbjct:   110 VKMSYLYGKRVIVLLREVEGLSSQGVFDIVT-EAAPIAEVEELPIQST-----IVGQDSM 163

Query:   160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQ-AKENNLFEKVISSRVSQTPQIKE 218
             L  + + L      ++G+YGMGG+GKTTL+ ++  + +K    F+ VI   VS+   + +
Sbjct:   164 LDKVWNCLMEDKVWIVGLYGMGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHK 223

Query:   219 IQREIAEKLGL---KIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLAD 275
             IQ+ I EKLGL     D+++++ RA  +   L+++ K +++LDDIW  ++L+ IG+P   
Sbjct:   224 IQKSIGEKLGLVGKNWDEKNKNQRALDIHNVLRRK-KFVLLLDDIWEKVELKVIGVPYPS 282

Query:   276 DNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCI--ENGELKSVV 333
                GCKV  T  S++V    M       +  L+   AW L KK  G+     + ++  + 
Sbjct:   283 GENGCKVAFTTHSKEVCG-RMGVDNPMEISCLDTGNAWDLLKKKVGENTLGSHPDIPQLA 341

Query:   334 TEVVKECAGLPIAIVPIAKALKNKSPY-EWRNALRQLKRNFLRSFSGTQAVAAYSTIQLS 392
              +V ++C GLP+A+  I + +  K    EWR+A   L       FSG +       ++ S
Sbjct:   342 RKVSEKCCGLPLALNVIGETMSFKRTIQEWRHATEVLTS--ATDFSGMED-EILPILKYS 398

Query:   393 YNQLGGEELRKTFL 406
             Y+ L GE+ +  FL
Sbjct:   399 YDSLNGEDAKSCFL 412

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:2166320 AT5G63020 [Arabidopsis thaliana (taxid:3702)]

 Score = 368 (134.6 bits), Expect = 8.7e-33, P = 8.7e-33
 Identities = 103/354 (29%), Positives = 175/354 (49%)

Query:    63 GIQQ--PVEEWLITVDEAINEVETLIADKEKSNNR-CLKGLCP-NLKTRYQLSKKAEREA 118
             G+Q+   V+ W+  V+  +  V  L+  +     R CL G C  NL + Y+  K+  +  
Sbjct:    64 GLQRLSVVQGWVSKVEAIVPRVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVMKMI 123

Query:   119 NAIVGLHEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVY 178
               +  L  +G F  V+ R        + T+  +  +     L+   + L      ++G++
Sbjct:   124 EEVEVLRYQGDFAVVAERVDAARVEERPTRPMVAMDPM---LESAWNRLMEDEIGILGLH 180

Query:   179 GMGGIGKTTLVKEVG-RQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL---GLKIDQE 234
             GMGG+GKTTL+  +  R ++    F+ VI   VS+  QI+ IQ EI EKL     K  Q+
Sbjct:   181 GMGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDNEKWKQK 240

Query:   235 SESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSC 294
             +E ++A  +   LK + + +++LDDIW  +DL  +G+P      GCK++ T R +++   
Sbjct:   241 TEDIKASNIYNVLKHK-RFVLLLDDIWSKVDLTEVGVPFPSRENGCKIVFTTRLKEICG- 298

Query:   295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAK 352
              M    +  V  L   +AW LF K  G+     + E+ +V   V K+C GLP+A+  I +
Sbjct:   299 RMGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALNVIGE 358

Query:   353 ALKNK-SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTF 405
              +  K +  EWR+A+  L  +    FSG +       ++ SY+ L  E+L+  F
Sbjct:   359 TMAYKRTVQEWRSAIDVLTSS-AAEFSGMED-EILPILKYSYDNLKSEQLKLCF 410

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 359 (131.4 bits), Expect = 8.0e-32, P = 8.0e-32
 Identities = 107/362 (29%), Positives = 179/362 (49%)

Query:    63 GIQQ--PVEEWLITVDEAINEVETLIADKEKSNNRCLKGLC------PNLKTRYQLSKKA 114
             G+Q+   ++ WL    + +  +E+   D + S    L+ LC       NL+  Y   ++ 
Sbjct:    64 GLQRLHQIKVWL----KRVKTIESQFNDLDSSRTVELQRLCCCGVGSRNLRLSYDYGRRV 119

Query:   115 EREANAIVGLHEKGRFDSVSF---RTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRN 171
                 N +  L  KG F+ V+    R + EE  L+ T        +++ L+   D L +  
Sbjct:   120 FLMLNIVEDLKSKGIFEEVAHPATRAVGEERPLQPT-----IVGQETILEKAWDHLMDDG 174

Query:   172 FNMIGVYGMGGIGKTTLVKEVG-RQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG-- 228
               ++G+YGMGG+GKTTL+ ++  R    ++  E VI   VS   QI +IQ+EI EK+G  
Sbjct:   175 TKIMGLYGMGGVGKTTLLTQINNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGEKIGFI 234

Query:   229 -LKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTAR 287
              ++ +Q+SE+ +A  +L  L K+ + +++LDDIW  ++L  IGIP      GCK+  T R
Sbjct:   235 GVEWNQKSENQKAVDILNFLSKK-RFVLLLDDIWKRVELTEIGIPNPTSENGCKIAFTTR 293

Query:   288 SQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPI 345
              Q V +  M       V  L   +AW LFKK  GD     + ++  +  +V + C GLP+
Sbjct:   294 CQSVCA-SMGVHDPMEVRCLGADDAWDLFKKKVGDITLSSHPDIPEIARKVAQACCGLPL 352

Query:   346 AIVPIAKALK-NKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKT 404
             A+  I + +   K+  EW  A+  +   +  +F G         ++ SY+ L  E ++  
Sbjct:   353 ALNVIGETMACKKTTQEWDRAV-DVSTTYAANF-GAVKERILPILKYSYDNLESESVKTC 410

Query:   405 FL 406
             FL
Sbjct:   411 FL 412

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:2153474 AT5G05400 [Arabidopsis thaliana (taxid:3702)]

 Score = 358 (131.1 bits), Expect = 9.9e-32, P = 9.9e-32
 Identities = 110/390 (28%), Positives = 194/390 (49%)

Query:    53 KVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADK-EKSNNRCLKGLCPN-LKTRYQL 110
             KV + R  G  +   V++WL  V+  + E   +++   E+ +N C    C    K  Y  
Sbjct:    58 KVQEDR--GLNLLDEVQQWLSEVESRVCEAHDILSQSDEEIDNLCCGQYCSKRCKYSYDY 115

Query:   111 SKKAEREANAIVGLHEKGRFDSVSFR-TIPEETWLKSTQDFMHFE--SRKSTLKGILDAL 167
             SK    +   +  L  KG FD V+ +  IP     K  +   H E   +++ ++   +++
Sbjct:   116 SKSVINKLQDVENLLSKGVFDEVAQKGPIP-----KVEERLFHQEIVGQEAIVESTWNSM 170

Query:   168 SNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE-NNLFEKVISSRVSQTPQIKEIQREIAEK 226
                   ++G+YGMGG+GKTTL+ ++  + +  +N F+  I   VS+ P +K IQ +I ++
Sbjct:   171 MEVGVGLLGIYGMGGVGKTTLLSQINNKFRTVSNDFDIAIWVVVSKNPTVKRIQEDIGKR 230

Query:   227 LGLKID---QESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVL 283
             L L  +   Q++E+  A  +   L+ + K +++LDD+W  +DL  IGIP+   NG  K+ 
Sbjct:   231 LDLYNEGWEQKTENEIASTIKRSLENK-KYMLLLDDMWTKVDLANIGIPVPKRNGS-KIA 288

Query:   284 LTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENG-ELKSVVTEVVKECAG 342
              T+RS +V   +M   +   V  L   +AW LF +   + +E+  ++  V   + ++C G
Sbjct:   289 FTSRSNEVCG-KMGVDKEIEVTCLMWDDAWDLFTRNMKETLESHPKIPEVAKSIARKCNG 347

Query:   343 LPIAIVPIAKAL-KNKSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEEL 401
             LP+A+  I + + + KS  EW +A+          FSG +A    S ++ SY+ L  E+ 
Sbjct:   348 LPLALNVIGETMARKKSIEEWHDAVGV--------FSGIEA-DILSILKFSYDDLKCEKT 398

Query:   402 RKTFL---LIGYSYICNVKDLL--YRGMGL 426
             +  FL   L    Y     DL+  + G G+
Sbjct:   399 KSCFLFSALFPEDYEIGKDDLIEYWVGQGI 428

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0006826 "iron ion transport" evidence=RCA

GO:0010106 "cellular response to iron ion starvation" evidence=RCA

GO:0010167 "response to nitrate" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	426
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	3e-43
pfam13401	124	pfam13401, AAA_22, AAA domain	3e-06
smart00382	148	smart00382, AAA, ATPases associated with a variety	3e-05
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	2e-04
COG1474	366	COG1474, CDC6, Cdc6-related protein, AAA superfami	0.004
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	0.004

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

 Score =  152 bits (387), Expect = 3e-43
 Identities = 82/260 (31%), Positives = 133/260 (51%), Gaps = 15/260 (5%)

Query: 156 RKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT 213
           R+  ++ +++ L   + N  ++G+ GMGG+GKTTL K++         F+ V    VS+T
Sbjct: 1   REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKT 60

Query: 214 PQIKEIQREIAEKLGLK---IDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIG 270
                +Q++I ++LGL      +++ES  A ++ E L    + L++LDD+W   D + IG
Sbjct: 61  YTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALL-RKRFLLVLDDVWEKNDWDKIG 119

Query: 271 IPLADDNGGCKVLLTARSQDVLSCEMDCQQNFV-VDVLNDKEAWSLFKKMTG--DCIENG 327
           +P  D   G +V++T RS+ V    M        V+ L  +E+W LF       +     
Sbjct: 120 VPFPDGENGSRVIVTTRSESVAG-RMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCP 178

Query: 328 ELKSVVTEVVKECAGLPIAIVPIAKALKNKS-PYEWRNALRQLKRNFLRSFSGTQAVAAY 386
           EL+ V  E+V++C GLP+A+  +   L  KS   EW + L QL  N L    G   V   
Sbjct: 179 ELEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQL-NNELAGRDGLNEV--L 235

Query: 387 STIQLSYNQLGGEELRKTFL 406
           S + LSY+ L    L++ FL
Sbjct: 236 SILSLSYDNL-PMHLKRCFL 254

Length = 285

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

 Score = 45.7 bits (109), Expect = 3e-06
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 177 VYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESE 236
           + G  G GKTTL++ + RQ         V+          K++ R+I   LGL +   + 
Sbjct: 9   LTGESGSGKTTLLRRLARQLPNRR----VVYVEAPSLGTPKDLLRKILRALGLPLSGGTT 64

Query: 237 SVRAWRLLEQLKKETKILIILDDI 260
           +     +L+ LK+  + L+I+D+ 
Sbjct: 65  AELLEAILDALKRRGRPLLIIDEA 88

Length = 124

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

 Score = 43.5 bits (102), Expect = 3e-05
 Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID 232
            +I + G  G GKTTL + + R+          I         + ++   I         
Sbjct: 3   EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS 62

Query: 233 QESESVRAWRLLEQLKKETKILIILDDIWGSLDLE 267
            E   +R    L   +K    ++ILD+I   LD E
Sbjct: 63  GELR-LR--LALALARKLKPDVLILDEITSLLDAE 94

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148

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

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 24/150 (16%), Positives = 49/150 (32%), Gaps = 21/150 (14%)

Query: 154 ESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT 213
           E     L   L    +     + + G  G GKT+L++E+           K   +  +  
Sbjct: 6   EEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLV--AAGKCDQAERNPP 63

Query: 214 PQIKEIQREIAEKLGLKIDQESESVRAW------------------RLLEQLKKETKILI 255
               +  RE+  +L  ++  E   +R                     L   L +   +++
Sbjct: 64  YAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARPLVL 123

Query: 256 ILDDI-WGSLDLEAIGIPLADDNGGCKVLL 284
           +LDD+ W   +   +   L        +L+
Sbjct: 124 VLDDLQWADEESLDLLAALLRRLERLPLLV 153

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

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

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 29/113 (25%), Positives = 49/113 (43%), Gaps = 5/113 (4%)

Query: 152 HFESRKSTLKGILDA--LSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSR 209
           H E   + L   L       R  N+I +YG  G GKT  VK V  + +E++   +V+   
Sbjct: 21  HREEEINQLASFLAPALRGERPSNII-IYGPTGTGKTATVKFVMEELEESSANVEVVYIN 79

Query: 210 VSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL--KKETKILIILDDI 260
             +     ++  +I  KLG        S+   + L     KK   +++ILD++
Sbjct: 80  CLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEV 132

Length = 366

>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 26/142 (18%), Positives = 46/142 (32%), Gaps = 25/142 (17%)

Query: 153 FESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ 212
            E     L+  L+    +N   + +YG  G GKTTL + +  +          +    S 
Sbjct: 3   QEEAIEALREALELPPPKN---LLLYGPPGTGKTTLARAIANELFRPGA--PFLYLNAS- 56

Query: 213 TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDI--------WGSL 264
                    ++ E L +        VR   L E  +K    ++ +D+I           L
Sbjct: 57  ---------DLLEGLVVAELFGHFLVR--LLFELAEKAKPGVLFIDEIDSLSRGAQNALL 105

Query: 265 DLEAIGIPLADDNGGCKVLLTA 286
            +      L  D    +V+   
Sbjct: 106 RVLETLNDLRIDRENVRVIGAT 127

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases. Length = 151

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	426
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
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.53
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.49
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.45
PRK04841	903	transcriptional regulator MalT; Provisional	99.45
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.39
PF05729	166	NACHT: NACHT domain	99.36
PRK13342	413	recombination factor protein RarA; Reviewed	99.17
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.16
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.14
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.14
COG3899	849	Predicted ATPase [General function prediction only	99.14
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.09
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.03
PRK12402	337	replication factor C small subunit 2; Reviewed	98.98
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.97
PRK06893	229	DNA replication initiation factor; Validated	98.97
PF13173	128	AAA_14: AAA domain	98.94
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.91
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.9
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.88
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.88
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.86
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.86
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.85
PLN03025	319	replication factor C subunit; Provisional	98.85
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.84
KOG2028	554	consensus ATPase related to the helicase subunit o	98.82
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.82
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.82
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.8
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.79
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.77
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.75
PRK04195	482	replication factor C large subunit; Provisional	98.75
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.75
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.75
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.74
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.73
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.73
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.71
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.71
cd01128	249	rho_factor Transcription termination factor rho is	98.71
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.71
PRK13341	725	recombination factor protein RarA/unknown domain f	98.7
PTZ00202	550	tuzin; Provisional	98.7
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.7
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.69
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.68
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.67
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.66
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.65
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.65
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.65
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.61
PRK08084	235	DNA replication initiation factor; Provisional	98.6
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.6
PRK08727	233	hypothetical protein; Validated	98.58
PRK09376	416	rho transcription termination factor Rho; Provisio	98.58
PRK09087	226	hypothetical protein; Validated	98.58
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.58
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.57
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.56
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.56
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.56
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.54
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.54
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.52
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.49
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.47
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.47
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.46
PF14516	331	AAA_35: AAA-like domain	98.46
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.45
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.44
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.44
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.44
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.43
TIGR00767	415	rho transcription termination factor Rho. Members	98.43
PHA02544	316	44 clamp loader, small subunit; Provisional	98.43
PRK05642	234	DNA replication initiation factor; Validated	98.42
CHL00095	821	clpC Clp protease ATP binding subunit	98.41
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.38
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.37
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.37
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.37
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.34
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.33
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.33
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	98.32
COG3903	414	Predicted ATPase [General function prediction only	98.31
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.29
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.29
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.29
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.28
CHL00181	287	cbbX CbbX; Provisional	98.27
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.25
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.25
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.25
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.23
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.22
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.22
PRK07399	314	DNA polymerase III subunit delta'; Validated	98.2
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.19
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.16
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.15
PRK10865	857	protein disaggregation chaperone; Provisional	98.12
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.11
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.1
PF00004	132	AAA: ATPase family associated with various cellula	98.1
smart00382	148	AAA ATPases associated with a variety of cellular	98.1
CHL00176	638	ftsH cell division protein; Validated	98.1
PRK06620	214	hypothetical protein; Validated	98.08
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.08
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	98.05
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.03
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.03
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	98.02
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.98
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.94
CHL00195	489	ycf46 Ycf46; Provisional	97.91
PRK10536	262	hypothetical protein; Provisional	97.9
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.9
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.89
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.87
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.82
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.82
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.8
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.79
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.79
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.79
PRK12422	445	chromosomal replication initiation protein; Provis	97.79
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.78
PRK12608	380	transcription termination factor Rho; Provisional	97.77
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.76
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.74
PHA00729	226	NTP-binding motif containing protein	97.74
PRK08116	268	hypothetical protein; Validated	97.73
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.73
PRK08118	167	topology modulation protein; Reviewed	97.71
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.68
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.67
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.67
PRK04132	846	replication factor C small subunit; Provisional	97.66
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.66
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	97.64
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.62
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.62
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.61
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	97.58
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	97.55
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.51
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.51
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.49
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.49
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.49
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.48
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.48
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	97.47
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.47
PRK08181	269	transposase; Validated	97.45
PRK07261	171	topology modulation protein; Provisional	97.42
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	97.42
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.4
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.38
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.36
PRK08939	306	primosomal protein DnaI; Reviewed	97.36
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.35
PRK10865	857	protein disaggregation chaperone; Provisional	97.35
PRK06526	254	transposase; Provisional	97.34
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.3
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.28
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.28
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.27
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	97.27
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.27
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.26
PRK12377	248	putative replication protein; Provisional	97.25
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.24
KOG0736	953	consensus Peroxisome assembly factor 2 containing	97.21
KOG1969	877	consensus DNA replication checkpoint protein CHL12	97.2
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.2
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.19
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.18
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	97.18
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.16
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.16
PRK09183	259	transposase/IS protein; Provisional	97.16
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.15
PRK06696	223	uridine kinase; Validated	97.14
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.14
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.12
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.12
CHL00095	821	clpC Clp protease ATP binding subunit	97.11
PRK05541	176	adenylylsulfate kinase; Provisional	97.1
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.1
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	97.09
PRK04296	190	thymidine kinase; Provisional	97.09
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.07
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.05
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	97.05
PRK07952	244	DNA replication protein DnaC; Validated	97.04
PRK08699	325	DNA polymerase III subunit delta'; Validated	97.03
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.03
PRK09354	349	recA recombinase A; Provisional	97.02
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.02
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	97.02
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	97.0
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.97
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.95
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.94
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.93
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.93
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.92
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.91
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.86
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	96.86
PHA02244	383	ATPase-like protein	96.86
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.86
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	96.85
PTZ00494	664	tuzin-like protein; Provisional	96.85
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.85
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.84
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.83
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.82
PRK06921	266	hypothetical protein; Provisional	96.82
PTZ00035	337	Rad51 protein; Provisional	96.81
PRK06547	172	hypothetical protein; Provisional	96.81
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.78
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	96.78
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.78
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.78
PRK06835	329	DNA replication protein DnaC; Validated	96.77
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.77
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.76
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.75
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.72
PRK15455	644	PrkA family serine protein kinase; Provisional	96.72
PRK04328	249	hypothetical protein; Provisional	96.72
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.71
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.7
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.69
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.67
PRK07667	193	uridine kinase; Provisional	96.66
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.66
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.66
CHL00206	2281	ycf2 Ycf2; Provisional	96.66
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.66
PRK05439	311	pantothenate kinase; Provisional	96.66
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.66
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.65
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.64
PRK06067	234	flagellar accessory protein FlaH; Validated	96.64
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.64
PRK14974	336	cell division protein FtsY; Provisional	96.64
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.63
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.63
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.61
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	96.61
TIGR00959	428	ffh signal recognition particle protein. This mode	96.6
PRK07132	299	DNA polymerase III subunit delta'; Validated	96.6
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	96.59
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.59
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.59
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.59
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	96.58
PRK10867	433	signal recognition particle protein; Provisional	96.58
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.58
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	96.56
PRK05480	209	uridine/cytidine kinase; Provisional	96.54
PRK13531	498	regulatory ATPase RavA; Provisional	96.53
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.53
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.51
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.51
PRK08233	182	hypothetical protein; Provisional	96.5
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.5
PRK00409	782	recombination and DNA strand exchange inhibitor pr	96.49
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	96.49
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	96.48
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.48
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.46
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.46
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	96.46
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	96.45
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.44
PTZ00301	210	uridine kinase; Provisional	96.43
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.43
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.42
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.4
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.4
PRK06762	166	hypothetical protein; Provisional	96.4
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.39
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.39
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.36
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.35
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.34
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.31
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	96.29
PF00154	322	RecA: recA bacterial DNA recombination protein; In	96.28
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	96.28
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.28
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.28
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	96.27
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	96.27
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	96.26
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.26
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	96.23
PRK13765	637	ATP-dependent protease Lon; Provisional	96.23
PRK01184	184	hypothetical protein; Provisional	96.23
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.22
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.21
) 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	96.2
PF13245	76	AAA_19: Part of AAA domain	96.2
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.2
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	96.19
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.19
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.18
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.16
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.15
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.15
PRK00131	175	aroK shikimate kinase; Reviewed	96.13
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.12
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.12
PRK05917	290	DNA polymerase III subunit delta'; Validated	96.12
PRK11823	446	DNA repair protein RadA; Provisional	96.11
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.11
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	96.1
PRK03839	180	putative kinase; Provisional	96.09
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	96.07
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.07
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.07
COG4240	300	Predicted kinase [General function prediction only	96.06
PRK04040	188	adenylate kinase; Provisional	96.05
PTZ00088	229	adenylate kinase 1; Provisional	96.04
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	96.01
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.98
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.97
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.97
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.97
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.96
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.96
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	95.94
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	95.94
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	95.94
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.93
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.92
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.91
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.91
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	95.91
PRK15453	290	phosphoribulokinase; Provisional	95.9
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	95.9
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	95.89
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	95.88
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.88
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.88
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	95.87
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.87
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	95.84
PRK00625	173	shikimate kinase; Provisional	95.84
cd03246	173	ABCC_Protease_Secretion This family represents the	95.83
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	95.83
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.82
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.82
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	95.8
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	95.79
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	95.78
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	95.78
PRK00889	175	adenylylsulfate kinase; Provisional	95.77
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	95.76
PRK12678	672	transcription termination factor Rho; Provisional	95.75
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.75
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	95.74
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	95.74
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	95.74
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	95.74
PRK08149	428	ATP synthase SpaL; Validated	95.74
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	95.74
PRK06217	183	hypothetical protein; Validated	95.74
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.74
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.74
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.73
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.72
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	95.71
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.7
PRK14527	191	adenylate kinase; Provisional	95.7
PTZ00185	574	ATPase alpha subunit; Provisional	95.67
PRK13975	196	thymidylate kinase; Provisional	95.67
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.66
PRK03846	198	adenylylsulfate kinase; Provisional	95.66
COG0714	329	MoxR-like ATPases [General function prediction onl	95.66
PRK06936	439	type III secretion system ATPase; Provisional	95.66
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.65
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	95.64
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.63
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	95.62
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.62
PRK00300	205	gmk guanylate kinase; Provisional	95.6
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	95.6
PRK14737	186	gmk guanylate kinase; Provisional	95.6
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	95.6
PF07726	131	AAA_3: ATPase family associated with various cellu	95.59
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.59
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	95.59
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	95.58
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.58
PRK04196	460	V-type ATP synthase subunit B; Provisional	95.58
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	95.57
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.56
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.56
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	95.56
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	95.56
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	95.55
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.54
PRK14531	183	adenylate kinase; Provisional	95.53
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.53
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.53
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	95.53
CHL00060	494	atpB ATP synthase CF1 beta subunit	95.52
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	95.51
PRK10875	615	recD exonuclease V subunit alpha; Provisional	95.51
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.5
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	95.5
PRK05922	434	type III secretion system ATPase; Validated	95.5
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	95.49
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.48
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.48
PRK14530	215	adenylate kinase; Provisional	95.48
PRK10416	318	signal recognition particle-docking protein FtsY;	95.48
PRK09099	441	type III secretion system ATPase; Provisional	95.48
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	95.47
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	95.47
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.47
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.45
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	95.43
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	95.42
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	95.42
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.42
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.42
PRK13949	169	shikimate kinase; Provisional	95.41
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	95.41
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.41
PRK00279	215	adk adenylate kinase; Reviewed	95.41
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.4
PRK13947	171	shikimate kinase; Provisional	95.4
PRK06851	367	hypothetical protein; Provisional	95.4
PRK05022	509	anaerobic nitric oxide reductase transcription reg	95.39
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	95.38
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	95.37
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	95.37
PRK14529	223	adenylate kinase; Provisional	95.35
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	95.35
PRK14738	206	gmk guanylate kinase; Provisional	95.35
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.33
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	95.32
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.32
PRK00698	205	tmk thymidylate kinase; Validated	95.31
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.3
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.3
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.29
PRK05057	172	aroK shikimate kinase I; Reviewed	95.29
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	95.27
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.23
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.22
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	95.21
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.21
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	95.21
PHA02774	613	E1; Provisional	95.2
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.2
PRK13695	174	putative NTPase; Provisional	95.18
PLN02200	234	adenylate kinase family protein	95.11
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	95.1
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.1
PRK09302	509	circadian clock protein KaiC; Reviewed	95.07
PRK13948	182	shikimate kinase; Provisional	95.06
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	95.05
cd03116	159	MobB Molybdenum is an essential trace element in t	95.05
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	95.04
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	95.03
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.02
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	95.01
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	95.0
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	95.0
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	95.0
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	94.96
PRK13946	184	shikimate kinase; Provisional	94.96
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	94.96
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	94.93
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	94.91
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	94.9
PRK09825	176	idnK D-gluconate kinase; Provisional	94.88
PRK04182	180	cytidylate kinase; Provisional	94.88
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	94.85
PF00005	137	ABC_tran: ABC transporter This structure is on hol	94.83
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	94.82
KOG0066	807	consensus eIF2-interacting protein ABC50 (ABC supe	94.82
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	94.8
PLN02348	395	phosphoribulokinase	94.8
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.79

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=8.1e-58  Score=473.24  Aligned_cols=388  Identities=29%  Similarity=0.473  Sum_probs=308.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHhhhhhhh-----------------cc
Q 044858           33 LEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKEKSN-----------------NR   95 (426)
Q Consensus        33 ~~~l~~~l~~l~~~l~~i~~~l~~a~~~~~~~~~~~~~Wl~~l~~~~yd~ed~ld~~~~~~-----------------~~   95 (426)
                      +.+.++.+..|+..+..++.++++++.+++ ....+..|.+.+++++|++||.++.+....                 +-
T Consensus        23 ~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~-~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~~  101 (889)
T KOG4658|consen   23 LDGKDNYILELKENLKALQSALEDLDAKRD-DLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKANDLLSTRSVERQRL  101 (889)
T ss_pred             HhchHHHHHHHHHHHHHHHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHH
Confidence            344455677777777777788888887763 357889999999999999999988653111                 11


Q ss_pred             cccccC-CChHHHhHHHHHHHHHHHHHHHhhhcCCcceeccc-CCCccccccccCCcccccchHHHHHHHHHHhccCCcc
Q 044858           96 CLKGLC-PNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFR-TIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFN  173 (426)
Q Consensus        96 ~~~~~~-~~~~~r~~~~~~i~~l~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~gR~~~~~~l~~~l~~~~~~  173 (426)
                      |+...+ ......+.+++++-++...++.+..++.|..+... .+++.....|..+... +|.+..++++.+.|.+.+..
T Consensus       102 c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~~  180 (889)
T KOG4658|consen  102 CLCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQSESD-VGLETMLEKLWNRLMEDDVG  180 (889)
T ss_pred             hhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcccCCCCcccc-ccHHHHHHHHHHHhccCCCC
Confidence            111111 22333344555555555555555444445544431 1112222333333334 99999999999999987779


Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh-hcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCc---HHHHHHHHHHHhc
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK-ENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESE---SVRAWRLLEQLKK  249 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~-~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~---~~~~~~l~~~l~~  249 (426)
                      +++|+||||+||||||++++|+.. +.++|+.++||+||+.++..+++.+|++.++.......+   ......+.+.|. 
T Consensus       181 iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~-  259 (889)
T KOG4658|consen  181 IVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLE-  259 (889)
T ss_pred             EEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhc-
Confidence            999999999999999999999988 899999999999999999999999999998874443322   344555666665 


Q ss_pred             CCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCC--CCCC
Q 044858          250 ETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDC--IENG  327 (426)
Q Consensus       250 ~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~--~~~~  327 (426)
                      +|||+|||||||+..+|+.+..++|...+||+|++|||++.|+...+++...++++.|+++|||.||++.++..  ...+
T Consensus       260 ~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~  339 (889)
T KOG4658|consen  260 GKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHP  339 (889)
T ss_pred             cCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhccccccccc
Confidence            69999999999999999999999999999999999999999987668888999999999999999999999854  2335


Q ss_pred             chHHHHHHHHHHcCCchHHHHHHHHHhhcC-CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHH
Q 044858          328 ELKSVVTEVVKECAGLPIAIVPIAKALKNK-SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFL  406 (426)
Q Consensus       328 ~~~~~~~~i~~~c~GlPlai~~~~~~l~~~-~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl  406 (426)
                      .++++|++++++|+|+|||++++|+.|+.+ +..+|+++.+.+.+....+.++.. +.++.+|++||++||++ +|.||+
T Consensus       340 ~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~-~~i~~iLklSyd~L~~~-lK~CFL  417 (889)
T KOG4658|consen  340 DIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGME-ESILPILKLSYDNLPEE-LKSCFL  417 (889)
T ss_pred             cHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchh-hhhHHhhhccHhhhhHH-HHHHHH
Confidence            589999999999999999999999999987 888999999999887555554444 89999999999999976 999999


Q ss_pred             Hhhc---CCccChhhHhhhccC
Q 044858          407 LIGY---SYICNVKDLLYRGMG  425 (426)
Q Consensus       407 ~~s~---~~~i~~~~Li~~Wi~  425 (426)
                      |||+   ||+|+++.||.+|||
T Consensus       418 ycalFPED~~I~~e~Li~yWia  439 (889)
T KOG4658|consen  418 YCALFPEDYEIKKEKLIEYWIA  439 (889)
T ss_pred             hhccCCcccccchHHHHHHHHh
Confidence            9999   999999999999996

>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=4.9e-45  Score=341.46  Aligned_cols=266  Identities=30%  Similarity=0.508  Sum_probs=213.3

Q ss_pred             hHHHHHHHHHHhcc--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcc-
Q 044858          156 RKSTLKGILDALSN--RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID-  232 (426)
Q Consensus       156 R~~~~~~l~~~l~~--~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~-  232 (426)
                      |+.++++|.+.|.+  ++.++|+|+|+||+||||||.+++++...+.+|+.++|+.++...+...++..|+.+++.... 
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            78899999999987  788999999999999999999999997777899999999999999999999999999987743 


Q ss_pred             ---ccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhccCCceeeEEccCCCH
Q 044858          233 ---QESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLND  309 (426)
Q Consensus       233 ---~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~~~~~~~~~~l~~L~~  309 (426)
                         ..+.......+.+.+. ++++||||||||+...|+.+...++....||+||||||+..++.........|++++|++
T Consensus        81 ~~~~~~~~~~~~~l~~~L~-~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~  159 (287)
T PF00931_consen   81 ISDPKDIEELQDQLRELLK-DKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSE  159 (287)
T ss_dssp             SSCCSSHHHHHHHHHHHHC-CTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--H
T ss_pred             cccccccccccccchhhhc-cccceeeeeeeccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence               2334445566666665 579999999999999998888888777789999999999988743333368999999999


Q ss_pred             HHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCchHHHHHHHHHhhcC-CHHHHHHHHHHHhhccccCCCCcchhhhh
Q 044858          310 KEAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGLPIAIVPIAKALKNK-SPYEWRNALRQLKRNFLRSFSGTQAVAAY  386 (426)
Q Consensus       310 ~e~~~Lf~~~~~~~~--~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~-~~~~w~~~l~~l~~~~~~~~~~~~~~~~~  386 (426)
                      +++++||.+.++...  .++.+.+.+++|+++|+|+||||.++|++|+.+ +..+|+.+++++........ +.. ..+.
T Consensus       160 ~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~-~~~-~~~~  237 (287)
T PF00931_consen  160 EEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESR-DYD-RSVF  237 (287)
T ss_dssp             HHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSS-GSC-HHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccc-cccc
Confidence            999999999997443  345556789999999999999999999999644 77899999999877654322 112 8899


Q ss_pred             hhHHhhhcCCCCChhHHHHHHhhc---CCccChhhHhhhccC
Q 044858          387 STIQLSYNQLGGEELRKTFLLIGY---SYICNVKDLLYRGMG  425 (426)
Q Consensus       387 ~~l~~sy~~L~~~~lk~cfl~~s~---~~~i~~~~Li~~Wi~  425 (426)
                      .++.+||+.||++ +|+||+|||+   ++.|+++.|+++|++
T Consensus       238 ~~l~~s~~~L~~~-~~~~f~~L~~f~~~~~i~~~~li~lW~~  278 (287)
T PF00931_consen  238 SALELSYDSLPDE-LRRCFLYLSIFPEGVPIPRERLIRLWVA  278 (287)
T ss_dssp             HHHHHHHHSSHTC-CHHHHHHGGGSGTTS-EEHHHHHHHHTT
T ss_pred             ccceechhcCCcc-HHHHHhhCcCCCCCceECHHHHHHHHHH
Confidence            9999999999998 9999999999   889999999999986

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=1.4e-33  Score=306.99  Aligned_cols=249  Identities=19%  Similarity=0.303  Sum_probs=193.2

Q ss_pred             CCcccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe---cCC---------
Q 044858          148 QDFMHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV---SQT---------  213 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v---~~~---------  213 (426)
                      .+..+++|++..++++..++.  .+++++|+|+||||+||||||+.+|+....  +|+..+|+..   +..         
T Consensus       181 ~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~--~F~g~vfv~~~~v~~~~~~~~~~~~  258 (1153)
T PLN03210        181 NDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSR--QFQSSVFIDRAFISKSMEIYSSANP  258 (1153)
T ss_pred             cccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhh--cCCeEEEeeccccccchhhcccccc
Confidence            355679999999999988875  456889999999999999999999998764  5888777642   111         


Q ss_pred             --cC-HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchh
Q 044858          214 --PQ-IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQD  290 (426)
Q Consensus       214 --~~-~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~  290 (426)
                        ++ ...+..+++..+........  .....+.+.+. ++|+||||||||+..+|+.+.......++||+||||||+..
T Consensus       259 ~~~~~~~~l~~~~l~~il~~~~~~~--~~~~~~~~~L~-~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~~  335 (1153)
T PLN03210        259 DDYNMKLHLQRAFLSEILDKKDIKI--YHLGAMEERLK-HRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKH  335 (1153)
T ss_pred             cccchhHHHHHHHHHHHhCCCCccc--CCHHHHHHHHh-CCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcHH
Confidence              01 12234444444322111100  01133445554 68999999999999999988766655678999999999999


Q ss_pred             hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCC-CCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHHH
Q 044858          291 VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCI-ENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQL  369 (426)
Q Consensus       291 va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~l  369 (426)
                      ++. ..+..++|+++.|++++||+||+..++... +++++.+++++|+++|+|+||||+++|++|++++..+|+.+++++
T Consensus       336 vl~-~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~~~l~~L  414 (1153)
T PLN03210        336 FLR-AHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDMLPRL  414 (1153)
T ss_pred             HHH-hcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            874 344567999999999999999999998543 445678999999999999999999999999999999999999998


Q ss_pred             hhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHHHhhc
Q 044858          370 KRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGY  410 (426)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s~  410 (426)
                      ....       + ..+..+|++||+.|+++..|.||+++|+
T Consensus       415 ~~~~-------~-~~I~~~L~~SYd~L~~~~~k~~Fl~ia~  447 (1153)
T PLN03210        415 RNGL-------D-GKIEKTLRVSYDGLNNKKDKAIFRHIAC  447 (1153)
T ss_pred             HhCc-------c-HHHHHHHHHhhhccCccchhhhhheehh
Confidence            7522       2 6789999999999987448999999998

syringae 6; Provisional

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

Probab=99.53  E-value=5.3e-12  Score=116.86  Aligned_cols=183  Identities=15%  Similarity=0.189  Sum_probs=119.2

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHH---
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLE---  245 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~---  245 (426)
                      ....+.+.|+|++|+|||||++.+++...... + ...|+ +....+..+++..|+..++.+............+..   
T Consensus        40 ~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~-~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~  116 (269)
T TIGR03015        40 SQREGFILITGEVGAGKTTLIRNLLKRLDQER-V-VAAKL-VNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLI  116 (269)
T ss_pred             hcCCCEEEEEcCCCCCHHHHHHHHHHhcCCCC-e-EEeee-eCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHH
Confidence            34456899999999999999999998865321 1 12233 334457788999999998876544333333333332   


Q ss_pred             -HHhcCCeEEEEEeCCCCcc--ChhhhcC---CCCCCCCCeEEEEeecchhhhh--------ccCCceeeEEccCCCHHH
Q 044858          246 -QLKKETKILIILDDIWGSL--DLEAIGI---PLADDNGGCKVLLTARSQDVLS--------CEMDCQQNFVVDVLNDKE  311 (426)
Q Consensus       246 -~l~~~k~~LlVlDdv~~~~--~~~~l~~---~l~~~~~~s~iivTtr~~~va~--------~~~~~~~~~~l~~L~~~e  311 (426)
                       ....++++++|+||++...  .++.+..   ..........|++|........        ........+++++|+.+|
T Consensus       117 ~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e  196 (269)
T TIGR03015       117 EQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPLDREE  196 (269)
T ss_pred             HHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCCCHHH
Confidence             2335788999999998753  3444321   1112223345667665432110        011124578999999999


Q ss_pred             HHHHHHHhhCCCC---CCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          312 AWSLFKKMTGDCI---ENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       312 ~~~Lf~~~~~~~~---~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      ..+++...+....   ...-..+..+.|++.|+|.|..|..++..+
T Consensus       197 ~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       197 TREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            9999988774211   122335789999999999999999998877

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.49  E-value=1.3e-11  Score=120.82  Aligned_cols=242  Identities=17%  Similarity=0.107  Sum_probs=148.5

Q ss_pred             CcccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .+..|.||++++++|...+.    +..+..+.|+|++|+|||++++.+++........-..+++++....+...++..|+
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~  107 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIA  107 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHH
Confidence            44568999999999988874    33456788999999999999999999876543233466777777778889999999


Q ss_pred             HHhCC-Ccc--ccCcHHHHHHHHHHHhc-CCeEEEEEeCCCCcc------ChhhhcCCCCCCCC--CeEEEEeecchhhh
Q 044858          225 EKLGL-KID--QESESVRAWRLLEQLKK-ETKILIILDDIWGSL------DLEAIGIPLADDNG--GCKVLLTARSQDVL  292 (426)
Q Consensus       225 ~~l~~-~~~--~~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~------~~~~l~~~l~~~~~--~s~iivTtr~~~va  292 (426)
                      .++.. ..+  ..+.......+.+.+.. +++.+||||+++...      .+..+...+ ....  +..+|.++....+.
T Consensus       108 ~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~-~~~~~~~v~vI~i~~~~~~~  186 (394)
T PRK00411        108 RQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAH-EEYPGARIGVIGISSDLTFL  186 (394)
T ss_pred             HHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhh-hccCCCeEEEEEEECCcchh
Confidence            99865 222  12233445566666643 567899999998643      122222211 1112  23366666654332


Q ss_pred             hc------cCCceeeEEccCCCHHHHHHHHHHhhCC-----CCCCCchHHHHHHHHHHcCCchHHHHHHHHHh--h---c
Q 044858          293 SC------EMDCQQNFVVDVLNDKEAWSLFKKMTGD-----CIENGELKSVVTEVVKECAGLPIAIVPIAKAL--K---N  356 (426)
Q Consensus       293 ~~------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~-----~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l--~---~  356 (426)
                      ..      ..-....+.+.+++.++..+++...+..     ...+..++.+++......|..+.|+..+-...  +   +
T Consensus       187 ~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~  266 (394)
T PRK00411        187 YILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREG  266 (394)
T ss_pred             hhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcC
Confidence            10      0111357899999999999999988632     11222223333333333466777777764332  1   1


Q ss_pred             C---CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHHHh
Q 044858          357 K---SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLI  408 (426)
Q Consensus       357 ~---~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~  408 (426)
                      .   +......+.+...               .....-.+..||.+  +.+|++.
T Consensus       267 ~~~I~~~~v~~a~~~~~---------------~~~~~~~~~~L~~~--~k~~L~a  304 (394)
T PRK00411        267 SRKVTEEDVRKAYEKSE---------------IVHLSEVLRTLPLH--EKLLLRA  304 (394)
T ss_pred             CCCcCHHHHHHHHHHHH---------------HHHHHHHHhcCCHH--HHHHHHH
Confidence            1   5666666666541               12234457788876  4444443

>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=99.45  E-value=6.5e-13  Score=120.05  Aligned_cols=195  Identities=23%  Similarity=0.297  Sum_probs=105.9

Q ss_pred             ccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH---------
Q 044858          153 FESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI---------  223 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i---------  223 (426)
                      |+||++++++|.+++..+..+.+.|+|+.|+|||+|++.+.+...... + ..+|+....... ......+         
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~-~-~~~y~~~~~~~~-~~~~~~~~~~~~~~~~   77 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEKG-Y-KVVYIDFLEESN-ESSLRSFIEETSLADE   77 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT--E-E-CCCHHCCTTBSH-HHHHHHHHHHHHHHCH
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcC-C-cEEEEecccchh-hhHHHHHHHHHHHHHH
Confidence            789999999999998877678999999999999999999999874321 2 233444333322 2212221         


Q ss_pred             -HHHhCCCc-----------cccCcHHHHHHHHHHHhc-CCeEEEEEeCCCCcc-Ch---hh----hcCCCC--CCCCCe
Q 044858          224 -AEKLGLKI-----------DQESESVRAWRLLEQLKK-ETKILIILDDIWGSL-DL---EA----IGIPLA--DDNGGC  280 (426)
Q Consensus       224 -~~~l~~~~-----------~~~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~-~~---~~----l~~~l~--~~~~~s  280 (426)
                       ...+....           ...........+.+.+.+ +++++|||||+.... ..   ..    +...+.  ......
T Consensus        78 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  157 (234)
T PF01637_consen   78 LSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNV  157 (234)
T ss_dssp             CHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTE
T ss_pred             HHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCc
Confidence             11121110           011223445566666653 345999999997655 11   11    111111  123344


Q ss_pred             EEEEeecchhhhhc-------cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          281 KVLLTARSQDVLSC-------EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       281 ~iivTtr~~~va~~-------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      .+|+++........       ..+....+.+++|+.+++++++...+.....-+.-.+..++|+..+||+|..|..+
T Consensus       158 ~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~gG~P~~l~~~  234 (234)
T PF01637_consen  158 SIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLTGGNPRYLQEL  234 (234)
T ss_dssp             EEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC------HHHHHHHHHHHTT-HHHHHHH
T ss_pred             eEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHhCCCHHHHhcC
Confidence            45555554433211       22334559999999999999999976433111123456799999999999988653

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

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.45  E-value=5.1e-12  Score=136.82  Aligned_cols=244  Identities=16%  Similarity=0.166  Sum_probs=151.4

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec-CCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS-QTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~il~~i~~~  226 (426)
                      .....++.|...++.+-.   ....+++.|+|++|.||||++.++.+.      ++.++|+++. .+.++..++..++..
T Consensus        11 ~~~~~~~~R~rl~~~l~~---~~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~~   81 (903)
T PRK04841         11 VRLHNTVVRERLLAKLSG---ANNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIAA   81 (903)
T ss_pred             CCccccCcchHHHHHHhc---ccCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHHH
Confidence            344567778766665533   245689999999999999999998853      2258899996 445667777777776


Q ss_pred             hCCCccc--------------cCcHHHHHHHHHHHhc-CCeEEEEEeCCCCccC--hh-hhcCCCCCCCCCeEEEEeecc
Q 044858          227 LGLKIDQ--------------ESESVRAWRLLEQLKK-ETKILIILDDIWGSLD--LE-AIGIPLADDNGGCKVLLTARS  288 (426)
Q Consensus       227 l~~~~~~--------------~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~~--~~-~l~~~l~~~~~~s~iivTtr~  288 (426)
                      ++...+.              .+.......+...+.. +.+++|||||++..++  .. .+...+.....+.++|||||.
T Consensus        82 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~  161 (903)
T PRK04841         82 LQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRN  161 (903)
T ss_pred             HHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCC
Confidence            6421111              1112233445555543 6799999999976532  22 222222233456789899998


Q ss_pred             hhhhhc-c-CCceeeEEcc----CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHH
Q 044858          289 QDVLSC-E-MDCQQNFVVD----VLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEW  362 (426)
Q Consensus       289 ~~va~~-~-~~~~~~~~l~----~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w  362 (426)
                      ...... . .-......+.    +|+.+|+.+||....+....    .+....|.+.|+|.|+++..++..+...+.. .
T Consensus       162 ~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~----~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~-~  236 (903)
T PRK04841        162 LPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPIE----AAESSRLCDDVEGWATALQLIALSARQNNSS-L  236 (903)
T ss_pred             CCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCCC----HHHHHHHHHHhCChHHHHHHHHHHHhhCCCc-h
Confidence            532110 0 0012234455    99999999999887664332    3457889999999999999988777643210 0


Q ss_pred             HHHHHHHhhccccCCCCcchhhhhhhHH-hhhcCCCCChhHHHHHHhhc-CCccC
Q 044858          363 RNALRQLKRNFLRSFSGTQAVAAYSTIQ-LSYNQLGGEELRKTFLLIGY-SYICN  415 (426)
Q Consensus       363 ~~~l~~l~~~~~~~~~~~~~~~~~~~l~-~sy~~L~~~~lk~cfl~~s~-~~~i~  415 (426)
                      ......+.    ..    +...+...+. -.|+.||++ .+..++..|+ + .|+
T Consensus       237 ~~~~~~~~----~~----~~~~~~~~l~~~v~~~l~~~-~~~~l~~~a~~~-~~~  281 (903)
T PRK04841        237 HDSARRLA----GI----NASHLSDYLVEEVLDNVDLE-TRHFLLRCSVLR-SMN  281 (903)
T ss_pred             hhhhHhhc----CC----CchhHHHHHHHHHHhcCCHH-HHHHHHHhcccc-cCC
Confidence            11111110    00    0023444433 348899998 9999999999 4 444

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.39  E-value=2.4e-10  Score=110.73  Aligned_cols=244  Identities=15%  Similarity=0.172  Sum_probs=146.3

Q ss_pred             cccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhc-Ccc---ceEEEEEecCCcCHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLF---EKVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f---~~~~wv~v~~~~~~~~il~  221 (426)
                      +..+.||++++++|...+.    +...+.+.|+|++|+|||++++.+++..... ...   -..+|+++....+...++.
T Consensus        14 p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~   93 (365)
T TIGR02928        14 PDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLV   93 (365)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHH
Confidence            4468999999999999886    3445679999999999999999999876431 111   2456777777778889999


Q ss_pred             HHHHHh---CCCccc--cCcHHHHHHHHHHHh-cCCeEEEEEeCCCCcc-C----hhhhcCCC-CCCC--CCeEEEEeec
Q 044858          222 EIAEKL---GLKIDQ--ESESVRAWRLLEQLK-KETKILIILDDIWGSL-D----LEAIGIPL-ADDN--GGCKVLLTAR  287 (426)
Q Consensus       222 ~i~~~l---~~~~~~--~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~-~----~~~l~~~l-~~~~--~~s~iivTtr  287 (426)
                      .|+.++   +...+.  .+.......+.+.+. .+++++||||+++... .    +..+.... ....  ....+|.+|.
T Consensus        94 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n  173 (365)
T TIGR02928        94 ELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISN  173 (365)
T ss_pred             HHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEEC
Confidence            999988   333222  122334455666654 3568999999998662 1    11221110 1111  2334555554


Q ss_pred             chhhh----hccC-C-ceeeEEccCCCHHHHHHHHHHhhCC----CCCCCchHHHHHHHHHHcCCchHHHHHHHHH-h--
Q 044858          288 SQDVL----SCEM-D-CQQNFVVDVLNDKEAWSLFKKMTGD----CIENGELKSVVTEVVKECAGLPIAIVPIAKA-L--  354 (426)
Q Consensus       288 ~~~va----~~~~-~-~~~~~~l~~L~~~e~~~Lf~~~~~~----~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~-l--  354 (426)
                      .....    .... . ....+.++|++.++..+++..++..    ...+++..+....++..+.|.|..+..+... .  
T Consensus       174 ~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~  253 (365)
T TIGR02928       174 DLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEI  253 (365)
T ss_pred             CcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            43221    1000 1 1256899999999999999988741    1122333344556777777888554333221 1  


Q ss_pred             h---c---CCHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHHHhh
Q 044858          355 K---N---KSPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG  409 (426)
Q Consensus       355 ~---~---~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s  409 (426)
                      .   +   -+.+..+.+.+.+.               .....-++..||.+ .|..+..+.
T Consensus       254 a~~~~~~~it~~~v~~a~~~~~---------------~~~~~~~i~~l~~~-~~~~l~ai~  298 (365)
T TIGR02928       254 AEREGAERVTEDHVEKAQEKIE---------------KDRLLELIRGLPTH-SKLVLLAIA  298 (365)
T ss_pred             HHHcCCCCCCHHHHHHHHHHHH---------------HHHHHHHHHcCCHH-HHHHHHHHH
Confidence            1   1   15566665555432               12234466788876 554444443

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.

>PF05729 NACHT: NACHT domain

Probab=99.36  E-value=7.2e-12  Score=106.92  Aligned_cols=144  Identities=19%  Similarity=0.263  Sum_probs=92.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEEEEecCCcCHH---HHHHHHHHHhCCCccccCcHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVISSRVSQTPQIK---EIQREIAEKLGLKIDQESESVRAWRLLE  245 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~---~il~~i~~~l~~~~~~~~~~~~~~~l~~  245 (426)
                      +++.|+|.+|+||||+++.++........    +...+|.+.+......   .+...|..+..........     .+..
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~-----~~~~   75 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEE-----LLQE   75 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHH-----HHHH
Confidence            57899999999999999999988776543    3456677665544322   3444444333222111111     2233


Q ss_pred             HHhcCCeEEEEEeCCCCccC---------hhhhc-CCCCC-CCCCeEEEEeecchhhh--hccCCceeeEEccCCCHHHH
Q 044858          246 QLKKETKILIILDDIWGSLD---------LEAIG-IPLAD-DNGGCKVLLTARSQDVL--SCEMDCQQNFVVDVLNDKEA  312 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~~~~~---------~~~l~-~~l~~-~~~~s~iivTtr~~~va--~~~~~~~~~~~l~~L~~~e~  312 (426)
                      .+...++++||||++++...         +..+. ..+.. ..+++++|||+|.....  .........+.+.+|++++.
T Consensus        76 ~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~  155 (166)
T PF05729_consen   76 LLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDI  155 (166)
T ss_pred             HHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHH
Confidence            34457899999999976532         22221 22222 24589999999997762  22334446899999999999


Q ss_pred             HHHHHHhhC
Q 044858          313 WSLFKKMTG  321 (426)
Q Consensus       313 ~~Lf~~~~~  321 (426)
                      .+++.+.+.
T Consensus       156 ~~~~~~~f~  164 (166)
T PF05729_consen  156 KQYLRKYFS  164 (166)
T ss_pred             HHHHHHHhh
Confidence            999988763

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.17  E-value=2.5e-09  Score=104.83  Aligned_cols=194  Identities=14%  Similarity=0.150  Sum_probs=116.5

Q ss_pred             CcccccchHHHHHH---HHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKG---ILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       149 ~~~~~~gR~~~~~~---l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      ....|+|+++.+..   +...+..+..+.+.++|++|+||||||+.+++.....       |+.++......+-+++++.
T Consensus        10 ~l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~~~-------~~~l~a~~~~~~~ir~ii~   82 (413)
T PRK13342         10 TLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP-------FEALSAVTSGVKDLREVIE   82 (413)
T ss_pred             CHHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhCCC-------EEEEecccccHHHHHHHHH
Confidence            45678888887665   7777777777788999999999999999998876432       2333222111111222221


Q ss_pred             HhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEE--eecchhhh--hccCCce
Q 044858          226 KLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLL--TARSQDVL--SCEMDCQ  299 (426)
Q Consensus       226 ~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iiv--Ttr~~~va--~~~~~~~  299 (426)
                      .                .......+++.+|+||+++...  ..+.+...+.   .+..+++  ||.+....  .......
T Consensus        83 ~----------------~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le---~~~iilI~att~n~~~~l~~aL~SR~  143 (413)
T PRK13342         83 E----------------ARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVE---DGTITLIGATTENPSFEVNPALLSRA  143 (413)
T ss_pred             H----------------HHHhhhcCCceEEEEechhhhCHHHHHHHHHHhh---cCcEEEEEeCCCChhhhccHHHhccc
Confidence            1                1111223578999999998653  3333333322   2444444  33433211  1122334


Q ss_pred             eeEEccCCCHHHHHHHHHHhhCCCC-CC-CchHHHHHHHHHHcCCchHHHHHHHHHhh---c-CCHHHHHHHHHH
Q 044858          300 QNFVVDVLNDKEAWSLFKKMTGDCI-EN-GELKSVVTEVVKECAGLPIAIVPIAKALK---N-KSPYEWRNALRQ  368 (426)
Q Consensus       300 ~~~~l~~L~~~e~~~Lf~~~~~~~~-~~-~~~~~~~~~i~~~c~GlPlai~~~~~~l~---~-~~~~~w~~~l~~  368 (426)
                      ..+.+.+++.++...++.+.+.... .. +-..+..+.|++.|+|.|..+..+.....   . .+.+..+.++..
T Consensus       144 ~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~~~~~~~~It~~~v~~~~~~  218 (413)
T PRK13342        144 QVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLELAALGVDSITLELLEEALQK  218 (413)
T ss_pred             eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHccCCCCHHHHHHHHhh
Confidence            7899999999999999998764211 11 22356788899999999987766554442   1 155555555544

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.16  E-value=1.2e-09  Score=103.08  Aligned_cols=189  Identities=13%  Similarity=0.090  Sum_probs=108.5

Q ss_pred             cccccchHHHHHHHHHHhc-----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALS-----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~-----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      +..|+|+++.++.|..++.     ...+..+.++|++|+|||+||+.+.+.....  +   ..+..+......+ +...+
T Consensus         3 ~~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~--~---~~~~~~~~~~~~~-l~~~l   76 (305)
T TIGR00635         3 LAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVN--L---KITSGPALEKPGD-LAAIL   76 (305)
T ss_pred             HHHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC--E---EEeccchhcCchh-HHHHH
Confidence            4579999999999888776     2345678899999999999999999876532  2   1222221112222 22222


Q ss_pred             HHhCCCc-------cccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhc-cC
Q 044858          225 EKLGLKI-------DQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSC-EM  296 (426)
Q Consensus       225 ~~l~~~~-------~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~-~~  296 (426)
                      ..++...       +..+ ......++..+. +.+..+|+++..+...+..   .++   +.+-|..||+...+... ..
T Consensus        77 ~~~~~~~vl~iDEi~~l~-~~~~e~l~~~~~-~~~~~~v~~~~~~~~~~~~---~~~---~~~li~~t~~~~~l~~~l~s  148 (305)
T TIGR00635        77 TNLEEGDVLFIDEIHRLS-PAVEELLYPAME-DFRLDIVIGKGPSARSVRL---DLP---PFTLVGATTRAGMLTSPLRD  148 (305)
T ss_pred             HhcccCCEEEEehHhhhC-HHHHHHhhHHHh-hhheeeeeccCccccceee---cCC---CeEEEEecCCccccCHHHHh
Confidence            3322111       0000 011122222222 3345555665544433321   111   24555666776544321 11


Q ss_pred             CceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          297 DCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       297 ~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      .....+.+++++.++..+++.+.+..... .-..+....|++.|+|.|..+..++..
T Consensus       149 R~~~~~~l~~l~~~e~~~il~~~~~~~~~-~~~~~al~~ia~~~~G~pR~~~~ll~~  204 (305)
T TIGR00635       149 RFGIILRLEFYTVEELAEIVSRSAGLLNV-EIEPEAALEIARRSRGTPRIANRLLRR  204 (305)
T ss_pred             hcceEEEeCCCCHHHHHHHHHHHHHHhCC-CcCHHHHHHHHHHhCCCcchHHHHHHH
Confidence            22357899999999999999988753221 222456788999999999877655543

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=99.14  E-value=9.1e-10  Score=102.24  Aligned_cols=178  Identities=16%  Similarity=0.155  Sum_probs=110.9

Q ss_pred             CCcccccchHHHHH---HHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLK---GILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       148 ~~~~~~~gR~~~~~---~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .....++|.++.+.   -|...+..+++....+||++|+||||||+.+.......       |..++...+-..-+++++
T Consensus        21 ~~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~-------f~~~sAv~~gvkdlr~i~   93 (436)
T COG2256          21 KSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAA-------FEALSAVTSGVKDLREII   93 (436)
T ss_pred             CCHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhhCCc-------eEEeccccccHHHHHHHH
Confidence            34556666665542   24445556778888899999999999999999876543       344444433333333333


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-hhhhcCCCCCCCCCeEEEE--eecchhhh--hccCCce
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-LEAIGIPLADDNGGCKVLL--TARSQDVL--SCEMDCQ  299 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-~~~l~~~l~~~~~~s~iiv--Ttr~~~va--~~~~~~~  299 (426)
                      +.                ..+....+++.+|++|+|+.... -++.  .||.-.+|.-|+|  ||.++.-.  +...+..
T Consensus        94 e~----------------a~~~~~~gr~tiLflDEIHRfnK~QQD~--lLp~vE~G~iilIGATTENPsF~ln~ALlSR~  155 (436)
T COG2256          94 EE----------------ARKNRLLGRRTILFLDEIHRFNKAQQDA--LLPHVENGTIILIGATTENPSFELNPALLSRA  155 (436)
T ss_pred             HH----------------HHHHHhcCCceEEEEehhhhcChhhhhh--hhhhhcCCeEEEEeccCCCCCeeecHHHhhhh
Confidence            21                22233347899999999985532 1222  2344556777776  55555322  2234556


Q ss_pred             eeEEccCCCHHHHHHHHHHhhCC-C-----CCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          300 QNFVVDVLNDKEAWSLFKKMTGD-C-----IENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       300 ~~~~l~~L~~~e~~~Lf~~~~~~-~-----~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      .++.+++|+.++..+++.+.+.. .     ....--++...-+++.++|---+.-..
T Consensus       156 ~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~  212 (436)
T COG2256         156 RVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNL  212 (436)
T ss_pred             heeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHH
Confidence            89999999999999999985421 1     111122457788999999976544333

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.14  E-value=2e-09  Score=108.61  Aligned_cols=242  Identities=17%  Similarity=0.154  Sum_probs=153.9

Q ss_pred             ccCCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHH
Q 044858          146 STQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIA  224 (426)
Q Consensus       146 ~~~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~  224 (426)
                      +|..+...+-|....+.+-.   ....+.+.|..|+|.|||||+.+.......   -..+.|.+.+. +.++..+...++
T Consensus        14 ~P~~~~~~v~R~rL~~~L~~---~~~~RL~li~APAGfGKttl~aq~~~~~~~---~~~v~Wlslde~dndp~rF~~yLi   87 (894)
T COG2909          14 RPVRPDNYVVRPRLLDRLRR---ANDYRLILISAPAGFGKTTLLAQWRELAAD---GAAVAWLSLDESDNDPARFLSYLI   87 (894)
T ss_pred             CCCCcccccccHHHHHHHhc---CCCceEEEEeCCCCCcHHHHHHHHHHhcCc---ccceeEeecCCccCCHHHHHHHHH
Confidence            33445566777765555433   346789999999999999999999873322   34688999864 557888888888


Q ss_pred             HHhCCCccccCc--------------HHHHHHHHHHHhc-CCeEEEEEeCCCCc---cChhhhcCCCCCCCCCeEEEEee
Q 044858          225 EKLGLKIDQESE--------------SVRAWRLLEQLKK-ETKILIILDDIWGS---LDLEAIGIPLADDNGGCKVLLTA  286 (426)
Q Consensus       225 ~~l~~~~~~~~~--------------~~~~~~l~~~l~~-~k~~LlVlDdv~~~---~~~~~l~~~l~~~~~~s~iivTt  286 (426)
                      ..++.-.+...+              ......++..+.. .+++.+||||-.-.   .--..+.-.+.....+-.+||||
T Consensus        88 ~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~S  167 (894)
T COG2909          88 AALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTS  167 (894)
T ss_pred             HHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEe
Confidence            887643332221              1233445544432 56899999997633   22222322233344588999999


Q ss_pred             cchhhhhc--cCCceeeEEcc----CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcC-CH
Q 044858          287 RSQDVLSC--EMDCQQNFVVD----VLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNK-SP  359 (426)
Q Consensus       287 r~~~va~~--~~~~~~~~~l~----~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~-~~  359 (426)
                      |+..-...  ..-....+++.    .|+.+|+.++|....+...+    +.-.+.+....+|-+-|+..++=.+++. +.
T Consensus       168 R~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld----~~~~~~L~~~teGW~~al~L~aLa~~~~~~~  243 (894)
T COG2909         168 RSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPLD----AADLKALYDRTEGWAAALQLIALALRNNTSA  243 (894)
T ss_pred             ccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCCC----hHHHHHHHhhcccHHHHHHHHHHHccCCCcH
Confidence            99753210  00112234444    48999999999987654333    3447789999999999999999888833 33


Q ss_pred             HHHHHHHHHHhhccccCCCCcchhhhhh-hHHhhhcCCCCChhHHHHHHhhc
Q 044858          360 YEWRNALRQLKRNFLRSFSGTQAVAAYS-TIQLSYNQLGGEELRKTFLLIGY  410 (426)
Q Consensus       360 ~~w~~~l~~l~~~~~~~~~~~~~~~~~~-~l~~sy~~L~~~~lk~cfl~~s~  410 (426)
                      +.--..+.-..            +.+.. ...--++.||++ +|..++-||+
T Consensus       244 ~q~~~~LsG~~------------~~l~dYL~eeVld~Lp~~-l~~FLl~~sv  282 (894)
T COG2909         244 EQSLRGLSGAA------------SHLSDYLVEEVLDRLPPE-LRDFLLQTSV  282 (894)
T ss_pred             HHHhhhccchH------------HHHHHHHHHHHHhcCCHH-HHHHHHHHHh
Confidence            33222221100            11111 233457889998 9999999998

>COG3899 Predicted ATPase [General function prediction only]

Probab=99.14  E-value=1.1e-09  Score=115.63  Aligned_cols=262  Identities=17%  Similarity=0.180  Sum_probs=158.3

Q ss_pred             cccchHHHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEEEEecCCc---CHHHHHHHHH
Q 044858          152 HFESRKSTLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQTP---QIKEIQREIA  224 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~---~~~~il~~i~  224 (426)
                      .++||+.+++.|...+.   .+...++.+.|..|+|||+|+++|......+ +.|-.-.+-......   ...+.+++++
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~~~~i~~~f~q~~~~ipl~~lvq~~r~l~   80 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRGYFIKGKFDQFERNIPLSPLVQAFRDLM   80 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhccceeeeHhhcccccCCCchHHHHHHHHHHH
Confidence            36899999999999887   4556799999999999999999999887654 222111111111221   1223333333


Q ss_pred             HHh-------------------CCCccc-----------------------cCcHH-----HHHHHHHHHhcCCeEEEEE
Q 044858          225 EKL-------------------GLKIDQ-----------------------ESESV-----RAWRLLEQLKKETKILIIL  257 (426)
Q Consensus       225 ~~l-------------------~~~~~~-----------------------~~~~~-----~~~~l~~~l~~~k~~LlVl  257 (426)
                      .++                   +.....                       .....     ....+.....+.++.++|+
T Consensus        81 ~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi~l  160 (849)
T COG3899          81 GQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVIVL  160 (849)
T ss_pred             HHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEEEE
Confidence            333                   111000                       00000     1112222334567999999


Q ss_pred             eCCCC--ccChhhh---cCCCCC-C--CCCeEEEEeecch-hhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCc
Q 044858          258 DDIWG--SLDLEAI---GIPLAD-D--NGGCKVLLTARSQ-DVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGE  328 (426)
Q Consensus       258 Ddv~~--~~~~~~l---~~~l~~-~--~~~s~iivTtr~~-~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~  328 (426)
                      ||++-  ...++-+   ...... .  .+..-.+.|.+.. ........+...|.|.||+..+...+....++.....  
T Consensus       161 eDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~~~~--  238 (849)
T COG3899         161 EDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGCTKLL--  238 (849)
T ss_pred             ecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCCcccc--
Confidence            99942  2222211   111110 0  0111122333332 1112234456899999999999999999998753322  


Q ss_pred             hHHHHHHHHHHcCCchHHHHHHHHHhhcC-------CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChh
Q 044858          329 LKSVVTEVVKECAGLPIAIVPIAKALKNK-------SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEEL  401 (426)
Q Consensus       329 ~~~~~~~i~~~c~GlPlai~~~~~~l~~~-------~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~l  401 (426)
                      ..+..+.|+++..|+|+.+..+-..+...       +...|..-..++..     .+. . +.+.+.+..-.+.||+. .
T Consensus       239 ~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~-----~~~-~-~~vv~~l~~rl~kL~~~-t  310 (849)
T COG3899         239 PAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGI-----LAT-T-DAVVEFLAARLQKLPGT-T  310 (849)
T ss_pred             cchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCC-----chh-h-HHHHHHHHHHHhcCCHH-H
Confidence            24568899999999999999999988742       33444333333221     111 1 33666799999999998 9


Q ss_pred             HHHHHHhhc-CCccChhhHhhhc
Q 044858          402 RKTFLLIGY-SYICNVKDLLYRG  423 (426)
Q Consensus       402 k~cfl~~s~-~~~i~~~~Li~~W  423 (426)
                      |..+-..|+ |..|+.+.|-..|
T Consensus       311 ~~Vl~~AA~iG~~F~l~~La~l~  333 (849)
T COG3899         311 REVLKAAACIGNRFDLDTLAALA  333 (849)
T ss_pred             HHHHHHHHHhCccCCHHHHHHHH
Confidence            999999999 9888888776554

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.09  E-value=4.4e-09  Score=100.01  Aligned_cols=192  Identities=13%  Similarity=0.066  Sum_probs=105.4

Q ss_pred             CCcccccchHHHHHHHHHHhc-----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALS-----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      ..+..|+|+++.++.+...+.     ...++.+.|+|++|+|||+||+.+.+.....  +   .++..+. ......+..
T Consensus        22 ~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~--~---~~~~~~~-~~~~~~l~~   95 (328)
T PRK00080         22 KSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVN--I---RITSGPA-LEKPGDLAA   95 (328)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCC--e---EEEeccc-ccChHHHHH
Confidence            356789999999988877664     2345678899999999999999999987532  1   1222211 111122223


Q ss_pred             HHHHhCCCc----cccC--cHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhc-c
Q 044858          223 IAEKLGLKI----DQES--ESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSC-E  295 (426)
Q Consensus       223 i~~~l~~~~----~~~~--~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~-~  295 (426)
                      ++..+....    ++..  .......++..+ .+.+..+++|+..+...+.   ..+   .+.+-|..||+...+... .
T Consensus        96 ~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~-e~~~~~~~l~~~~~~~~~~---~~l---~~~~li~at~~~~~l~~~L~  168 (328)
T PRK00080         96 ILTNLEEGDVLFIDEIHRLSPVVEEILYPAM-EDFRLDIMIGKGPAARSIR---LDL---PPFTLIGATTRAGLLTSPLR  168 (328)
T ss_pred             HHHhcccCCEEEEecHhhcchHHHHHHHHHH-HhcceeeeeccCcccccee---ecC---CCceEEeecCCcccCCHHHH
Confidence            333222110    0000  000111111222 1233444444433222111   011   123445566665443221 1


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      ......++++++++++..+++.+.+..... .--.+....|++.|+|.|-.+..+...
T Consensus       169 sRf~~~~~l~~~~~~e~~~il~~~~~~~~~-~~~~~~~~~ia~~~~G~pR~a~~~l~~  225 (328)
T PRK00080        169 DRFGIVQRLEFYTVEELEKIVKRSARILGV-EIDEEGALEIARRSRGTPRIANRLLRR  225 (328)
T ss_pred             HhcCeeeecCCCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHHcCCCchHHHHHHHH
Confidence            112357899999999999999988763221 122457889999999999766665553

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.03  E-value=1.9e-08  Score=101.76  Aligned_cols=183  Identities=14%  Similarity=0.175  Sum_probs=116.1

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------ccceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENN-------------------LFEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~-------------------~f~~~~w  207 (426)
                      ..+..++|.+..++.|.+++..+++ +.+.++|+.|+||||+|+.+.+......                   .|..+++
T Consensus        13 qtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviE   92 (830)
T PRK07003         13 KDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVE   92 (830)
T ss_pred             CcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEE
Confidence            3567789999999999999887664 4567999999999999999887654211                   1111222


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeE
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL----KKETKILIILDDIWGSL--DLEAIGIPLADDNGGCK  281 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~  281 (426)
                      ++.+....+.                     .+..+++..    ..++.-++|||+++...  .++.+...+..-..+++
T Consensus        93 IDAas~rgVD---------------------dIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~  151 (830)
T PRK07003         93 MDAASNRGVD---------------------EMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVK  151 (830)
T ss_pred             ecccccccHH---------------------HHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeE
Confidence            2222211111                     122222222    12455689999998663  36665544433344677


Q ss_pred             EEEeecchh-hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch-HHHHHHHH
Q 044858          282 VLLTARSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP-IAIVPIAK  352 (426)
Q Consensus       282 iivTtr~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP-lai~~~~~  352 (426)
                      +|+||.+.. +.....+....+++++++.++..+.+.+.+...... -..+....|++.++|.. -++..+-.
T Consensus       152 FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~-id~eAL~lIA~~A~GsmRdALsLLdQ  223 (830)
T PRK07003        152 FILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIA-FEPQALRLLARAAQGSMRDALSLTDQ  223 (830)
T ss_pred             EEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            777776643 322233445789999999999999999887533211 12456788999999865 45555443

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.98  E-value=1.9e-08  Score=96.35  Aligned_cols=202  Identities=13%  Similarity=0.099  Sum_probs=113.4

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcC-HHHHHH---HH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQ-IKEIQR---EI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~-~~~il~---~i  223 (426)
                      ....++|++..++.+..++..+..+.+.++|++|+||||+|+.+.+..... .+. ..+.++++...+ ....+.   ..
T Consensus        13 ~~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~   91 (337)
T PRK12402         13 LLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGD-PWENNFTEFNVADFFDQGKKYLVEDPRF   91 (337)
T ss_pred             cHHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCc-ccccceEEechhhhhhcchhhhhcCcch
Confidence            456788999999999998887776778899999999999999998876432 222 233444332110 000000   00


Q ss_pred             HHHhCCC-ccccCcHHHHHHHHHHHhc-----CCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecchh-hhhc
Q 044858          224 AEKLGLK-IDQESESVRAWRLLEQLKK-----ETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQD-VLSC  294 (426)
Q Consensus       224 ~~~l~~~-~~~~~~~~~~~~l~~~l~~-----~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~~-va~~  294 (426)
                      ...++.. ............+.+....     +.+-+||+||+....  ....+...+......+++|+||.... +...
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~  171 (337)
T PRK12402         92 AHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPP  171 (337)
T ss_pred             hhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchh
Confidence            0000000 0001111222233222211     234589999997552  22223322222234567887775432 2111


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      .......+.+.+++.++...++.+.+...... --.+....+++.++|.+-.+.....
T Consensus       172 L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~-~~~~al~~l~~~~~gdlr~l~~~l~  228 (337)
T PRK12402        172 IRSRCLPLFFRAPTDDELVDVLESIAEAEGVD-YDDDGLELIAYYAGGDLRKAILTLQ  228 (337)
T ss_pred             hcCCceEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            22334678999999999999998876422211 2245678888999887766554443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.97  E-value=1e-07  Score=97.26  Aligned_cols=255  Identities=20%  Similarity=0.170  Sum_probs=143.4

Q ss_pred             cccccchHHHHHHHHHHhc----cCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhc---Cccc--eEEEEEecCCcCHHHH
Q 044858          150 FMHFESRKSTLKGILDALS----NRN-FNMIGVYGMGGIGKTTLVKEVGRQAKEN---NLFE--KVISSRVSQTPQIKEI  219 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~----~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~---~~f~--~~~wv~v~~~~~~~~i  219 (426)
                      +..+.+|++|+++|...|.    ... ..++.|+|++|+|||++++.|.+.....   ....  .+++|.+..-.+...+
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            3457899999999988876    223 3467899999999999999998776421   1122  3567777666788889


Q ss_pred             HHHHHHHhCCCccc--cCcHHHHHHHHHHHhc--CCeEEEEEeCCCCccC-hhh-hcCCCC-CCCCCeEEEE--eecchh
Q 044858          220 QREIAEKLGLKIDQ--ESESVRAWRLLEQLKK--ETKILIILDDIWGSLD-LEA-IGIPLA-DDNGGCKVLL--TARSQD  290 (426)
Q Consensus       220 l~~i~~~l~~~~~~--~~~~~~~~~l~~~l~~--~k~~LlVlDdv~~~~~-~~~-l~~~l~-~~~~~s~iiv--Ttr~~~  290 (426)
                      ...|.+++....+.  .+....+..++..+..  +...+||||+++.... -+. |...+. ....+++|+|  +|....
T Consensus       834 YqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlD  913 (1164)
T PTZ00112        834 YQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMD  913 (1164)
T ss_pred             HHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchh
Confidence            99999888433322  2233455566665532  2346999999975431 111 111111 1123455444  332211


Q ss_pred             hh----hccC--CceeeEEccCCCHHHHHHHHHHhhCCC---CCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcC----
Q 044858          291 VL----SCEM--DCQQNFVVDVLNDKEAWSLFKKMTGDC---IENGELKSVVTEVVKECAGLPIAIVPIAKALKNK----  357 (426)
Q Consensus       291 va----~~~~--~~~~~~~l~~L~~~e~~~Lf~~~~~~~---~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~----  357 (426)
                      ..    ....  -....+...|++.++-.+++..++...   ..+..++-+++.++...|-.-.||.++-.+....    
T Consensus       914 LperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAgEikegsk  993 (1164)
T PTZ00112        914 LPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAFENKRGQK  993 (1164)
T ss_pred             cchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHHhhcCCCc
Confidence            11    1000  112347789999999999999988632   2222333334444444455566666655444311    


Q ss_pred             -CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHHHhhc------C-CccChhhHhh
Q 044858          358 -SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGY------S-YICNVKDLLY  421 (426)
Q Consensus       358 -~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s~------~-~~i~~~~Li~  421 (426)
                       +.+.-..+...+.               ...+.-....||.|  ..+||+..+      + ..++...+..
T Consensus       994 VT~eHVrkAleeiE---------------~srI~e~IktLPlH--qKLVLlALIlLlk~tg~~~i~TGEVYe 1048 (1164)
T PTZ00112        994 IVPRDITEATNQLF---------------DSPLTNAINYLPWP--FKMFLTCLIVELRMLNDFIIPYKKVLN 1048 (1164)
T ss_pred             cCHHHHHHHHHHHH---------------hhhHHHHHHcCCHH--HHHHHHHHHHHHhhcCCCceeHHHHHH
Confidence             3334444433321               11233455689987  555666433      1 2466555543

>PRK06893 DNA replication initiation factor; Validated

Probab=98.97  E-value=1.1e-08  Score=92.04  Aligned_cols=155  Identities=18%  Similarity=0.147  Sum_probs=93.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ..+.+.|+|++|+|||+|++.+++....+  ...+.|+++....   ...                    ..+.+.+.  
T Consensus        38 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~--~~~~~y~~~~~~~---~~~--------------------~~~~~~~~--   90 (229)
T PRK06893         38 QQPFFYIWGGKSSGKSHLLKAVSNHYLLN--QRTAIYIPLSKSQ---YFS--------------------PAVLENLE--   90 (229)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEeeHHHhh---hhh--------------------HHHHhhcc--
Confidence            34678999999999999999999987544  2345666653110   000                    01222222  


Q ss_pred             CeEEEEEeCCCCc---cChhh-hcCCCCCC-CCCeEEEEeecch----------hhhhccCCceeeEEccCCCHHHHHHH
Q 044858          251 TKILIILDDIWGS---LDLEA-IGIPLADD-NGGCKVLLTARSQ----------DVLSCEMDCQQNFVVDVLNDKEAWSL  315 (426)
Q Consensus       251 k~~LlVlDdv~~~---~~~~~-l~~~l~~~-~~~s~iivTtr~~----------~va~~~~~~~~~~~l~~L~~~e~~~L  315 (426)
                      +.-+|+|||+|..   ..|+. +...+... ..|..+||+|.+.          .+.+ .......++++++++++.+++
T Consensus        91 ~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~s-Rl~~g~~~~l~~pd~e~~~~i  169 (229)
T PRK06893         91 QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLAS-RLTWGEIYQLNDLTDEQKIIV  169 (229)
T ss_pred             cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHH-HHhcCCeeeCCCCCHHHHHHH
Confidence            2359999999864   34543 22222111 2355565554443          2212 123346889999999999999


Q ss_pred             HHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          316 FKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       316 f~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      +++.+....- .--+++..-|++.+.|..-.+..+-..|
T Consensus       170 L~~~a~~~~l-~l~~~v~~~L~~~~~~d~r~l~~~l~~l  207 (229)
T PRK06893        170 LQRNAYQRGI-ELSDEVANFLLKRLDRDMHTLFDALDLL  207 (229)
T ss_pred             HHHHHHHcCC-CCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            9988853221 1224677889999988776665554433

>PF13173 AAA_14: AAA domain

Probab=98.94  E-value=4.5e-09  Score=85.52  Aligned_cols=121  Identities=24%  Similarity=0.220  Sum_probs=81.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      .+++.|.|+.|+|||||+++++++..   ....+++++............+                ....+.+... .+
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~~~----------------~~~~~~~~~~-~~   61 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLADPD----------------LLEYFLELIK-PG   61 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhhhh----------------hHHHHHHhhc-cC
Confidence            36899999999999999999998765   2345667766543321110000                1112222222 35


Q ss_pred             eEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhh-----ccCCceeeEEccCCCHHHH
Q 044858          252 KILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLS-----CEMDCQQNFVVDVLNDKEA  312 (426)
Q Consensus       252 ~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~-----~~~~~~~~~~l~~L~~~e~  312 (426)
                      +.+|+||++....+|......+.+..+..+|++|+.+.....     ...+....+++.||+-.|.
T Consensus        62 ~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   62 KKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             CcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            789999999999888887666655556789999999876542     2334556889999997763

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.91  E-value=1.4e-07  Score=90.92  Aligned_cols=196  Identities=15%  Similarity=0.187  Sum_probs=111.7

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .....++|.+..++.+...+..++. +.+.++|+.|+||||+|+.+.+.........       ..+........++...
T Consensus        13 ~~~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~-------~~pc~~c~~c~~~~~~   85 (363)
T PRK14961         13 QYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGIT-------SNPCRKCIICKEIEKG   85 (363)
T ss_pred             CchhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCCCHHHHHHhcC
Confidence            3556788999999998888876654 4678999999999999999988764211110       0000000011111110


Q ss_pred             hCCCc---c--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecch-hhhhc
Q 044858          227 LGLKI---D--QESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQ-DVLSC  294 (426)
Q Consensus       227 l~~~~---~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~-~va~~  294 (426)
                      .....   +  ..........+.+.+.    .+++-++|+|+++...  .++.+...+......+++|++|.+. .+...
T Consensus        86 ~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~t  165 (363)
T PRK14961         86 LCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKT  165 (363)
T ss_pred             CCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHH
Confidence            00000   0  0011122223333221    2345699999998653  3555544443334466777766543 33222


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      ..+....+++.+++.++..+.+.+.+..... .--.+.+..|++.++|.|-.+....
T Consensus       166 I~SRc~~~~~~~l~~~el~~~L~~~~~~~g~-~i~~~al~~ia~~s~G~~R~al~~l  221 (363)
T PRK14961        166 ILSRCLQFKLKIISEEKIFNFLKYILIKESI-DTDEYALKLIAYHAHGSMRDALNLL  221 (363)
T ss_pred             HHhhceEEeCCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            2333578999999999999998887643221 1123567789999999886444433

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

Probab=98.90  E-value=5.9e-09  Score=85.19  Aligned_cols=115  Identities=24%  Similarity=0.345  Sum_probs=80.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc---CccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-cCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN---NLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-ESESVRAWRLLEQL  247 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~---~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-~~~~~~~~~l~~~l  247 (426)
                      .+.+.|+|++|+|||++++.+.+.....   ..-..++|+.++...+...+...|+.+++.+... .+.......+.+.+
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l   83 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDAL   83 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHH
Confidence            4678999999999999999999876431   0123467999988889999999999999987766 44555667777778


Q ss_pred             hcCCeEEEEEeCCCCc-c--ChhhhcCCCCCCCCCeEEEEeecc
Q 044858          248 KKETKILIILDDIWGS-L--DLEAIGIPLADDNGGCKVLLTARS  288 (426)
Q Consensus       248 ~~~k~~LlVlDdv~~~-~--~~~~l~~~l~~~~~~s~iivTtr~  288 (426)
                      .+.+..+|||||++.. .  .++.+....  +..+.++|+..+.
T Consensus        84 ~~~~~~~lviDe~~~l~~~~~l~~l~~l~--~~~~~~vvl~G~~  125 (131)
T PF13401_consen   84 DRRRVVLLVIDEADHLFSDEFLEFLRSLL--NESNIKVVLVGTP  125 (131)
T ss_dssp             HHCTEEEEEEETTHHHHTHHHHHHHHHHT--CSCBEEEEEEESS
T ss_pred             HhcCCeEEEEeChHhcCCHHHHHHHHHHH--hCCCCeEEEEECh
Confidence            7766789999999765 2  222332222  2567788888776

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.88  E-value=8.4e-08  Score=91.10  Aligned_cols=186  Identities=10%  Similarity=0.102  Sum_probs=109.9

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccce-EEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEK-VISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      ....++|+++.++.+..++..+..+.+.++|++|+||||+++.+.+...... +.. .+-++.+...... ...+.+..+
T Consensus        15 ~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~-~~~~~i~~~~~~~~~~~-~~~~~i~~~   92 (319)
T PRK00440         15 TLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGED-WRENFLELNASDERGID-VIRNKIKEF   92 (319)
T ss_pred             cHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCc-cccceEEeccccccchH-HHHHHHHHH
Confidence            4566889999999999998877777789999999999999999998764322 221 1122222222211 111221111


Q ss_pred             CCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecchh-hhhccCCceeeEEc
Q 044858          228 GLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQD-VLSCEMDCQQNFVV  304 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~~-va~~~~~~~~~~~l  304 (426)
                      ....+              .....+-++++|+++...  ....+...+......+.+|+++.... ...........+++
T Consensus        93 ~~~~~--------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~  158 (319)
T PRK00440         93 ARTAP--------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRF  158 (319)
T ss_pred             HhcCC--------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeee
Confidence            10000              001235689999987542  23333333322334567777764322 11111123457899


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      .++++++....+.+.+...... --.+....+++.++|.+.-+....
T Consensus       159 ~~l~~~ei~~~l~~~~~~~~~~-i~~~al~~l~~~~~gd~r~~~~~l  204 (319)
T PRK00440        159 SPLKKEAVAERLRYIAENEGIE-ITDDALEAIYYVSEGDMRKAINAL  204 (319)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999999999998877532211 124567889999999887654443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.88  E-value=3.8e-08  Score=101.58  Aligned_cols=185  Identities=15%  Similarity=0.198  Sum_probs=113.4

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccE-EEEEcCCCCcHHHHHHHHHHHhhhcCc-------------------cceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNM-IGVYGMGGIGKTTLVKEVGRQAKENNL-------------------FEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~v-i~I~G~~GiGKTtLa~~v~~~~~~~~~-------------------f~~~~w  207 (426)
                      ..+..++|.+..+..|.+++..++..- +.++|+.|+||||+|+.+++.......                   |..+++
T Consensus        13 ~tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviE   92 (944)
T PRK14949         13 ATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIE   92 (944)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEE
Confidence            356778999999999988888776654 589999999999999999987643211                   111122


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT  285 (426)
                      +..+....+.+ +++|...+                ...-..+++-++|||+++..  ...+.|...+-.-...+++|++
T Consensus        93 idAas~~kVDd-IReLie~v----------------~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949         93 VDAASRTKVDD-TRELLDNV----------------QYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             eccccccCHHH-HHHHHHHH----------------HhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEE
Confidence            22211111111 12222211                11111356779999999755  3455544444332345666655


Q ss_pred             ecc-hhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          286 ARS-QDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       286 tr~-~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      |.+ ..+..........|++.+|+.++....+.+.+.... -..-.+....|++.++|.|--+..+
T Consensus       156 TTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~Eg-I~~edeAL~lIA~~S~Gd~R~ALnL  220 (944)
T PRK14949        156 TTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQ-LPFEAEALTLLAKAANGSMRDALSL  220 (944)
T ss_pred             CCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            544 443322233457899999999999999988774322 1222456788999999988655444

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.86  E-value=2.7e-07  Score=87.25  Aligned_cols=176  Identities=15%  Similarity=0.195  Sum_probs=113.6

Q ss_pred             ccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhh----hcCccceEEEEEe-cCCcCHHHHHHHHH
Q 044858          151 MHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAK----ENNLFEKVISSRV-SQTPQIKEIQREIA  224 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~----~~~~f~~~~wv~v-~~~~~~~~il~~i~  224 (426)
                      .+++|.+..++.+...+..++. +.+.++|+.|+||||+|+.+++...    ...|+|...|... +....+.+ .+++.
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            4567888888889988876654 5678999999999999999998642    2346666555442 23333333 22333


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCC--CccChhhhcCCCCCCCCCeEEEEeecchhhh-hccCCceee
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIW--GSLDLEAIGIPLADDNGGCKVLLTARSQDVL-SCEMDCQQN  301 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~--~~~~~~~l~~~l~~~~~~s~iivTtr~~~va-~~~~~~~~~  301 (426)
                      +.+....               . .+++-++|+|+++  +...++.+...+..-..++.+|++|.+.... ....+....
T Consensus        83 ~~~~~~p---------------~-~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~  146 (313)
T PRK05564         83 EEVNKKP---------------Y-EGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQI  146 (313)
T ss_pred             HHHhcCc---------------c-cCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhcee
Confidence            3322110               0 1345567777764  4456777766665555688888888665432 212344579


Q ss_pred             EEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHH
Q 044858          302 FVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       302 ~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                      +++.++++++....+.+.... .    -.+.+..++..++|.|.-+.
T Consensus       147 ~~~~~~~~~~~~~~l~~~~~~-~----~~~~~~~l~~~~~g~~~~a~  188 (313)
T PRK05564        147 YKLNRLSKEEIEKFISYKYND-I----KEEEKKSAIAFSDGIPGKVE  188 (313)
T ss_pred             eeCCCcCHHHHHHHHHHHhcC-C----CHHHHHHHHHHcCCCHHHHH
Confidence            999999999998888765431 1    12346778899999886543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.86  E-value=3.3e-08  Score=88.94  Aligned_cols=170  Identities=16%  Similarity=0.167  Sum_probs=102.0

Q ss_pred             hHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccC
Q 044858          156 RKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQES  235 (426)
Q Consensus       156 R~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~  235 (426)
                      .+..++.+..++.......+.|+|++|+|||+||+.+++.....  ....++++++.-.+      ..            
T Consensus        22 ~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~--~~~~~~i~~~~~~~------~~------------   81 (226)
T TIGR03420        22 NAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER--GKSAIYLPLAELAQ------AD------------   81 (226)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc--CCcEEEEeHHHHHH------hH------------
Confidence            45567777776655566789999999999999999999876533  33455665432211      00            


Q ss_pred             cHHHHHHHHHHHhcCCeEEEEEeCCCCcc---Chh-hhcCCCCC-CCCCeEEEEeecchhhhh--------ccCCceeeE
Q 044858          236 ESVRAWRLLEQLKKETKILIILDDIWGSL---DLE-AIGIPLAD-DNGGCKVLLTARSQDVLS--------CEMDCQQNF  302 (426)
Q Consensus       236 ~~~~~~~l~~~l~~~k~~LlVlDdv~~~~---~~~-~l~~~l~~-~~~~s~iivTtr~~~va~--------~~~~~~~~~  302 (426)
                           ..+...+.  +.-+|||||++...   .|. .+...+.. ...+.++|+||+......        ........+
T Consensus        82 -----~~~~~~~~--~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i  154 (226)
T TIGR03420        82 -----PEVLEGLE--QADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVF  154 (226)
T ss_pred             -----HHHHhhcc--cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeE
Confidence                 01112222  23489999997653   232 23222211 122347888887543210        011123579


Q ss_pred             EccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          303 VVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       303 ~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      ++.++++++...++...+.... -+--.+..+.|.+.++|.|..+..+...
T Consensus       155 ~l~~l~~~e~~~~l~~~~~~~~-~~~~~~~l~~L~~~~~gn~r~L~~~l~~  204 (226)
T TIGR03420       155 QLPPLSDEEKIAALQSRAARRG-LQLPDEVADYLLRHGSRDMGSLMALLDA  204 (226)
T ss_pred             ecCCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHhccCCHHHHHHHHHH
Confidence            9999999999999987653211 1112455677888888888877666443

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.85  E-value=5.1e-08  Score=97.48  Aligned_cols=200  Identities=14%  Similarity=0.141  Sum_probs=113.8

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ..+..++|.+..++.|.+.+..++.. .+.++|+.|+||||+|+.+.+.......-... -+ .+..+......+.|...
T Consensus        13 qtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~-g~-~~~PCG~C~sC~~I~aG   90 (700)
T PRK12323         13 RDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEG-GI-TAQPCGQCRACTEIDAG   90 (700)
T ss_pred             CcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccc-cC-CCCCCcccHHHHHHHcC
Confidence            35667899999999999998877654 56899999999999999998765431000000 00 00000001111111100


Q ss_pred             -----hCCCccccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEE-eecchhhhhc
Q 044858          227 -----LGLKIDQESESVRAWRLLEQL----KKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLL-TARSQDVLSC  294 (426)
Q Consensus       227 -----l~~~~~~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iiv-Ttr~~~va~~  294 (426)
                           +..+.......+.+..+.+.+    ..++.-++|||+++..  ..++.|...+-.-..++++|+ ||....+...
T Consensus        91 ~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpT  170 (700)
T PRK12323         91 RFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVT  170 (700)
T ss_pred             CCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhH
Confidence                 000000001112222333332    1356679999999865  345555544433334555555 4444544422


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      ..+....+.+++++.++..+.+.+.+....... ..+..+.|++.++|.|.-...+
T Consensus       171 IrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~-d~eAL~~IA~~A~Gs~RdALsL  225 (700)
T PRK12323        171 VLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAH-EVNALRLLAQAAQGSMRDALSL  225 (700)
T ss_pred             HHHHHHhcccCCCChHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            334457899999999999999988775322111 2345688999999999755444

>PLN03025 replication factor C subunit; Provisional

Probab=98.85  E-value=9e-08  Score=90.65  Aligned_cols=187  Identities=12%  Similarity=0.091  Sum_probs=109.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .....++|.++.+..|..++..++.+.+.++|++|+||||+|..+.+..... .|. .++-++.+...+.. ..+++++.
T Consensus        10 ~~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~-~~~~~~~eln~sd~~~~~-~vr~~i~~   87 (319)
T PLN03025         10 TKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGP-NYKEAVLELNASDDRGID-VVRNKIKM   87 (319)
T ss_pred             CCHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcc-cCccceeeecccccccHH-HHHHHHHH
Confidence            3556788988888888887777777778899999999999999999876432 122 12222333322222 22222222


Q ss_pred             hCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecch-hhhhccCCceeeEE
Q 044858          227 LGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMDCQQNFV  303 (426)
Q Consensus       227 l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~~~~~~~  303 (426)
                      +.....             .+..++.-+++||+++...  ....+...+......+++|+++... .+..........++
T Consensus        88 ~~~~~~-------------~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~  154 (319)
T PLN03025         88 FAQKKV-------------TLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVR  154 (319)
T ss_pred             HHhccc-------------cCCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhccc
Confidence            110000             0012356799999998653  2222322222223456777766543 22111122346899


Q ss_pred             ccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          304 VDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       304 l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      ++++++++....+...+......- -.+....|++.++|..-.+...
T Consensus       155 f~~l~~~~l~~~L~~i~~~egi~i-~~~~l~~i~~~~~gDlR~aln~  200 (319)
T PLN03025        155 FSRLSDQEILGRLMKVVEAEKVPY-VPEGLEAIIFTADGDMRQALNN  200 (319)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            999999999999988774322111 1346788899999877554433

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.84  E-value=1.5e-07  Score=93.44  Aligned_cols=180  Identities=14%  Similarity=0.184  Sum_probs=111.6

Q ss_pred             CCcccccchHHHHHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCcc-----------------------c
Q 044858          148 QDFMHFESRKSTLKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLF-----------------------E  203 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f-----------------------~  203 (426)
                      ..+..++|.+..+..|...+..++ .+.+.++|+.|+||||+|+.+++........                       .
T Consensus        18 ~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~   97 (507)
T PRK06645         18 SNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHP   97 (507)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCC
Confidence            356678899998888888776655 3578899999999999999998876432110                       0


Q ss_pred             eEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCC
Q 044858          204 KVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDN  277 (426)
Q Consensus       204 ~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~  277 (426)
                      .++.+..+...++                     +.+..+.+...    .+++-++|+|+++..  ..++.+...+....
T Consensus        98 Dv~eidaas~~~v---------------------d~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp  156 (507)
T PRK06645         98 DIIEIDAASKTSV---------------------DDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPP  156 (507)
T ss_pred             cEEEeeccCCCCH---------------------HHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcC
Confidence            1111111111111                     22222222221    246679999999865  34666654444334


Q ss_pred             CCeEEEE-eecchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHH
Q 044858          278 GGCKVLL-TARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVP  349 (426)
Q Consensus       278 ~~s~iiv-Ttr~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~  349 (426)
                      ..+.+|+ ||+...+..........+++.+++.++....+.+.+....... ..+....|++.++|.+.-+..
T Consensus       157 ~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~i-e~eAL~~Ia~~s~GslR~al~  228 (507)
T PRK06645        157 PHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKT-DIEALRIIAYKSEGSARDAVS  228 (507)
T ss_pred             CCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHH
Confidence            4556554 4444444322233446899999999999999998885332221 234567799999998755433

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

Probab=98.82  E-value=7.1e-08  Score=88.41  Aligned_cols=160  Identities=17%  Similarity=0.198  Sum_probs=104.1

Q ss_pred             HHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHH
Q 044858          165 DALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLL  244 (426)
Q Consensus       165 ~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~  244 (426)
                      +.+..+..+.+.+||++|+||||||+.+.+..+...    ..||..|....-..-.+.|.++-.             . .
T Consensus       155 s~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq-------------~-~  216 (554)
T KOG2028|consen  155 SLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQ-------------N-E  216 (554)
T ss_pred             HHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHH-------------H-H
Confidence            344467888899999999999999999998877543    457777765544444455544321             1 1


Q ss_pred             HHHhcCCeEEEEEeCCCCccCh-hhhcCCCCCCCCCeEEEE--eecchhhh--hccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          245 EQLKKETKILIILDDIWGSLDL-EAIGIPLADDNGGCKVLL--TARSQDVL--SCEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       245 ~~l~~~k~~LlVlDdv~~~~~~-~~l~~~l~~~~~~s~iiv--Ttr~~~va--~~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      .. ..++|.+|++|+|+....- ++  ..+|...+|.-++|  ||.+....  ........++.|++|+.++...++.+.
T Consensus       217 ~~-l~krkTilFiDEiHRFNksQQD--~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~ra  293 (554)
T KOG2028|consen  217 KS-LTKRKTILFIDEIHRFNKSQQD--TFLPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRA  293 (554)
T ss_pred             Hh-hhcceeEEEeHHhhhhhhhhhh--cccceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHH
Confidence            11 2358999999999754221 22  24556667876666  66665331  123345679999999999999999885


Q ss_pred             hC---C------CCCCC---chHHHHHHHHHHcCCchH
Q 044858          320 TG---D------CIENG---ELKSVVTEVVKECAGLPI  345 (426)
Q Consensus       320 ~~---~------~~~~~---~~~~~~~~i~~~c~GlPl  345 (426)
                      ..   .      ..+.+   -...+.+-++..|+|-..
T Consensus       294 ia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR  331 (554)
T KOG2028|consen  294 IASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDAR  331 (554)
T ss_pred             HHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHH
Confidence            42   1      11221   124567778888998754

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

Probab=98.82  E-value=8.8e-07  Score=84.66  Aligned_cols=199  Identities=19%  Similarity=0.239  Sum_probs=128.0

Q ss_pred             cccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          152 HFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .+.+|+.+++++...|.    ++.+..+.|+|.+|+|||+.++.+.+.......=...++|++-...+...++..|++++
T Consensus        18 ~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~   97 (366)
T COG1474          18 ELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKL   97 (366)
T ss_pred             cccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHc
Confidence            37899999999988775    44555699999999999999999999887542222278999999999999999999999


Q ss_pred             C-CCccccCcHHHHHHHHHHHhc-CCeEEEEEeCCCCccCh--hhhcCCCCC-CCCCeEEEE--eecchhhh----hc--
Q 044858          228 G-LKIDQESESVRAWRLLEQLKK-ETKILIILDDIWGSLDL--EAIGIPLAD-DNGGCKVLL--TARSQDVL----SC--  294 (426)
Q Consensus       228 ~-~~~~~~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~~~--~~l~~~l~~-~~~~s~iiv--Ttr~~~va----~~--  294 (426)
                      + .+....+..+....+.+.+.. ++.+++|||+++....-  +.+...+.. ....++|++  .+-+....    ..  
T Consensus        98 ~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv~  177 (366)
T COG1474          98 GKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVK  177 (366)
T ss_pred             CCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhhh
Confidence            6 233334555566667777654 67899999999755322  222222211 112454443  33333211    00  


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhC----CCCCCCchHHHHHHHHHHcC-CchHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTG----DCIENGELKSVVTEVVKECA-GLPIAIVPI  350 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~----~~~~~~~~~~~~~~i~~~c~-GlPlai~~~  350 (426)
                      ..-....+..+|-+.+|-.+++..++.    ....+++.-+++..++..-+ ---.||..+
T Consensus       178 s~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidil  238 (366)
T COG1474         178 SSLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDIL  238 (366)
T ss_pred             hccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHH
Confidence            111233588999999999999998874    22223333334444444444 455555554

>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=98.82  E-value=8.1e-08  Score=83.61  Aligned_cols=180  Identities=15%  Similarity=0.165  Sum_probs=96.8

Q ss_pred             cCCcccccchHHHHHHHHHHhc-----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHH
Q 044858          147 TQDFMHFESRKSTLKGILDALS-----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       147 ~~~~~~~~gR~~~~~~l~~~l~-----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~  221 (426)
                      |....+|+|.++.+..+.-.+.     +....-+.++|++|+||||||..+.+.....  |.   +.+.+.-....++  
T Consensus        20 P~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~--~~---~~sg~~i~k~~dl--   92 (233)
T PF05496_consen   20 PKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVN--FK---ITSGPAIEKAGDL--   92 (233)
T ss_dssp             -SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT----EE---EEECCC--SCHHH--
T ss_pred             CCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCC--eE---eccchhhhhHHHH--
Confidence            3467889999988877554433     2346778999999999999999999998754  32   2222111111111  


Q ss_pred             HHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC---------hhhhcCC-CCCCC-----------CCe
Q 044858          222 EIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD---------LEAIGIP-LADDN-----------GGC  280 (426)
Q Consensus       222 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~---------~~~l~~~-l~~~~-----------~~s  280 (426)
                                         ..+...+.  ++-+|++|+++....         .++.... ....+           +-+
T Consensus        93 -------------------~~il~~l~--~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FT  151 (233)
T PF05496_consen   93 -------------------AAILTNLK--EGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFT  151 (233)
T ss_dssp             -------------------HHHHHT----TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----E
T ss_pred             -------------------HHHHHhcC--CCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCce
Confidence                               12222222  356788898875421         1111100 00111           123


Q ss_pred             EEEEeecchhhhhccCCce-eeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhh
Q 044858          281 KVLLTARSQDVLSCEMDCQ-QNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALK  355 (426)
Q Consensus       281 ~iivTtr~~~va~~~~~~~-~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~  355 (426)
                      -|=-|||...+........ ...+|+..+.+|-.+++.+.+..... +-.++.+.+|++.|.|-|--..-+.+..+
T Consensus       152 ligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i-~i~~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  152 LIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNI-EIDEDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             EEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT--EE-HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             EeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCC-CcCHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            3445888765543222223 45689999999999999887643221 22356799999999999987666555444

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=98.80  E-value=2.5e-07  Score=92.11  Aligned_cols=196  Identities=13%  Similarity=0.099  Sum_probs=111.7

Q ss_pred             CcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .+..++|.+..++.|..++..++.+ .+.++|++|+||||+|+.+++.....+.+...+|.|.+... +..-...-+..+
T Consensus        12 ~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~-i~~~~h~dv~el   90 (504)
T PRK14963         12 TFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLA-VRRGAHPDVLEI   90 (504)
T ss_pred             CHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHH-HhcCCCCceEEe
Confidence            4567889998888888888766654 56999999999999999998876532222212222211000 000000000000


Q ss_pred             CCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeec-chhhhhccCCcee
Q 044858          228 GLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTAR-SQDVLSCEMDCQQ  300 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr-~~~va~~~~~~~~  300 (426)
                      ..  ........+..+.+.+.    .+++-++|||+++..  ..++.+...+......+.+|++|. ...+.........
T Consensus        91 ~~--~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~  168 (504)
T PRK14963         91 DA--ASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQ  168 (504)
T ss_pred             cc--cccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceE
Confidence            00  00011122222322221    245679999999754  335555444433334555555554 3333222234456


Q ss_pred             eEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHH
Q 044858          301 NFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       301 ~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                      .+++.+++.++....+.+.+....... -.+....|++.++|.+--+.
T Consensus       169 ~~~f~~ls~~el~~~L~~i~~~egi~i-~~~Al~~ia~~s~GdlR~al  215 (504)
T PRK14963        169 HFRFRRLTEEEIAGKLRRLLEAEGREA-EPEALQLVARLADGAMRDAE  215 (504)
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHH
Confidence            899999999999999998875322111 24567889999999886554

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.79  E-value=1.3e-07  Score=94.89  Aligned_cols=181  Identities=12%  Similarity=0.176  Sum_probs=112.8

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------ccceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENN-------------------LFEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~-------------------~f~~~~w  207 (426)
                      ..+..++|.+.....|..++..++. ..+.++|+.|+||||+|+.+.+......                   .|..++.
T Consensus        12 ktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviE   91 (702)
T PRK14960         12 RNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIE   91 (702)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEE
Confidence            3567789999999999999887664 5778999999999999999987753211                   1111222


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeE
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL----KKETKILIILDDIWGS--LDLEAIGIPLADDNGGCK  281 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~  281 (426)
                      +..+....+.                     .+..++...    ..+++-++|||+++..  ...+.+...+.....+++
T Consensus        92 IDAAs~~~Vd---------------------dIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~  150 (702)
T PRK14960         92 IDAASRTKVE---------------------DTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVK  150 (702)
T ss_pred             ecccccCCHH---------------------HHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcE
Confidence            2222111211                     222222222    1246679999999865  344444443433334567


Q ss_pred             EEEeecch-hhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          282 VLLTARSQ-DVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       282 iivTtr~~-~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      +|++|.+. .+..........+++.+++.++....+.+.+...... --.+....|++.++|.+..+..+
T Consensus       151 FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~-id~eAL~~IA~~S~GdLRdALnL  219 (702)
T PRK14960        151 FLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIA-ADQDAIWQIAESAQGSLRDALSL  219 (702)
T ss_pred             EEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            77777553 2221123445789999999999999998877532221 22456778999999987555443

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.77  E-value=4.3e-07  Score=86.40  Aligned_cols=198  Identities=14%  Similarity=0.093  Sum_probs=115.1

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCc--cceEEEEEecCCcCHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNL--FEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~--f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .....++|.++....+...+..++. ..+.|+|+.|+||||+|..+.+..-....  +...   .....+......+.+.
T Consensus        20 ~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~---~~~~~~~~c~~c~~i~   96 (351)
T PRK09112         20 SENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPE---TLADPDPASPVWRQIA   96 (351)
T ss_pred             CchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcc---ccCCCCCCCHHHHHHH
Confidence            3566789999999999998887664 46899999999999999999887643110  1110   0011111112333332


Q ss_pred             HHhC-------CCccc-------cCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeE-EE
Q 044858          225 EKLG-------LKIDQ-------ESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCK-VL  283 (426)
Q Consensus       225 ~~l~-------~~~~~-------~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~-ii  283 (426)
                      ..-.       .+.+.       .-..+.+..+.+++.    .+++-++|+|+++...  ..+.+...+..-..++. |+
T Consensus        97 ~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiL  176 (351)
T PRK09112         97 QGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFIL  176 (351)
T ss_pred             cCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEE
Confidence            2210       01000       011233444555543    3567799999998652  23333333322222344 44


Q ss_pred             EeecchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          284 LTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       284 vTtr~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      +|++...+.....+....+++.+++.++..+++.+......   ...+....+++.++|.|.....+.
T Consensus       177 it~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~---~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        177 ISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG---SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             EECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC---CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            55444433322233457999999999999999987432211   124457789999999998665443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.75  E-value=4e-07  Score=90.95  Aligned_cols=186  Identities=14%  Similarity=0.175  Sum_probs=110.9

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhc-------------------CccceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKEN-------------------NLFEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~-------------------~~f~~~~w  207 (426)
                      ..+..++|.+..+..|...+..++. ..+.++|+.|+||||+|+.+.+.....                   +.|...++
T Consensus        13 ~~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlie   92 (546)
T PRK14957         13 QSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIE   92 (546)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEE
Confidence            3566788999999999988886654 457899999999999999998765321                   11222233


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT  285 (426)
                      +.......+.++ ++++..+                ...-..+++-++|+|+++..  ...+.+...+......+.+|++
T Consensus        93 idaas~~gvd~i-r~ii~~~----------------~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~  155 (546)
T PRK14957         93 IDAASRTGVEET-KEILDNI----------------QYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILA  155 (546)
T ss_pred             eecccccCHHHH-HHHHHHH----------------HhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEE
Confidence            332222222211 1121111                11111245679999999754  3344554444333345555554


Q ss_pred             e-cchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHHH
Q 044858          286 A-RSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPIA  351 (426)
Q Consensus       286 t-r~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~~  351 (426)
                      | ....+..........+++.+++.++....+.+.+..... ..-......|++.++|.+- |+..+-
T Consensus       156 Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi-~~e~~Al~~Ia~~s~GdlR~alnlLe  222 (546)
T PRK14957        156 TTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENI-NSDEQSLEYIAYHAKGSLRDALSLLD  222 (546)
T ss_pred             ECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4 433333222344579999999999999888876643221 1224566789999999665 444443

>PRK04195 replication factor C large subunit; Provisional

Probab=98.75  E-value=2.5e-07  Score=92.56  Aligned_cols=185  Identities=15%  Similarity=0.158  Sum_probs=112.1

Q ss_pred             CCcccccchHHHHHHHHHHhcc----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSN----RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~----~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      .....++|++..++.+.+|+..    ...+.+.|+|++|+||||+|+.+++...    |+ .+-++.+...+. +.+..+
T Consensus        11 ~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~----~~-~ielnasd~r~~-~~i~~~   84 (482)
T PRK04195         11 KTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG----WE-VIELNASDQRTA-DVIERV   84 (482)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC----CC-EEEEcccccccH-HHHHHH
Confidence            3456789999999998888762    2267899999999999999999998864    32 233444433322 233333


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC------hhhhcCCCCCCCCCeEEEEeecchhhh-h-cc
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD------LEAIGIPLADDNGGCKVLLTARSQDVL-S-CE  295 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~------~~~l~~~l~~~~~~s~iivTtr~~~va-~-~~  295 (426)
                      +.......              .+...++-+||||+++....      +..+...+.  ..++.||+|+.+..-. . ..
T Consensus        85 i~~~~~~~--------------sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~~k~L  148 (482)
T PRK04195         85 AGEAATSG--------------SLFGARRKLILLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPYDPSLREL  148 (482)
T ss_pred             HHHhhccC--------------cccCCCCeEEEEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCccccchhhH
Confidence            32211100              01112578999999976532      333333222  2344566666443211 1 11


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhh
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALK  355 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~  355 (426)
                      ......+.+.+++.++....+.+.+......- -.+....|++.++|..-.+......+.
T Consensus       149 rsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i-~~eaL~~Ia~~s~GDlR~ain~Lq~~a  207 (482)
T PRK04195        149 RNACLMIEFKRLSTRSIVPVLKRICRKEGIEC-DDEALKEIAERSGGDLRSAINDLQAIA  207 (482)
T ss_pred             hccceEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            23356899999999999999888774222111 145678899999997776655444443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.75  E-value=1.7e-07  Score=95.07  Aligned_cols=196  Identities=14%  Similarity=0.157  Sum_probs=112.9

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ..+..++|.+..+..|...+..++.. .+.++|+.|+||||+|+.+.+.......+.       +..+......+.|...
T Consensus        13 ~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~-------~~pCg~C~~C~~i~~g   85 (647)
T PRK07994         13 QTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGIT-------ATPCGECDNCREIEQG   85 (647)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCC-------CCCCCCCHHHHHHHcC
Confidence            35677899999999999888876654 468999999999999999987654321100       0011111122222110


Q ss_pred             hCCC---ccc--cCcHHHHHHHHHHH----hcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhc
Q 044858          227 LGLK---IDQ--ESESVRAWRLLEQL----KKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSC  294 (426)
Q Consensus       227 l~~~---~~~--~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~  294 (426)
                      -...   .+.  ....+.+..+.+.+    ..+++-++|||+++..  ...+.+...+-.-...+++|++|.+ ..+...
T Consensus        86 ~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~T  165 (647)
T PRK07994         86 RFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVT  165 (647)
T ss_pred             CCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchH
Confidence            0000   000  01112222333322    1356779999999755  3445444333222335555554444 444322


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      .......|++.+|+.++....+.+.+...... ........|++.++|.|--+..+.
T Consensus       166 I~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~-~e~~aL~~Ia~~s~Gs~R~Al~ll  221 (647)
T PRK07994        166 ILSRCLQFHLKALDVEQIRQQLEHILQAEQIP-FEPRALQLLARAADGSMRDALSLT  221 (647)
T ss_pred             HHhhheEeeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            23345799999999999999998876422211 224566789999999887554443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.75  E-value=3e-07  Score=89.60  Aligned_cols=196  Identities=14%  Similarity=0.135  Sum_probs=114.4

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ..+..++|.+..+..|..++..++.+ .+.++|+.|+||||+|+.+.+..........   ..+....+-    ..+...
T Consensus        15 ~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~---~pCg~C~sC----~~i~~g   87 (484)
T PRK14956         15 QFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGN---EPCNECTSC----LEITKG   87 (484)
T ss_pred             CCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCc---cccCCCcHH----HHHHcc
Confidence            35677899999999988888877754 5899999999999999999887543211000   000001111    111111


Q ss_pred             hCCC---cc--ccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEE-eecchhhhhc
Q 044858          227 LGLK---ID--QESESVRAWRLLEQL----KKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLL-TARSQDVLSC  294 (426)
Q Consensus       227 l~~~---~~--~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iiv-Ttr~~~va~~  294 (426)
                      ....   .+  .....+.+..+.+.+    ..++.-++|||+++..  ..++.+...+......+.+|+ ||....+...
T Consensus        88 ~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~T  167 (484)
T PRK14956         88 ISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPET  167 (484)
T ss_pred             CCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHH
Confidence            1000   00  001112223333322    2356679999999855  446665444433233555554 4444444332


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      .......|.+.+++.++..+.+.+.+...... --.+....|++.++|.+.-...+.
T Consensus       168 I~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~-~e~eAL~~Ia~~S~Gd~RdAL~lL  223 (484)
T PRK14956        168 ILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQ-YDQEGLFWIAKKGDGSVRDMLSFM  223 (484)
T ss_pred             HHhhhheeeecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCChHHHHHHHH
Confidence            33445789999999999999998876532211 124567889999999986444443

>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=98.74  E-value=1.2e-07  Score=78.68  Aligned_cols=122  Identities=17%  Similarity=0.149  Sum_probs=72.1

Q ss_pred             chHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc
Q 044858          155 SRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE  234 (426)
Q Consensus       155 gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~  234 (426)
                      |++..+..+...+..+..+.+.|+|++|+|||++++.+++.....  -..++++..............+...        
T Consensus         2 ~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~~~~~~~~~~~~~~~--------   71 (151)
T cd00009           2 GQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP--GAPFLYLNASDLLEGLVVAELFGHF--------   71 (151)
T ss_pred             chHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC--CCCeEEEehhhhhhhhHHHHHhhhh--------
Confidence            678888888888877666789999999999999999999987522  2345566554433322211111100        


Q ss_pred             CcHHHHHHHHHHHhcCCeEEEEEeCCCCc-----cChhhhcCCCCC---CCCCeEEEEeecchh
Q 044858          235 SESVRAWRLLEQLKKETKILIILDDIWGS-----LDLEAIGIPLAD---DNGGCKVLLTARSQD  290 (426)
Q Consensus       235 ~~~~~~~~l~~~l~~~k~~LlVlDdv~~~-----~~~~~l~~~l~~---~~~~s~iivTtr~~~  290 (426)
                          ............++.++++||++..     ..+..+...+..   ...+..+|+||....
T Consensus        72 ----~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          72 ----LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             ----hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                0001111112346789999999854     122222222211   135778888888654

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.73  E-value=4.6e-07  Score=89.56  Aligned_cols=201  Identities=18%  Similarity=0.205  Sum_probs=115.7

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCc-------------------cceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNL-------------------FEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~-------------------f~~~~w  207 (426)
                      .....++|.+.....|...+..++. +.+.++|++|+||||+|+.+.+.......                   +.....
T Consensus        11 ~~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~e   90 (472)
T PRK14962         11 KTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIE   90 (472)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEE
Confidence            3566789998888888887777665 45789999999999999999876542110                   011222


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT  285 (426)
                      +..+......++ ++|......                .-..+++-++|+|+++..  ...+.+...+......+.+|++
T Consensus        91 l~aa~~~gid~i-R~i~~~~~~----------------~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ila  153 (472)
T PRK14962         91 LDAASNRGIDEI-RKIRDAVGY----------------RPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLA  153 (472)
T ss_pred             EeCcccCCHHHH-HHHHHHHhh----------------ChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEE
Confidence            222222222221 122221110                001245679999999754  2334443333322234555544


Q ss_pred             ecc-hhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-chHHHHHHHHHhh--c-C-CH
Q 044858          286 ARS-QDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAG-LPIAIVPIAKALK--N-K-SP  359 (426)
Q Consensus       286 tr~-~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G-lPlai~~~~~~l~--~-~-~~  359 (426)
                      |.+ ..+..........+.+.+++.++....+.+.+..... .--.+....|++.++| ++.++..+-.+..  + . +.
T Consensus       154 ttn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi-~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~~~~It~  232 (472)
T PRK14962        154 TTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGI-EIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITL  232 (472)
T ss_pred             eCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCH
Confidence            443 3333223344578999999999999998887742211 1124567788887765 5677777765443  1 2 55


Q ss_pred             HHHHHHH
Q 044858          360 YEWRNAL  366 (426)
Q Consensus       360 ~~w~~~l  366 (426)
                      +....++
T Consensus       233 e~V~~~l  239 (472)
T PRK14962        233 ETVHEAL  239 (472)
T ss_pred             HHHHHHH
Confidence            5554443

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

Probab=98.73  E-value=5.4e-08  Score=84.49  Aligned_cols=49  Identities=22%  Similarity=0.349  Sum_probs=35.1

Q ss_pred             cccchHHHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC
Q 044858          152 HFESRKSTLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN  200 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~  200 (426)
                      .|+||+++++++.+.+.   ....+++.|+|++|+|||+|.+.++.......
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~   52 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAERG   52 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            48999999999999993   44578999999999999999999999887653

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.71  E-value=4.5e-07  Score=92.83  Aligned_cols=204  Identities=15%  Similarity=0.100  Sum_probs=119.5

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc---eEEEEEecCC---cCHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE---KVISSRVSQT---PQIKEIQR  221 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~---~~~wv~v~~~---~~~~~il~  221 (426)
                      ..+..++|++..+..+...+.......+.|+|++|+||||||+.+++.......+.   ..-|+.+...   .+...+..
T Consensus       151 ~~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~  230 (615)
T TIGR02903       151 RAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTN  230 (615)
T ss_pred             CcHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhH
Confidence            34567889998888888877766677899999999999999999988765433331   2234444321   12222211


Q ss_pred             HH---------------HHHhCCCcc------------------ccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cCh
Q 044858          222 EI---------------AEKLGLKID------------------QESESVRAWRLLEQLKKETKILIILDDIWGS--LDL  266 (426)
Q Consensus       222 ~i---------------~~~l~~~~~------------------~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~  266 (426)
                      .+               +...+....                  ..-+......+.+.+. .+++.++-|+.|..  ..|
T Consensus       231 ~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le-~~~v~~~~~~~~~~~~~~~  309 (615)
T TIGR02903       231 PLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLE-DKRVEFSSSYYDPDDPNVP  309 (615)
T ss_pred             HhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHh-hCeEEeecceeccCCcccc
Confidence            11               111111100                  0012233455666665 46777776666543  346


Q ss_pred             hhhcCCCCCCCCCeEEEE--eecchhhh-hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          267 EAIGIPLADDNGGCKVLL--TARSQDVL-SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       267 ~~l~~~l~~~~~~s~iiv--Ttr~~~va-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                      ..+...+....+...+++  ||++.... .........+.+.+++.++.+.++.+.+..... .--.++.+.|.+.+..-
T Consensus       310 ~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v-~ls~eal~~L~~ys~~g  388 (615)
T TIGR02903       310 KYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINV-HLAAGVEELIARYTIEG  388 (615)
T ss_pred             hhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHCCCcH
Confidence            666655555455444555  55544321 111223457889999999999999998753211 11245566677766655


Q ss_pred             hHHHHHHHHH
Q 044858          344 PIAIVPIAKA  353 (426)
Q Consensus       344 Plai~~~~~~  353 (426)
                      +.++..++..
T Consensus       389 Rraln~L~~~  398 (615)
T TIGR02903       389 RKAVNILADV  398 (615)
T ss_pred             HHHHHHHHHH
Confidence            7777766554

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.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.71  E-value=2.8e-07  Score=92.04  Aligned_cols=186  Identities=11%  Similarity=0.171  Sum_probs=112.7

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------ccceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENN-------------------LFEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~-------------------~f~~~~w  207 (426)
                      ..+.+++|.+..+..|..++..++.+ .+.++|+.|+||||+|+.+.+......                   .|..++.
T Consensus        13 ~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~e   92 (509)
T PRK14958         13 RCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFE   92 (509)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEE
Confidence            35677899999999999999876655 578999999999999999988654221                   1222333


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT  285 (426)
                      +..+....+.++ ++++..+...                -..++.-++|||+++..  ...+.+...+..-...+++|++
T Consensus        93 idaas~~~v~~i-R~l~~~~~~~----------------p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIla  155 (509)
T PRK14958         93 VDAASRTKVEDT-RELLDNIPYA----------------PTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILA  155 (509)
T ss_pred             EcccccCCHHHH-HHHHHHHhhc----------------cccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEE
Confidence            333323333332 2222221110                01255678999999854  3444444333332345666665


Q ss_pred             ecc-hhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          286 ARS-QDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       286 tr~-~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      |.+ ..+.....+....+++++++.++....+.+.+......- ..+....|++.++|.|.-+..+.
T Consensus       156 ttd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~-~~~al~~ia~~s~GslR~al~lL  221 (509)
T PRK14958        156 TTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEF-ENAALDLLARAANGSVRDALSLL  221 (509)
T ss_pred             ECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHHHHH
Confidence            543 333221233346789999999998888777764322211 23456788999999886554443

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

Probab=98.71  E-value=4.8e-08  Score=88.23  Aligned_cols=92  Identities=15%  Similarity=0.121  Sum_probs=63.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC--cCHHHHHHHHHHHhCCCccccCcHH-------HHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT--PQIKEIQREIAEKLGLKIDQESESV-------RAW  241 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~il~~i~~~l~~~~~~~~~~~-------~~~  241 (426)
                      +-..+.|+|++|+|||||++.+++..... +|+..+|+.+.+.  .++.++++.+...+-...-..+...       ...
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~   93 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLE   93 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHH
Confidence            34578999999999999999999988764 8999999997766  7999999999333211111111111       112


Q ss_pred             HHHHHHhcCCeEEEEEeCCCCc
Q 044858          242 RLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       242 ~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      ........+++.++++|++...
T Consensus        94 ~a~~~~~~G~~vll~iDei~r~  115 (249)
T cd01128          94 KAKRLVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHHHHHCCCCEEEEEECHHHh
Confidence            2222234589999999999644

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.71  E-value=6e-07  Score=88.47  Aligned_cols=185  Identities=12%  Similarity=0.135  Sum_probs=113.0

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhc-------------------CccceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKEN-------------------NLFEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~-------------------~~f~~~~w  207 (426)
                      ..+.+++|.+..++.|...+..++.+ .+.++|+.|+||||+|+.+.......                   +.+..++.
T Consensus        10 ~~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~e   89 (491)
T PRK14964         10 SSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIE   89 (491)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEE
Confidence            35677899999998888888776655 78999999999999999998643210                   11122334


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT  285 (426)
                      ++.+...++.++ ++|+......               - ..+++-++|+|+++..  ...+.+...+..-.+.+.+|++
T Consensus        90 idaas~~~vddI-R~Iie~~~~~---------------P-~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIla  152 (491)
T PRK14964         90 IDAASNTSVDDI-KVILENSCYL---------------P-ISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILA  152 (491)
T ss_pred             EecccCCCHHHH-HHHHHHHHhc---------------c-ccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEE
Confidence            444433333332 2222211100               0 0245668999999754  2344444444333345666665


Q ss_pred             ec-chhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          286 AR-SQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       286 tr-~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      |. ...+..........+.+.+++.++....+.+.+...... --.+....|++.++|.+..+...
T Consensus       153 tte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~-i~~eAL~lIa~~s~GslR~alsl  217 (491)
T PRK14964        153 TTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIE-HDEESLKLIAENSSGSMRNALFL  217 (491)
T ss_pred             eCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            53 344432233445789999999999999999887532221 12456778999999987644443

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

Probab=98.70  E-value=2.4e-07  Score=95.90  Aligned_cols=177  Identities=18%  Similarity=0.243  Sum_probs=102.5

Q ss_pred             CCcccccchHHHHH---HHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLK---GILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       148 ~~~~~~~gR~~~~~---~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .....|+|++..+.   .+...+..++.+.+.++|++|+||||||+.+++....  +|.   .++.+. ....++ +++ 
T Consensus        25 ~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~~--~f~---~lna~~-~~i~di-r~~-   96 (725)
T PRK13341         25 RTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRA--HFS---SLNAVL-AGVKDL-RAE-   96 (725)
T ss_pred             CcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhcC--cce---eehhhh-hhhHHH-HHH-
Confidence            45667889888774   4556666667778899999999999999999987542  231   111110 011111 111 


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHh-cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe--ecchh--hhhccCC
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLK-KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT--ARSQD--VLSCEMD  297 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT--tr~~~--va~~~~~  297 (426)
                                     .....+.+. .+++.+|+|||++..  ...+.+...+   ..++.++++  |.+..  +......
T Consensus        97 ---------------i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~l---E~g~IiLI~aTTenp~~~l~~aL~S  158 (725)
T PRK13341         97 ---------------VDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWV---ENGTITLIGATTENPYFEVNKALVS  158 (725)
T ss_pred             ---------------HHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHh---cCceEEEEEecCCChHhhhhhHhhc
Confidence                           111111111 145689999999754  3344443322   235545553  33321  1111222


Q ss_pred             ceeeEEccCCCHHHHHHHHHHhhCC------CCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          298 CQQNFVVDVLNDKEAWSLFKKMTGD------CIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       298 ~~~~~~l~~L~~~e~~~Lf~~~~~~------~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      ....+.+++|+.++...++.+.+..      .....--.+....|++.+.|..-.+..+
T Consensus       159 R~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~  217 (725)
T PRK13341        159 RSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNA  217 (725)
T ss_pred             cccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHH
Confidence            3467999999999999999887641      1111222556788999999875544333

>PTZ00202 tuzin; Provisional

Probab=98.70  E-value=1.6e-06  Score=82.54  Aligned_cols=166  Identities=16%  Similarity=0.215  Sum_probs=105.3

Q ss_pred             cccCCcccccchHHHHHHHHHHhcc---CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHH
Q 044858          145 KSTQDFMHFESRKSTLKGILDALSN---RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       145 ~~~~~~~~~~gR~~~~~~l~~~l~~---~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~  221 (426)
                      ..|.+..+|+||+.++..|...|.+   ..++++.|+|++|+|||||++.+.....    +. ..+++..   +..++++
T Consensus       256 ~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~----~~-qL~vNpr---g~eElLr  327 (550)
T PTZ00202        256 SAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----MP-AVFVDVR---GTEDTLR  327 (550)
T ss_pred             CCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC----ce-EEEECCC---CHHHHHH
Confidence            3345677899999999999888863   2346889999999999999999986543    11 2222222   7799999


Q ss_pred             HHHHHhCCCccccCcHHHHHHHHHHH----hc-CCeEEEEEeCCCCccChhhhc---CCCCCCCCCeEEEEeecchhhh-
Q 044858          222 EIAEKLGLKIDQESESVRAWRLLEQL----KK-ETKILIILDDIWGSLDLEAIG---IPLADDNGGCKVLLTARSQDVL-  292 (426)
Q Consensus       222 ~i~~~l~~~~~~~~~~~~~~~l~~~l----~~-~k~~LlVlDdv~~~~~~~~l~---~~l~~~~~~s~iivTtr~~~va-  292 (426)
                      .|+.+||.+.. ....+....+.+.+    .. +++.+||+- +.+...+..+.   ..+.....-|.|++---.+..- 
T Consensus       328 ~LL~ALGV~p~-~~k~dLLrqIqeaLl~~~~e~GrtPVLII~-lreg~~l~rvyne~v~la~drr~ch~v~evpleslt~  405 (550)
T PTZ00202        328 SVVKALGVPNV-EACGDLLDFISEACRRAKKMNGETPLLVLK-LREGSSLQRVYNEVVALACDRRLCHVVIEVPLESLTI  405 (550)
T ss_pred             HHHHHcCCCCc-ccHHHHHHHHHHHHHHHHHhCCCCEEEEEE-ecCCCcHHHHHHHHHHHHccchhheeeeeehHhhcch
Confidence            99999997432 22233344444433    22 566666663 22222222211   1233344567788765554432 


Q ss_pred             -hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          293 -SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       293 -~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                       ......-..|.+++|+.+++.++-.+..
T Consensus       406 ~~~~lprldf~~vp~fsr~qaf~y~~h~~  434 (550)
T PTZ00202        406 ANTLLPRLDFYLVPNFSRSQAFAYTQHAI  434 (550)
T ss_pred             hcccCccceeEecCCCCHHHHHHHHhhcc
Confidence             1123344678899999999998877664

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.70  E-value=1e-06  Score=84.26  Aligned_cols=197  Identities=13%  Similarity=0.063  Sum_probs=112.9

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEE----EEEecCCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVI----SSRVSQTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~----wv~v~~~~~~~~il~~  222 (426)
                      .....++|.+.....+.+.+..++.+ .+.++|+.|+||+|+|..+.+..-.........    -.+.. ........+.
T Consensus        16 ~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~-~~~~c~~c~~   94 (365)
T PRK07471         16 RETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLA-IDPDHPVARR   94 (365)
T ss_pred             CchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCcccccccccc-CCCCChHHHH
Confidence            34567899999999999988877654 688999999999999999887654321110000    00000 0000011111


Q ss_pred             HHHHhCCC-------cccc-------CcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEE
Q 044858          223 IAEKLGLK-------IDQE-------SESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKV  282 (426)
Q Consensus       223 i~~~l~~~-------~~~~-------~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~i  282 (426)
                      |...-...       .+..       -..+.+..+.+.+.    .+.+-++|+||++..  ...+.+...+..-..++.+
T Consensus        95 i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~  174 (365)
T PRK07471         95 IAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEPPARSLF  174 (365)
T ss_pred             HHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEE
Confidence            11110000       0000       01233444444442    356779999999754  3344444333333345666


Q ss_pred             EEeecch-hhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          283 LLTARSQ-DVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       283 ivTtr~~-~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      |++|.+. .+.....+....+.+.+++.++..+++.+.....   +  ......+++.++|.|+....+
T Consensus       175 IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~~---~--~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        175 LLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPDL---P--DDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             EEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcccC---C--HHHHHHHHHHcCCCHHHHHHH
Confidence            6666654 3333234456799999999999999998764221   1  122367899999999865444

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.69  E-value=3.1e-07  Score=92.94  Aligned_cols=182  Identities=14%  Similarity=0.189  Sum_probs=111.0

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCc-------------------cceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNL-------------------FEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~-------------------f~~~~w  207 (426)
                      ..+..++|.+..+..|..++..++. ..+.++|+.|+||||+|+.+.+.......                   |...+.
T Consensus        13 ~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlE   92 (709)
T PRK08691         13 KTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLE   92 (709)
T ss_pred             CCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEE
Confidence            3567789999999999999887664 46899999999999999999876432111                   111122


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeE
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL----KKETKILIILDDIWGSL--DLEAIGIPLADDNGGCK  281 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~  281 (426)
                      +..+....+.                     .+..++...    ..+++-++|||+++...  ..+.+...+..-...++
T Consensus        93 idaAs~~gVd---------------------~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~  151 (709)
T PRK08691         93 IDAASNTGID---------------------NIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVK  151 (709)
T ss_pred             EeccccCCHH---------------------HHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcE
Confidence            2222222211                     122222211    12456799999997543  23333333322233566


Q ss_pred             EEEeecch-hhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          282 VLLTARSQ-DVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       282 iivTtr~~-~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      +|++|.+. .+.....+....+.+.+++.++....+.+.+......- -......|++.++|.+.-+..+.
T Consensus       152 fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~i-d~eAL~~Ia~~A~GslRdAlnLL  221 (709)
T PRK08691        152 FILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAY-EPPALQLLGRAAAGSMRDALSLL  221 (709)
T ss_pred             EEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCc-CHHHHHHHHHHhCCCHHHHHHHH
Confidence            66666543 33211223446788999999999999988875322211 24567889999999986555443

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.68  E-value=1.2e-06  Score=84.48  Aligned_cols=184  Identities=13%  Similarity=0.139  Sum_probs=109.9

Q ss_pred             CcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------ccceEEE
Q 044858          149 DFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENN--------------------LFEKVIS  207 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~--------------------~f~~~~w  207 (426)
                      ....++|.++.++.+.+.+.+++. +.+.++|++|+||||+|+.+........                    +++. ++
T Consensus        12 ~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~-~~   90 (355)
T TIGR02397        12 TFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDV-IE   90 (355)
T ss_pred             cHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EE
Confidence            456788999999999998887654 4678999999999999999987753211                    1221 22


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT  285 (426)
                      +..+...+.. -.+++...+....                ..+++-++|+|++...  ...+.+...+......+.+|++
T Consensus        91 ~~~~~~~~~~-~~~~l~~~~~~~p----------------~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~  153 (355)
T TIGR02397        91 IDAASNNGVD-DIREILDNVKYAP----------------SSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILA  153 (355)
T ss_pred             eeccccCCHH-HHHHHHHHHhcCc----------------ccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEE
Confidence            2222111111 1122222111000                0134558899998654  3344444444333345666666


Q ss_pred             ecchh-hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          286 ARSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       286 tr~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      |.+.. +..........+++.++++++..+++...+...... --.+.+..+++.++|.|..+....
T Consensus       154 ~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~-i~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       154 TTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIK-IEDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             eCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCChHHHHHHH
Confidence            65443 221122334678999999999999998876422211 114577889999999987665554

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.67  E-value=7.5e-07  Score=90.24  Aligned_cols=198  Identities=13%  Similarity=0.137  Sum_probs=112.4

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCcc--ceEEEEEecCCcCHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLF--EKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f--~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ..+.+++|.+..+..|.+++..++. ..+.++|+.|+||||+|+.+.+........  ....    ...+......+.|.
T Consensus        13 ~~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~----~~pCg~C~~C~~i~   88 (618)
T PRK14951         13 RSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGIT----ATPCGVCQACRDID   88 (618)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCC----CCCCCccHHHHHHH
Confidence            3567789999999999998887665 466899999999999999997664321100  0000    00111111111111


Q ss_pred             HHhC-----CCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEee-cchhhh
Q 044858          225 EKLG-----LKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTA-RSQDVL  292 (426)
Q Consensus       225 ~~l~-----~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTt-r~~~va  292 (426)
                      ..-.     .+.......+.+..+.+...    .++.-++|||+++..  ..++.+...+..-...+.+|++| ....+.
T Consensus        89 ~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil  168 (618)
T PRK14951         89 SGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVP  168 (618)
T ss_pred             cCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhh
Confidence            0000     00000011122223333321    244568999999865  34555554443333455666555 434333


Q ss_pred             hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          293 SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       293 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      .........+++++++.++..+.+.+.+......- ..+....|++.++|.+.-+..+
T Consensus       169 ~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~i-e~~AL~~La~~s~GslR~al~l  225 (618)
T PRK14951        169 VTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPA-EPQALRLLARAARGSMRDALSL  225 (618)
T ss_pred             HHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            22334457899999999999999988775322221 2456788999999987655444

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.66  E-value=1e-06  Score=85.03  Aligned_cols=175  Identities=20%  Similarity=0.272  Sum_probs=103.2

Q ss_pred             CCcccccchHHHHHHHHHHhc----c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALS----N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~----~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..+.++.|.+..++++.+.+.    .         ..++-+.++|++|+|||++|+.+++.....  |     +.+..  
T Consensus       119 ~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~--~-----~~v~~--  189 (364)
T TIGR01242       119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT--F-----IRVVG--  189 (364)
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCC--E-----Eecch--
Confidence            345678899999888887663    1         234568999999999999999999876532  2     22211  


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------------ChhhhcCCCC--CC
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL----------------DLEAIGIPLA--DD  276 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~----------------~~~~l~~~l~--~~  276 (426)
                        .++....   .+      ........+++......+.+|+|||++...                .+..+...+.  ..
T Consensus       190 --~~l~~~~---~g------~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~  258 (364)
T TIGR01242       190 --SELVRKY---IG------EGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDP  258 (364)
T ss_pred             --HHHHHHh---hh------HHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCC
Confidence              1111111   10      011223344444444568999999987531                0111111111  12


Q ss_pred             CCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          277 NGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       277 ~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      ..+..||.||.......    ........+.+...+.++..++|...+......++.  ....+++.+.|..
T Consensus       259 ~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~--~~~~la~~t~g~s  328 (364)
T TIGR01242       259 RGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDV--DLEAIAKMTEGAS  328 (364)
T ss_pred             CCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccC--CHHHHHHHcCCCC
Confidence            34677888887643221    112234578999999999999999887543322211  1456777887764

Many proteins may score above the trusted cutoff because an internal

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.65  E-value=1e-06  Score=85.07  Aligned_cols=172  Identities=9%  Similarity=0.033  Sum_probs=103.3

Q ss_pred             cccccchHHHHHHHHHHhccCC----------ccEEEEEcCCCCcHHHHHHHHHHHhhhc-------------------C
Q 044858          150 FMHFESRKSTLKGILDALSNRN----------FNMIGVYGMGGIGKTTLVKEVGRQAKEN-------------------N  200 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~----------~~vi~I~G~~GiGKTtLa~~v~~~~~~~-------------------~  200 (426)
                      +..++|.+..++.|...+..+.          ++.+.++|+.|+|||++|+.+.+..-..                   .
T Consensus         4 f~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~   83 (394)
T PRK07940          4 WDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGT   83 (394)
T ss_pred             hhhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCC
Confidence            4467888888888888887543          4568899999999999999987754321                   1


Q ss_pred             ccceEEEEEec-CCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCC
Q 044858          201 LFEKVISSRVS-QTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPL  273 (426)
Q Consensus       201 ~f~~~~wv~v~-~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l  273 (426)
                      |.|. .++... ....+                     +.+..+.+.+.    .+++-++++|+++..  ...+.+...+
T Consensus        84 hpD~-~~i~~~~~~i~i---------------------~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~L  141 (394)
T PRK07940         84 HPDV-RVVAPEGLSIGV---------------------DEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAV  141 (394)
T ss_pred             CCCE-EEeccccccCCH---------------------HHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHh
Confidence            1111 111111 11111                     12223333321    245568899999755  2333343333


Q ss_pred             CCCCCCeEEEEeecc-hhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHH
Q 044858          274 ADDNGGCKVLLTARS-QDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVP  349 (426)
Q Consensus       274 ~~~~~~s~iivTtr~-~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~  349 (426)
                      .....++.+|++|.+ ..+.....+....+.+.+++.++..+.+.+..+.   +   .+.+..+++.++|.|.....
T Consensus       142 Eep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~~---~---~~~a~~la~~s~G~~~~A~~  212 (394)
T PRK07940        142 EEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDGV---D---PETARRAARASQGHIGRARR  212 (394)
T ss_pred             hcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcCC---C---HHHHHHHHHHcCCCHHHHHH
Confidence            222335555555555 3443323344579999999999999888754321   1   34577899999999975533

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.65  E-value=1.2e-06  Score=76.33  Aligned_cols=159  Identities=17%  Similarity=0.167  Sum_probs=92.6

Q ss_pred             HHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhc--------------------CccceEEEEEec-CCcCHHHHH
Q 044858          163 ILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKEN--------------------NLFEKVISSRVS-QTPQIKEIQ  220 (426)
Q Consensus       163 l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~v~-~~~~~~~il  220 (426)
                      +.+.+..++. ..+.++|+.|+|||++|+.+.+.....                    .+.+. .++... ..... +..
T Consensus         4 l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~-~~~~~~~~~~~~-~~i   81 (188)
T TIGR00678         4 LKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDL-HRLEPEGQSIKV-DQV   81 (188)
T ss_pred             HHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcE-EEeccccCcCCH-HHH
Confidence            4444445554 578999999999999999998775432                    11121 122111 11111 111


Q ss_pred             HHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecch-hhhhccCC
Q 044858          221 REIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMD  297 (426)
Q Consensus       221 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~  297 (426)
                      +++...+....                ..+.+-++|+||++...  ..+.+...+......+.+|++|++. .+......
T Consensus        82 ~~i~~~~~~~~----------------~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~s  145 (188)
T TIGR00678        82 RELVEFLSRTP----------------QESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRS  145 (188)
T ss_pred             HHHHHHHccCc----------------ccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHh
Confidence            12222211000                02456789999997542  3444544443333456677766643 22221223


Q ss_pred             ceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH
Q 044858          298 CQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIA  346 (426)
Q Consensus       298 ~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla  346 (426)
                      ....+++.+++.++..+.+.+. +  . +   .+.+..|++.++|.|..
T Consensus       146 r~~~~~~~~~~~~~~~~~l~~~-g--i-~---~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       146 RCQVLPFPPLSEEALLQWLIRQ-G--I-S---EEAAELLLALAGGSPGA  187 (188)
T ss_pred             hcEEeeCCCCCHHHHHHHHHHc-C--C-C---HHHHHHHHHHcCCCccc
Confidence            4468999999999999998876 2  2 1   45688999999999853

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.65  E-value=5.4e-07  Score=87.87  Aligned_cols=200  Identities=13%  Similarity=0.110  Sum_probs=112.1

Q ss_pred             CcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEE-ecCCcCHHHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSR-VSQTPQIKEIQREIAEK  226 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~-v~~~~~~~~il~~i~~~  226 (426)
                      ....++|.+..++.|..++.+++.+ .+.++|+.|+||||+|..+.+.......+....|.. ...........+.+...
T Consensus        14 ~~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~   93 (397)
T PRK14955         14 KFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAG   93 (397)
T ss_pred             cHhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcC
Confidence            4567889999888888888876654 588999999999999999988764321111100110 00111111111111111


Q ss_pred             hCCCc---c--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEee-cchhhhhc
Q 044858          227 LGLKI---D--QESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTA-RSQDVLSC  294 (426)
Q Consensus       227 l~~~~---~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTt-r~~~va~~  294 (426)
                      ...+.   +  .....+.+..+.+.+.    .+.+-++|+|+++..  ..++.+...+..-.+.+.+|++| +...+...
T Consensus        94 ~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~t  173 (397)
T PRK14955         94 TSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPAT  173 (397)
T ss_pred             CCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHH
Confidence            00000   0  0011223333333331    235668999999755  34555554444333466666555 33333221


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVP  349 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~  349 (426)
                      .......+++.++++++..+.+...+..... .--.+.+..|++.++|.+--+..
T Consensus       174 l~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~-~i~~~al~~l~~~s~g~lr~a~~  227 (397)
T PRK14955        174 IASRCQRFNFKRIPLEEIQQQLQGICEAEGI-SVDADALQLIGRKAQGSMRDAQS  227 (397)
T ss_pred             HHHHHHHhhcCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHH
Confidence            1223467899999999999888887642211 11245688899999998764444

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.61  E-value=2.5e-06  Score=86.03  Aligned_cols=198  Identities=15%  Similarity=0.133  Sum_probs=111.4

Q ss_pred             CcccccchHHHHHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .+..++|.+..+..|...+..++ .+.+.++|+.|+||||+|+.+.+..........       ..++.....+.|....
T Consensus        14 sf~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~-------~pCg~C~sC~~i~~g~   86 (624)
T PRK14959         14 TFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTG-------EPCNTCEQCRKVTQGM   86 (624)
T ss_pred             CHHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCC-------CCCcccHHHHHHhcCC
Confidence            45677898888888888887665 467889999999999999999877643110000       0011111111111110


Q ss_pred             CCCc---cc--cCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhcc
Q 044858          228 GLKI---DQ--ESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSCE  295 (426)
Q Consensus       228 ~~~~---~~--~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~  295 (426)
                      ....   +.  ....+.+..+.+.+.    .+++-++|||+++..  ...+.|...+..-...+.+|++|.. ..+....
T Consensus        87 hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI  166 (624)
T PRK14959         87 HVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTI  166 (624)
T ss_pred             CCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHH
Confidence            0000   00  000112222222221    245679999999765  3344454444322234556555544 4333212


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch-HHHHHHHHHh
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP-IAIVPIAKAL  354 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP-lai~~~~~~l  354 (426)
                      ......+++.+++.++....+...+..... .-..+.+..|++.++|.+ .|+..+..++
T Consensus       167 ~SRcq~i~F~pLs~~eL~~~L~~il~~egi-~id~eal~lIA~~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        167 VSRCQHFTFTRLSEAGLEAHLTKVLGREGV-DYDPAAVRLIARRAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             HhhhhccccCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            233468899999999999999887643221 112456788999999965 6777665544

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.60  E-value=8.3e-07  Score=80.10  Aligned_cols=167  Identities=15%  Similarity=0.095  Sum_probs=98.0

Q ss_pred             HHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHH
Q 044858          159 TLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESV  238 (426)
Q Consensus       159 ~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~  238 (426)
                      .+..+..+......+.+.|+|+.|+|||+|++.+++.....  ...+.++++....+                       
T Consensus        32 a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~--~~~v~y~~~~~~~~-----------------------   86 (235)
T PRK08084         32 LLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR--GRAVGYVPLDKRAW-----------------------   86 (235)
T ss_pred             HHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEEHHHHhh-----------------------
Confidence            44444444444455689999999999999999999876543  23455665532110                       


Q ss_pred             HHHHHHHHHhcCCeEEEEEeCCCCc---cChhh-hcCCCCC--CCCCeEEEEeecchhhh--------hccCCceeeEEc
Q 044858          239 RAWRLLEQLKKETKILIILDDIWGS---LDLEA-IGIPLAD--DNGGCKVLLTARSQDVL--------SCEMDCQQNFVV  304 (426)
Q Consensus       239 ~~~~l~~~l~~~k~~LlVlDdv~~~---~~~~~-l~~~l~~--~~~~s~iivTtr~~~va--------~~~~~~~~~~~l  304 (426)
                      ....+.+.+.+  --+|+|||+...   ..|+. +...+..  ...+.++|+||+...-.        ........++++
T Consensus        87 ~~~~~~~~~~~--~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l  164 (235)
T PRK08084         87 FVPEVLEGMEQ--LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKL  164 (235)
T ss_pred             hhHHHHHHhhh--CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeee
Confidence            00112222221  248899999754   33443 1111111  12234799999865322        011233468999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      +++++++-.+++.+.+.... -.--+++..-|++.+.|..-.+..+-..
T Consensus       165 ~~~~~~~~~~~l~~~a~~~~-~~l~~~v~~~L~~~~~~d~r~l~~~l~~  212 (235)
T PRK08084        165 QPLSDEEKLQALQLRARLRG-FELPEDVGRFLLKRLDREMRTLFMTLDQ  212 (235)
T ss_pred             cCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHhhcCCHHHHHHHHHH
Confidence            99999999999988664221 1122567788888888776655544433

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.60  E-value=1.2e-06  Score=88.04  Aligned_cols=178  Identities=15%  Similarity=0.192  Sum_probs=108.1

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------ccceEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENN-------------------LFEKVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~-------------------~f~~~~w  207 (426)
                      ..+..++|.+..++.+..++..++.+ .+.++|+.|+||||+|+.+.+......                   .|...++
T Consensus        13 ~~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~e   92 (527)
T PRK14969         13 KSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIE   92 (527)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeE
Confidence            35667889999999999888876654 568999999999999999987653211                   1112222


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeE
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCK  281 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~  281 (426)
                      +..+....+.                     .+..+.....    .+++-++|+|+++...  ..+.+...+..-...+.
T Consensus        93 i~~~~~~~vd---------------------~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~  151 (527)
T PRK14969         93 VDAASNTQVD---------------------AMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVK  151 (527)
T ss_pred             eeccccCCHH---------------------HHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEE
Confidence            2222111211                     1222222221    2456799999997553  34444434433334566


Q ss_pred             EEEeecc-hhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          282 VLLTARS-QDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       282 iivTtr~-~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      +|++|.+ +.+..........+++++++.++....+.+.+...... .-......|++.++|.+--+
T Consensus       152 fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~-~~~~al~~la~~s~Gslr~a  217 (527)
T PRK14969        152 FILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIP-FDATALQLLARAAAGSMRDA  217 (527)
T ss_pred             EEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHH
Confidence            6665544 33321112334689999999999998888876422211 12455688999999977633

>PRK08727 hypothetical protein; Validated

Probab=98.58  E-value=1.2e-06  Score=79.01  Aligned_cols=173  Identities=14%  Similarity=0.100  Sum_probs=99.9

Q ss_pred             cccccchH-HHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC
Q 044858          150 FMHFESRK-STLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG  228 (426)
Q Consensus       150 ~~~~~gR~-~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~  228 (426)
                      +..|++.. ..+..+.....+.....+.|+|+.|+|||+|++.+++....+  ...+.|++..+      ....+     
T Consensus        18 f~~f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~--~~~~~y~~~~~------~~~~~-----   84 (233)
T PRK08727         18 FDSYIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQA--GRSSAYLPLQA------AAGRL-----   84 (233)
T ss_pred             hhhccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEeHHH------hhhhH-----
Confidence            44454433 333333333333334569999999999999999999886644  23455665322      11111     


Q ss_pred             CCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc---Chhh-hcCCCCC-CCCCeEEEEeecchhhh-----h---cc
Q 044858          229 LKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL---DLEA-IGIPLAD-DNGGCKVLLTARSQDVL-----S---CE  295 (426)
Q Consensus       229 ~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~---~~~~-l~~~l~~-~~~~s~iivTtr~~~va-----~---~~  295 (426)
                                  ...++.+.  +.-+|||||+....   .|.. +...+.. ..++..||+||+...-.     .   ..
T Consensus        85 ------------~~~~~~l~--~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SR  150 (233)
T PRK08727         85 ------------RDALEALE--GRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSR  150 (233)
T ss_pred             ------------HHHHHHHh--cCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHH
Confidence                        11223332  34599999997542   2332 2211111 12356799999864321     0   01


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      ......+++++++.++-.+++.+.+....- .--.+...-|++.++|-.-.+..+
T Consensus       151 l~~~~~~~l~~~~~e~~~~iL~~~a~~~~l-~l~~e~~~~La~~~~rd~r~~l~~  204 (233)
T PRK08727        151 LAQCIRIGLPVLDDVARAAVLRERAQRRGL-ALDEAAIDWLLTHGERELAGLVAL  204 (233)
T ss_pred             HhcCceEEecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhCCCCHHHHHHH
Confidence            122458999999999999999987642211 122456778888888766655333

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.58  E-value=2.1e-07  Score=87.81  Aligned_cols=90  Identities=14%  Similarity=0.142  Sum_probs=62.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc--CHHHHHHHHHHHhCCCccccCcHHH-------HHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP--QIKEIQREIAEKLGLKIDQESESVR-------AWRL  243 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~--~~~~il~~i~~~l~~~~~~~~~~~~-------~~~l  243 (426)
                      +-..|+|++|+|||||++.+|+....+ +|+..+|+.+.+..  ++.++++.|...+-......+....       ....
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~A  248 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKA  248 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHH
Confidence            457899999999999999999998875 89999999998887  7788888886322111111111111       1112


Q ss_pred             HHHHhcCCeEEEEEeCCCCc
Q 044858          244 LEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       244 ~~~l~~~k~~LlVlDdv~~~  263 (426)
                      ......+++++|++|++...
T Consensus       249 e~~~e~G~dVlL~iDsItR~  268 (416)
T PRK09376        249 KRLVEHGKDVVILLDSITRL  268 (416)
T ss_pred             HHHHHcCCCEEEEEEChHHH
Confidence            22223579999999999643

>PRK09087 hypothetical protein; Validated

Probab=98.58  E-value=1.1e-06  Score=78.57  Aligned_cols=168  Identities=16%  Similarity=0.087  Sum_probs=95.8

Q ss_pred             ccccc--chHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          150 FMHFE--SRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       150 ~~~~~--gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      +..|+  +.....-.+++.+.+...+.+.|+|+.|+|||+|++.+++....       .+++..      .+..++.   
T Consensus        20 ~~~Fi~~~~N~~a~~~l~~~~~~~~~~l~l~G~~GsGKThLl~~~~~~~~~-------~~i~~~------~~~~~~~---   83 (226)
T PRK09087         20 RDDLLVTESNRAAVSLVDHWPNWPSPVVVLAGPVGSGKTHLASIWREKSDA-------LLIHPN------EIGSDAA---   83 (226)
T ss_pred             hhceeecCchHHHHHHHHhcccCCCCeEEEECCCCCCHHHHHHHHHHhcCC-------EEecHH------HcchHHH---
Confidence            44554  22333333333322333467899999999999999988876432       133321      1111111   


Q ss_pred             CCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-ChhhhcCCCC-CCCCCeEEEEeecchhhh--------hccCC
Q 044858          228 GLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-DLEAIGIPLA-DDNGGCKVLLTARSQDVL--------SCEMD  297 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-~~~~l~~~l~-~~~~~s~iivTtr~~~va--------~~~~~  297 (426)
                                       ..+.+   -+|++||+.... .-..+...+. ....|..||+|++.....        .....
T Consensus        84 -----------------~~~~~---~~l~iDDi~~~~~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~  143 (226)
T PRK09087         84 -----------------NAAAE---GPVLIEDIDAGGFDETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLK  143 (226)
T ss_pred             -----------------Hhhhc---CeEEEECCCCCCCCHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHh
Confidence                             11111   278889996432 1111221111 112367799988754321        11223


Q ss_pred             ceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          298 CQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       298 ~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      ....+++++++.++-.+++.+.+....- .--+++..-|++.+.|..-++..+...|
T Consensus       144 ~gl~~~l~~pd~e~~~~iL~~~~~~~~~-~l~~ev~~~La~~~~r~~~~l~~~l~~L  199 (226)
T PRK09087        144 AATVVEIGEPDDALLSQVIFKLFADRQL-YVDPHVVYYLVSRMERSLFAAQTIVDRL  199 (226)
T ss_pred             CCceeecCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            4578999999999999999998853211 1225677888888888877776544333

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.58  E-value=1.5e-06  Score=87.19  Aligned_cols=197  Identities=14%  Similarity=0.141  Sum_probs=108.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ..+..++|++..++.+...+..++. +.+.++|+.|+||||+|+.+.+......      |.... .+......+.+...
T Consensus        13 ~~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~------~~~~~-~Cg~C~sCr~i~~~   85 (605)
T PRK05896         13 HNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLN------PKDGD-CCNSCSVCESINTN   85 (605)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCC------CCCCC-CCcccHHHHHHHcC
Confidence            3566789999999999998876554 4688999999999999999988754211      11100 11111111111111


Q ss_pred             hCCCc---cc--cCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEee-cchhhhhc
Q 044858          227 LGLKI---DQ--ESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTA-RSQDVLSC  294 (426)
Q Consensus       227 l~~~~---~~--~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTt-r~~~va~~  294 (426)
                      .....   +.  ....+.+..+.+.+.    .+++-++|+|+++..  ..++.+...+......+.+|++| ....+...
T Consensus        86 ~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~T  165 (605)
T PRK05896         86 QSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLT  165 (605)
T ss_pred             CCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHH
Confidence            00000   00  001111222222211    123447999999754  34444444332222345555444 43333221


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPIAK  352 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~~~  352 (426)
                      .......+++.++++++....+...+......- -.+.+..+++.++|.|. |+..+-.
T Consensus       166 I~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~I-s~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        166 IISRCQRYNFKKLNNSELQELLKSIAKKEKIKI-EDNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             HHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            223356899999999999999988764221111 13457789999999665 4444433

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.57  E-value=3.3e-06  Score=81.74  Aligned_cols=181  Identities=12%  Similarity=0.170  Sum_probs=104.6

Q ss_pred             CcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhc------Cccce-EEEEEecCCcCHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKEN------NLFEK-VISSRVSQTPQIKEIQ  220 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~------~~f~~-~~wv~v~~~~~~~~il  220 (426)
                      ...+++|.+..++.+...+.+++. +.+.++|+.|+||||+|+.+.+.....      ..|.. .+-+......+..+ .
T Consensus        15 ~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-i   93 (367)
T PRK14970         15 TFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD-I   93 (367)
T ss_pred             cHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHH-H
Confidence            566788999999999999887654 478899999999999999998765431      11221 11111111111111 1


Q ss_pred             HHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecc-hhhhhccCC
Q 044858          221 REIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARS-QDVLSCEMD  297 (426)
Q Consensus       221 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~~~  297 (426)
                      +++...+...               .. .+++-++++|++....  .++.+...+......+.+|++|.. .........
T Consensus        94 ~~l~~~~~~~---------------p~-~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~s  157 (367)
T PRK14970         94 RNLIDQVRIP---------------PQ-TGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILS  157 (367)
T ss_pred             HHHHHHHhhc---------------cc-cCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHh
Confidence            1222211100               00 1345689999986542  344443333222234555555533 222211223


Q ss_pred             ceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          298 CQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       298 ~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      ....+++.++++++....+.+.+...... --.+....|++.++|.+-.+
T Consensus       158 r~~~v~~~~~~~~~l~~~l~~~~~~~g~~-i~~~al~~l~~~~~gdlr~~  206 (367)
T PRK14970        158 RCQIFDFKRITIKDIKEHLAGIAVKEGIK-FEDDALHIIAQKADGALRDA  206 (367)
T ss_pred             cceeEecCCccHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhCCCCHHHH
Confidence            34579999999999999988876422211 11456788888999876644

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

Probab=98.56  E-value=3.5e-06  Score=76.94  Aligned_cols=193  Identities=15%  Similarity=0.136  Sum_probs=115.5

Q ss_pred             HHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCcc----ceEEEEEecCCcCHHHHHHHHHHHhCCC
Q 044858          158 STLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLF----EKVISSRVSQTPQIKEIQREIAEKLGLK  230 (426)
Q Consensus       158 ~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----~~~~wv~v~~~~~~~~il~~i~~~l~~~  230 (426)
                      +.++.|.+.+.   ....+.+.|+|.+|.|||++++.+.........-    -.++.+.....++...+...|+.+++.+
T Consensus        44 ~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP  123 (302)
T PF05621_consen   44 EALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAP  123 (302)
T ss_pred             HHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcc
Confidence            34555555554   3356789999999999999999999876432111    1467788889999999999999999988


Q ss_pred             ccccCcHHH-HHHHHHHHhcCCeEEEEEeCCCCccC---------hhhhcCCCCCCCCCeEEEEeecchhhhh----ccC
Q 044858          231 IDQESESVR-AWRLLEQLKKETKILIILDDIWGSLD---------LEAIGIPLADDNGGCKVLLTARSQDVLS----CEM  296 (426)
Q Consensus       231 ~~~~~~~~~-~~~l~~~l~~~k~~LlVlDdv~~~~~---------~~~l~~~l~~~~~~s~iivTtr~~~va~----~~~  296 (426)
                      ......... ..+..+.+..-+--+||||++++...         .+.++ .+.+.-.=+-|.+-|+.-.-+-    ...
T Consensus       124 ~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK-~L~NeL~ipiV~vGt~~A~~al~~D~QLa  202 (302)
T PF05621_consen  124 YRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALK-FLGNELQIPIVGVGTREAYRALRTDPQLA  202 (302)
T ss_pred             cCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHH-HHhhccCCCeEEeccHHHHHHhccCHHHH
Confidence            755443333 33444555444566999999987511         11111 1212222234555555432221    012


Q ss_pred             CceeeEEccCCCH-HHHHHHHHHhh---C-CCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          297 DCQQNFVVDVLND-KEAWSLFKKMT---G-DCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       297 ~~~~~~~l~~L~~-~e~~~Lf~~~~---~-~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      +....+.|+.... ++...|+...-   . .....-...++++.|...++|+.=-+..+-
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            2345677776544 34444543332   1 111122336789999999999875554443

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

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.56  E-value=2.2e-06  Score=89.93  Aligned_cols=177  Identities=12%  Similarity=0.100  Sum_probs=108.4

Q ss_pred             CcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCcc---------------------ceEE
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLF---------------------EKVI  206 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f---------------------~~~~  206 (426)
                      .+..++|.+..++.|...+..+++. .+.++|+.|+||||+|+.+.+........                     ..++
T Consensus        13 ~f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~   92 (824)
T PRK07764         13 TFAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVT   92 (824)
T ss_pred             CHHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEE
Confidence            4567889999999999998876654 57899999999999999998776421111                     0011


Q ss_pred             EEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCe
Q 044858          207 SSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL----KKETKILIILDDIWGS--LDLEAIGIPLADDNGGC  280 (426)
Q Consensus       207 wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s  280 (426)
                      ++.......+                     +.+..+.+.+    ..++.-++|||+++..  ...+.|...+..-...+
T Consensus        93 eidaas~~~V---------------------d~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~  151 (824)
T PRK07764         93 EIDAASHGGV---------------------DDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHL  151 (824)
T ss_pred             EecccccCCH---------------------HHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCe
Confidence            2211111111                     1222222221    1245568899999755  34455544443333455


Q ss_pred             EEEEee-cchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          281 KVLLTA-RSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       281 ~iivTt-r~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      .+|++| ....+..........|++.+++.++..+++.+.+....... -......|++.++|.+..+
T Consensus       152 ~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~i-d~eal~lLa~~sgGdlR~A  218 (824)
T PRK07764        152 KFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPV-EPGVLPLVIRAGGGSVRDS  218 (824)
T ss_pred             EEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            655555 44444322334567899999999999998888764222111 2345678899999988544

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.56  E-value=1.3e-06  Score=78.69  Aligned_cols=153  Identities=12%  Similarity=0.071  Sum_probs=88.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ....+.|+|+.|+|||+||+.+++.....+ + ...+++.....      ..+                     ...  .
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~~~~~~-~-~~~~i~~~~~~------~~~---------------------~~~--~   89 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVADASYGG-R-NARYLDAASPL------LAF---------------------DFD--P   89 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCC-C-cEEEEehHHhH------HHH---------------------hhc--c
Confidence            446789999999999999999998764321 2 23444433211      000                     111  1


Q ss_pred             CeEEEEEeCCCCccChh--hhcCCCCC-CCCCe-EEEEeecchhhhhc-------cCCceeeEEccCCCHHHHHHHHHHh
Q 044858          251 TKILIILDDIWGSLDLE--AIGIPLAD-DNGGC-KVLLTARSQDVLSC-------EMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       251 k~~LlVlDdv~~~~~~~--~l~~~l~~-~~~~s-~iivTtr~~~va~~-------~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      ..-+|++||+.....+.  .+...+.. ...+. .+|+|++.......       .......+++.++++++-..++.+.
T Consensus        90 ~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~  169 (227)
T PRK08903         90 EAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAA  169 (227)
T ss_pred             cCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHH
Confidence            23478999997543222  22222211 11233 46666664332110       1122368999999998877777765


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhh
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALK  355 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~  355 (426)
                      +.... -.--++....+++.+.|.+..+..+...+.
T Consensus       170 ~~~~~-v~l~~~al~~L~~~~~gn~~~l~~~l~~l~  204 (227)
T PRK08903        170 AAERG-LQLADEVPDYLLTHFRRDMPSLMALLDALD  204 (227)
T ss_pred             HHHcC-CCCCHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            43211 112245778888899999988877766553

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.54  E-value=1e-06  Score=93.34  Aligned_cols=183  Identities=13%  Similarity=0.120  Sum_probs=105.6

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEE-EEecCCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVIS-SRVSQTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~w-v~v~~~~~~~~il~~  222 (426)
                      ....+++||++++..++..|.......+.++|++|+||||+|+.+.+.......    ....+| +..+.-..       
T Consensus       184 ~~ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~a-------  256 (852)
T TIGR03345       184 GKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQA-------  256 (852)
T ss_pred             CCCCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhc-------
Confidence            345789999999999999888766667789999999999999999988643211    122232 22221000       


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHh-cCCeEEEEEeCCCCcc-------Chh--hhcCCCCCCCCCeEEEEeecchhh-
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLK-KETKILIILDDIWGSL-------DLE--AIGIPLADDNGGCKVLLTARSQDV-  291 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~-------~~~--~l~~~l~~~~~~s~iivTtr~~~v-  291 (426)
                            ...........+..+++.+. .+++.+|++|+++...       .-+  .+..+... ...-++|-||..+.. 
T Consensus       257 ------g~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~-~G~l~~IgaTT~~e~~  329 (852)
T TIGR03345       257 ------GASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALA-RGELRTIAATTWAEYK  329 (852)
T ss_pred             ------ccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHhh-CCCeEEEEecCHHHHh
Confidence                  00000111123344444443 2468999999997542       111  12222211 224566666655321 


Q ss_pred             ---h--hccCCceeeEEccCCCHHHHHHHHHHhhC---CCCCCCchHHHHHHHHHHcCCch
Q 044858          292 ---L--SCEMDCQQNFVVDVLNDKEAWSLFKKMTG---DCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       292 ---a--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~---~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                         .  .........+.+++++.++..+++.....   ....-.-..+....+++.+.+.+
T Consensus       330 ~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi  390 (852)
T TIGR03345       330 KYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI  390 (852)
T ss_pred             hhhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHccccc
Confidence               0  11223457899999999999999755442   11111122455667777776643

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.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.54  E-value=3e-06  Score=86.07  Aligned_cols=199  Identities=12%  Similarity=0.132  Sum_probs=114.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccce--EEEEEecCCcCHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEK--VISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~--~~wv~v~~~~~~~~il~~i~  224 (426)
                      ..+..++|.+..++.|.+.+..++.+ .+.++|+.|+||||+|+.+.+..........  ..+    ..+....-.+.|.
T Consensus        21 ~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~----~~cg~c~~C~~i~   96 (598)
T PRK09111         21 QTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTI----DLCGVGEHCQAIM   96 (598)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCcc----ccCcccHHHHHHh
Confidence            35677899999999999998876644 6889999999999999999886542211000  000    0001111111121


Q ss_pred             HHhCCCc-----cccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEee-cchhhh
Q 044858          225 EKLGLKI-----DQESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTA-RSQDVL  292 (426)
Q Consensus       225 ~~l~~~~-----~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTt-r~~~va  292 (426)
                      ..-....     ......+.+..+.+.+.    .+++-++|+|+++...  ..+.+...+..-..++.+|++| ....+.
T Consensus        97 ~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll  176 (598)
T PRK09111         97 EGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVP  176 (598)
T ss_pred             cCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhh
Confidence            1111000     00111222333333332    2345689999997553  3444444443333456666555 434433


Q ss_pred             hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          293 SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       293 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      .........+.+.+++.++....+.+.+...... --.+....|++.++|.+.-+....
T Consensus       177 ~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~-i~~eAl~lIa~~a~Gdlr~al~~L  234 (598)
T PRK09111        177 VTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVE-VEDEALALIARAAEGSVRDGLSLL  234 (598)
T ss_pred             HHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            2223345789999999999999998877422211 123567889999999987665544

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.52  E-value=1.8e-06  Score=83.91  Aligned_cols=202  Identities=16%  Similarity=0.249  Sum_probs=113.1

Q ss_pred             CCcccccchHHHHHHHHHHhc----c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALS----N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~----~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..+..+.|++..++++.+.+.    .         ..++-|.++|++|+|||++|+.+++.....       |+.++.  
T Consensus       128 ~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~-------~i~v~~--  198 (389)
T PRK03992        128 VTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT-------FIRVVG--  198 (389)
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCC-------EEEeeh--
Confidence            345567899998888877653    1         345678999999999999999999876532       222221  


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------C-hhhhcCC---CC--CC
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------D-LEAIGIP---LA--DD  276 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~-~~~l~~~---l~--~~  276 (426)
                        .++....   .+      .....+..+++......+.+|+|||++...            . ...+...   +.  ..
T Consensus       199 --~~l~~~~---~g------~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~  267 (389)
T PRK03992        199 --SELVQKF---IG------EGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDP  267 (389)
T ss_pred             --HHHhHhh---cc------chHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCC
Confidence              1121111   00      111233444555444568999999997531            0 1111111   11  11


Q ss_pred             CCCeEEEEeecchhhhhc----cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch-HHHHHH-
Q 044858          277 NGGCKVLLTARSQDVLSC----EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP-IAIVPI-  350 (426)
Q Consensus       277 ~~~s~iivTtr~~~va~~----~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP-lai~~~-  350 (426)
                      ..+..||.||........    ...-...+++++.+.++-.++|+..+......++.  ....+++.+.|.- --|..+ 
T Consensus       268 ~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~--~~~~la~~t~g~sgadl~~l~  345 (389)
T PRK03992        268 RGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDV--DLEELAELTEGASGADLKAIC  345 (389)
T ss_pred             CCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcC--CHHHHHHHcCCCCHHHHHHHH
Confidence            235677777765432211    11234579999999999999999887543322211  1355677777753 222222 


Q ss_pred             --HHHhh---cC---CHHHHHHHHHHHhh
Q 044858          351 --AKALK---NK---SPYEWRNALRQLKR  371 (426)
Q Consensus       351 --~~~l~---~~---~~~~w~~~l~~l~~  371 (426)
                        |++.+   +.   +..+...+++....
T Consensus       346 ~eA~~~a~~~~~~~i~~~d~~~A~~~~~~  374 (389)
T PRK03992        346 TEAGMFAIRDDRTEVTMEDFLKAIEKVMG  374 (389)
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence              22221   11   56666666665543

>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=9.7e-06  Score=77.20  Aligned_cols=195  Identities=11%  Similarity=0.086  Sum_probs=121.9

Q ss_pred             CcccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .+....||+.+++.+..++.    .+..+.+-|.|-+|.|||.+...++.+......-.++++++...-.....++..|.
T Consensus       148 ~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI~  227 (529)
T KOG2227|consen  148 PPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKIF  227 (529)
T ss_pred             CCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHHH
Confidence            45678999999999888876    34567889999999999999999998876532223556776655456777888877


Q ss_pred             HHhCCCccc-cCcHHHHHHHHHHHhcCC-eEEEEEeCCCCccC--hhhhcCCC-CCCCCCeEEEEeecchhh--------
Q 044858          225 EKLGLKIDQ-ESESVRAWRLLEQLKKET-KILIILDDIWGSLD--LEAIGIPL-ADDNGGCKVLLTARSQDV--------  291 (426)
Q Consensus       225 ~~l~~~~~~-~~~~~~~~~l~~~l~~~k-~~LlVlDdv~~~~~--~~~l~~~l-~~~~~~s~iivTtr~~~v--------  291 (426)
                      ..+...... .........+.....+.+ .+|+|+|+.+....  -..+...| ...-+++++|+..--...        
T Consensus       228 ~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~Lp  307 (529)
T KOG2227|consen  228 SSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLP  307 (529)
T ss_pred             HHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhh
Confidence            766211111 112333444555555444 79999999975521  11122222 123346666654322211        


Q ss_pred             -hh-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          292 -LS-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       292 -a~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                       .. ........+...|.+.++..++|..++........+....+.++++|.|.
T Consensus       308 rL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~  361 (529)
T KOG2227|consen  308 RLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAP  361 (529)
T ss_pred             hhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccC
Confidence             11 01223568899999999999999999875544444444455555555543

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.47  E-value=7e-06  Score=82.95  Aligned_cols=181  Identities=13%  Similarity=0.135  Sum_probs=108.6

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccc---------------------eE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFE---------------------KV  205 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~---------------------~~  205 (426)
                      ..+..++|.+..++.|..++..++.. .+.++|+.|+||||+|+.+.+........+                     .+
T Consensus        10 ~~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~dv   89 (584)
T PRK14952         10 ATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSIDV   89 (584)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCceE
Confidence            35667899999999999998877655 478999999999999999987654211100                     11


Q ss_pred             EEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCC
Q 044858          206 ISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL----KKETKILIILDDIWGS--LDLEAIGIPLADDNGG  279 (426)
Q Consensus       206 ~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~  279 (426)
                      +.+..+....+                     +.+..+.+.+    ..+++-++|+|+++..  ...+.|...+..-...
T Consensus        90 ieidaas~~gv---------------------d~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~  148 (584)
T PRK14952         90 VELDAASHGGV---------------------DDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEH  148 (584)
T ss_pred             EEeccccccCH---------------------HHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCC
Confidence            12211111111                     1222222222    1245568999999754  3444444444333335


Q ss_pred             eEEEE-eecchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHH
Q 044858          280 CKVLL-TARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPI  350 (426)
Q Consensus       280 s~iiv-Ttr~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~  350 (426)
                      +.+|+ ||....+.....+....+++.+++.++..+.+.+.+......- -.+....|++.++|.+- ++..+
T Consensus       149 ~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i-~~~al~~Ia~~s~GdlR~aln~L  220 (584)
T PRK14952        149 LIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGVVV-DDAVYPLVIRAGGGSPRDTLSVL  220 (584)
T ss_pred             eEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            55554 4444444322233457899999999999988887764322111 23456778899999775 44443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.47  E-value=9.3e-06  Score=80.93  Aligned_cols=186  Identities=15%  Similarity=0.148  Sum_probs=109.8

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCc------------------cc-eEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNL------------------FE-KVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~------------------f~-~~~w  207 (426)
                      .....++|.+.....|...+..++.+ ++.++|+.|+||||+|+.+.+..-....                  +. .++.
T Consensus        11 ~~fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~e   90 (535)
T PRK08451         11 KHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIE   90 (535)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEE
Confidence            35667889998888888888776655 5689999999999999998876532110                  00 1122


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivT  285 (426)
                      +..+....+.++. +++.....                .-..+++-++|+|+++..  +..+.+...+-.-...+++|++
T Consensus        91 ldaas~~gId~IR-elie~~~~----------------~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~  153 (535)
T PRK08451         91 MDAASNRGIDDIR-ELIEQTKY----------------KPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILA  153 (535)
T ss_pred             eccccccCHHHHH-HHHHHHhh----------------CcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEE
Confidence            2211111222211 11111100                000145669999999755  2344443333222345666666


Q ss_pred             ecch-hhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          286 ARSQ-DVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       286 tr~~-~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      |.+. .+..........+++.+++.++....+.+.+...... --.+.+..|++.++|.+.-+..+.
T Consensus       154 ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~-i~~~Al~~Ia~~s~GdlR~alnlL  219 (535)
T PRK08451        154 TTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVS-YEPEALEILARSGNGSLRDTLTLL  219 (535)
T ss_pred             ECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCcHHHHHHHH
Confidence            6553 2221122345789999999999999988777532211 124567889999999986555443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.46  E-value=7e-06  Score=83.99  Aligned_cols=197  Identities=13%  Similarity=0.150  Sum_probs=113.4

Q ss_pred             CcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .+..++|.+..++.|..++..++. ..+.++|+.|+||||+|+.+.+.........      ....++.....+.|....
T Consensus        14 ~~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~------~~~~c~~c~~c~~i~~~~   87 (585)
T PRK14950         14 TFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP------KGRPCGTCEMCRAIAEGS   87 (585)
T ss_pred             CHHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCCCCccCHHHHHHhcCC
Confidence            456788999999999888876654 4568999999999999999987764211100      001112222333333222


Q ss_pred             CCCc---c--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhcc
Q 044858          228 GLKI---D--QESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSCE  295 (426)
Q Consensus       228 ~~~~---~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~  295 (426)
                      ....   +  .....+.+..+.+.+.    .+++-++|||+++..  ...+.+...+......+.+|++|.+ ..+....
T Consensus        88 ~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI  167 (585)
T PRK14950         88 AVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATI  167 (585)
T ss_pred             CCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHH
Confidence            1110   0  0111122233333222    145679999999754  3344444333333345666665543 3332212


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHH
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      ......+.+.+++..+....+...+...... --.+.+..|++.++|.+..+.....
T Consensus       168 ~SR~~~i~f~~l~~~el~~~L~~~a~~egl~-i~~eal~~La~~s~Gdlr~al~~Le  223 (585)
T PRK14950        168 LSRCQRFDFHRHSVADMAAHLRKIAAAEGIN-LEPGALEAIARAATGSMRDAENLLQ  223 (585)
T ss_pred             HhccceeeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            2334678899999999998888876532211 1245678899999998875554433

>PF14516 AAA_35: AAA-like domain

Probab=98.46  E-value=2.2e-05  Score=74.60  Aligned_cols=199  Identities=12%  Similarity=0.170  Sum_probs=116.8

Q ss_pred             ccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-----cCHHHHHHHHH-
Q 044858          151 MHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-----PQIKEIQREIA-  224 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-----~~~~~il~~i~-  224 (426)
                      ...+.|...-+.+.+.+.++ -..+.|.|+..+|||||...+.+..... .+. .+++++..-     .+...+++.++ 
T Consensus        11 ~~Yi~R~~~e~~~~~~i~~~-G~~~~I~apRq~GKTSll~~l~~~l~~~-~~~-~v~id~~~~~~~~~~~~~~f~~~~~~   87 (331)
T PF14516_consen   11 PFYIERPPAEQECYQEIVQP-GSYIRIKAPRQMGKTSLLLRLLERLQQQ-GYR-CVYIDLQQLGSAIFSDLEQFLRWFCE   87 (331)
T ss_pred             CcccCchHHHHHHHHHHhcC-CCEEEEECcccCCHHHHHHHHHHHHHHC-CCE-EEEEEeecCCCcccCCHHHHHHHHHH
Confidence            34567876666677776653 3579999999999999999999888764 243 446665431     24555555554 


Q ss_pred             ---HHhCCCcccc-------Cc-HHHHHHHHHHHh--cCCeEEEEEeCCCCccC---h-hhhcCCCC------C-C--CC
Q 044858          225 ---EKLGLKIDQE-------SE-SVRAWRLLEQLK--KETKILIILDDIWGSLD---L-EAIGIPLA------D-D--NG  278 (426)
Q Consensus       225 ---~~l~~~~~~~-------~~-~~~~~~l~~~l~--~~k~~LlVlDdv~~~~~---~-~~l~~~l~------~-~--~~  278 (426)
                         ++++....-.       +. ......+.+.+.  .+++.+|+||+++....   + .++...+.      . .  -.
T Consensus        88 ~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~  167 (331)
T PF14516_consen   88 EISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQ  167 (331)
T ss_pred             HHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccc
Confidence               4554432110       11 111122223332  25899999999975422   1 11111110      0 0  01


Q ss_pred             CeEEEEeecchh-h-h---hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          279 GCKVLLTARSQD-V-L---SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       279 ~s~iivTtr~~~-v-a---~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      .-++++....+. . .   .........++|++|+.+|...|+...-.. . .   ....++|...+||+|.-+..++..
T Consensus       168 ~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~-~-~---~~~~~~l~~~tgGhP~Lv~~~~~~  242 (331)
T PF14516_consen  168 KLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLE-F-S---QEQLEQLMDWTGGHPYLVQKACYL  242 (331)
T ss_pred             eEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhcc-C-C---HHHHHHHHHHHCCCHHHHHHHHHH
Confidence            122222221111 1 1   112233458999999999999998876322 1 1   223889999999999999999999


Q ss_pred             hhcC
Q 044858          354 LKNK  357 (426)
Q Consensus       354 l~~~  357 (426)
                      +...
T Consensus       243 l~~~  246 (331)
T PF14516_consen  243 LVEE  246 (331)
T ss_pred             HHHc
Confidence            9753

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.45  E-value=8.4e-06  Score=83.35  Aligned_cols=182  Identities=10%  Similarity=0.139  Sum_probs=109.8

Q ss_pred             CcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhh---------------------cCccceEE
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKE---------------------NNLFEKVI  206 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~---------------------~~~f~~~~  206 (426)
                      .+..++|.+...+.|...+..++.. .+.++|+.|+||||+|+.+......                     ..+|+. .
T Consensus        15 ~f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~-~   93 (614)
T PRK14971         15 TFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNI-H   93 (614)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCce-E
Confidence            5667889999999999998877654 5789999999999999998876531                     112332 2


Q ss_pred             EEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEE
Q 044858          207 SSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLL  284 (426)
Q Consensus       207 wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iiv  284 (426)
                      .+..+...+..++. +++.++....                ..+++-++|+|+++..  ...+.+...+..-..++.+|+
T Consensus        94 ~ld~~~~~~vd~Ir-~li~~~~~~P----------------~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL  156 (614)
T PRK14971         94 ELDAASNNSVDDIR-NLIEQVRIPP----------------QIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFIL  156 (614)
T ss_pred             EecccccCCHHHHH-HHHHHHhhCc----------------ccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEE
Confidence            22222222222221 2222211100                0134568899998765  335555444433334566555


Q ss_pred             ee-cchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHH
Q 044858          285 TA-RSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVP  349 (426)
Q Consensus       285 Tt-r~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~  349 (426)
                      +| ....+..........+++.+++.++....+.+.+...... --.+.+..|++.++|..--+..
T Consensus       157 ~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~-i~~~al~~La~~s~gdlr~al~  221 (614)
T PRK14971        157 ATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGIT-AEPEALNVIAQKADGGMRDALS  221 (614)
T ss_pred             EeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHH
Confidence            44 4444432223445789999999999999998876432211 1134678899999997754433

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.44  E-value=8.9e-06  Score=80.33  Aligned_cols=183  Identities=16%  Similarity=0.123  Sum_probs=110.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .-+.|+|..|+|||+|++.+.+.......-..+++++      ..++...+...+....      .......+.+.  +.
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~------~~~f~~~~~~~l~~~~------~~~~~~~~~~~--~~  207 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMS------GDEFARKAVDILQKTH------KEIEQFKNEIC--QN  207 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE------HHHHHHHHHHHHHHhh------hHHHHHHHHhc--cC
Confidence            4588999999999999999998765432222344543      3466667666553210      12233334443  34


Q ss_pred             EEEEEeCCCCcc---Chh-hhcCCCCC-CCCCeEEEEeecchhhhh--------ccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGSL---DLE-AIGIPLAD-DNGGCKVLLTARSQDVLS--------CEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~~---~~~-~l~~~l~~-~~~~s~iivTtr~~~va~--------~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      -+|+|||+....   .+. .+...+.. ...|..||+|+.......        ......-.+.+++++.++-.+++.+.
T Consensus       208 dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~  287 (450)
T PRK14087        208 DVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKE  287 (450)
T ss_pred             CEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHH
Confidence            589999997542   222 22222211 123457888876542110        11223457889999999999999998


Q ss_pred             hCCCCC-CCchHHHHHHHHHHcCCchHHHHHHHHHhh-----c---C--CHHHHHHHHHHH
Q 044858          320 TGDCIE-NGELKSVVTEVVKECAGLPIAIVPIAKALK-----N---K--SPYEWRNALRQL  369 (426)
Q Consensus       320 ~~~~~~-~~~~~~~~~~i~~~c~GlPlai~~~~~~l~-----~---~--~~~~w~~~l~~l  369 (426)
                      +..... ..--+++..-|++.++|.|-.+..+...+.     .   +  +...-+.++..+
T Consensus       288 ~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l~~~a~~~~~~~~it~~~v~~~l~~~  348 (450)
T PRK14087        288 IKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRLNFWSQQNPEEKIITIEIVSDLFRDI  348 (450)
T ss_pred             HHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHhhc
Confidence            853221 123367889999999999998876654431     1   2  555556666554

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.44  E-value=1.2e-05  Score=79.99  Aligned_cols=181  Identities=12%  Similarity=0.114  Sum_probs=107.0

Q ss_pred             CcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhc-------------------CccceEEEE
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKEN-------------------NLFEKVISS  208 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv  208 (426)
                      .+..++|.+.....+..++..++.. .+.++|+.|+||||+|+.+.......                   +.|...+.+
T Consensus        14 ~f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~ei   93 (486)
T PRK14953         14 FFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEI   93 (486)
T ss_pred             cHHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEE
Confidence            5567889999999999988876544 56789999999999999988764310                   001112222


Q ss_pred             EecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEE
Q 044858          209 RVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKV  282 (426)
Q Consensus       209 ~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~i  282 (426)
                      ..+......                     .+..+.+.+.    .+++-++|+|+++..  ...+.+...+....+.+.+
T Consensus        94 daas~~gvd---------------------~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~  152 (486)
T PRK14953         94 DAASNRGID---------------------DIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIF  152 (486)
T ss_pred             eCccCCCHH---------------------HHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEE
Confidence            221111111                     1222222221    246679999999754  2344443333322334455


Q ss_pred             EEee-cchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          283 LLTA-RSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       283 ivTt-r~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      |++| +...+..........+.+.+++.++....+.+.+...... .-.+....|++.++|.+..+....
T Consensus       153 Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~-id~~al~~La~~s~G~lr~al~~L  221 (486)
T PRK14953        153 ILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIE-YEEKALDLLAQASEGGMRDAASLL  221 (486)
T ss_pred             EEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            5544 4333321112334689999999999999888876422211 123567788999999876555444

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.44  E-value=8.2e-06  Score=83.06  Aligned_cols=198  Identities=14%  Similarity=0.130  Sum_probs=108.7

Q ss_pred             CcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEE-ecCCcCHHHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSR-VSQTPQIKEIQREIAEK  226 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~-v~~~~~~~~il~~i~~~  226 (426)
                      .+..++|.+..+..|...+..++.. .+.++|+.|+||||+|+.+.+..-.....+.-.|.. +...+......+.+...
T Consensus        14 ~f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g   93 (620)
T PRK14954         14 KFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFDAG   93 (620)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHhcc
Confidence            5667889999999988888776654 588999999999999999987764321111000110 00111111111111110


Q ss_pred             hCCCc---c--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEee-cchhhhhc
Q 044858          227 LGLKI---D--QESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTA-RSQDVLSC  294 (426)
Q Consensus       227 l~~~~---~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTt-r~~~va~~  294 (426)
                      -..+.   +  .....+.+..+.+.+.    .+.+-++|+|+++...  ..+.+...+..-...+.+|++| +...+...
T Consensus        94 ~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~T  173 (620)
T PRK14954         94 TSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPAT  173 (620)
T ss_pred             CCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHH
Confidence            00000   0  0011223333333331    2345688999987553  3444444443323345555444 43443322


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      .......+++.+++.++....+.+.+...... --.+.+..|++.++|.+--+
T Consensus       174 I~SRc~~vef~~l~~~ei~~~L~~i~~~egi~-I~~eal~~La~~s~Gdlr~a  225 (620)
T PRK14954        174 IASRCQRFNFKRIPLDEIQSQLQMICRAEGIQ-IDADALQLIARKAQGSMRDA  225 (620)
T ss_pred             HHhhceEEecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHhCCCHHHH
Confidence            23446789999999999988888766422111 12456788999999965533

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

Probab=98.43  E-value=3.3e-06  Score=88.76  Aligned_cols=158  Identities=16%  Similarity=0.210  Sum_probs=94.5

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc---c-ceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL---F-EKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~---f-~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ...+++||+++++.++..|......-+.++|++|+|||++|+.+.+.......   + ...+|. +    +...+...  
T Consensus       180 ~l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~-~----~~~~l~a~--  252 (731)
T TIGR02639       180 KIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS-L----DMGSLLAG--  252 (731)
T ss_pred             CCCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE-e----cHHHHhhh--
Confidence            45679999999999999888666667889999999999999999988643211   1 233332 1    11111110  


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------Chhh-hcCCCCCCCCCeEEEEeecchhh--
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL----------DLEA-IGIPLADDNGGCKVLLTARSQDV--  291 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~----------~~~~-l~~~l~~~~~~s~iivTtr~~~v--  291 (426)
                           ..........+..+++.+...++.+|++|+++...          +... +...+ . ...-++|-+|.....  
T Consensus       253 -----~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l-~-~g~i~~IgaTt~~e~~~  325 (731)
T TIGR02639       253 -----TKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPAL-S-SGKLRCIGSTTYEEYKN  325 (731)
T ss_pred             -----ccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHH-h-CCCeEEEEecCHHHHHH
Confidence                 00001122345556666554568999999997331          1112 22222 1 123455555543211  


Q ss_pred             --h--hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          292 --L--SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       292 --a--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                        .  .........+++++++.++..+++....
T Consensus       326 ~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       326 HFEKDRALSRRFQKIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             HhhhhHHHHHhCceEEeCCCCHHHHHHHHHHHH
Confidence              1  1112234689999999999999999655

>TIGR00767 rho transcription termination factor Rho

Probab=98.43  E-value=1.2e-06  Score=83.10  Aligned_cols=92  Identities=15%  Similarity=0.137  Sum_probs=64.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC--cCHHHHHHHHHHHhCCCccccCcHH------H-HH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT--PQIKEIQREIAEKLGLKIDQESESV------R-AW  241 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~il~~i~~~l~~~~~~~~~~~------~-~~  241 (426)
                      .-..+.|+|++|+|||||++.+++....+ +|+..+|+.+.+.  .++.++++.++..+-...-..+...      . .+
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e  245 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIE  245 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHH
Confidence            34678999999999999999999988764 8999899999865  7899999999543322111111111      1 11


Q ss_pred             HHHHHHhcCCeEEEEEeCCCCc
Q 044858          242 RLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       242 ~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      .......++++.+|++|++...
T Consensus       246 ~Ae~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       246 KAKRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHHHcCCCeEEEEEChhHH
Confidence            2222334689999999999643

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

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.43  E-value=2.9e-06  Score=80.47  Aligned_cols=177  Identities=15%  Similarity=0.095  Sum_probs=97.2

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .....++|.+...+.+..++..++. .++.++|++|+|||++|+.+++....     ....++.+. .... ..+..+..
T Consensus        18 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~~-----~~~~i~~~~-~~~~-~i~~~l~~   90 (316)
T PHA02544         18 STIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGA-----EVLFVNGSD-CRID-FVRNRLTR   90 (316)
T ss_pred             CcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCc-----cceEeccCc-ccHH-HHHHHHHH
Confidence            4567788999999999998876654 46667999999999999999886532     123344333 2211 11111111


Q ss_pred             hCCCccccCcHHHHHHHHHHH-hcCCeEEEEEeCCCCc--cCh-hhhcCCCCCCCCCeEEEEeecchhhh-hccCCceee
Q 044858          227 LGLKIDQESESVRAWRLLEQL-KKETKILIILDDIWGS--LDL-EAIGIPLADDNGGCKVLLTARSQDVL-SCEMDCQQN  301 (426)
Q Consensus       227 l~~~~~~~~~~~~~~~l~~~l-~~~k~~LlVlDdv~~~--~~~-~~l~~~l~~~~~~s~iivTtr~~~va-~~~~~~~~~  301 (426)
                      +                .... ..+.+-+|||||++..  ... ..+...+.....++++|+||...... ....+....
T Consensus        91 ~----------------~~~~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~  154 (316)
T PHA02544         91 F----------------ASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRV  154 (316)
T ss_pred             H----------------HHhhcccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceE
Confidence            1                0111 0124568999999754  111 22322222234567888888654321 111223356


Q ss_pred             EEccCCCHHHHHHHHHHhhC------CCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          302 FVVDVLNDKEAWSLFKKMTG------DCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       302 ~~l~~L~~~e~~~Lf~~~~~------~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      +.++..+.++..+++...+.      .....+-..+....+++..+|.-..+
T Consensus       155 i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~~~~~d~r~~  206 (316)
T PHA02544        155 IDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKKNFPDFRRT  206 (316)
T ss_pred             EEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhcCCCHHHH
Confidence            78877888887766543221      00111112334566776666644333

>PRK05642 DNA replication initiation factor; Validated

Probab=98.42  E-value=5.9e-06  Score=74.52  Aligned_cols=153  Identities=16%  Similarity=0.166  Sum_probs=91.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.|+|+.|+|||.|++.+++....+  -..++|++..      ++...                 ...+.+.+.+.  
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~--~~~v~y~~~~------~~~~~-----------------~~~~~~~~~~~--   98 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQR--GEPAVYLPLA------ELLDR-----------------GPELLDNLEQY--   98 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhC--CCcEEEeeHH------HHHhh-----------------hHHHHHhhhhC--
Confidence            568999999999999999998876543  2345666543      22211                 01233333321  


Q ss_pred             EEEEEeCCCCc---cChhh-hcCCCCC-CCCCeEEEEeecchhhhhc--------cCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGS---LDLEA-IGIPLAD-DNGGCKVLLTARSQDVLSC--------EMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~---~~~~~-l~~~l~~-~~~~s~iivTtr~~~va~~--------~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      =+|++||+...   ..|+. +...+.. ...|.++|+|++.....-.        .......+++++++.++-.++++.+
T Consensus        99 d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~k  178 (234)
T PRK05642         99 ELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLR  178 (234)
T ss_pred             CEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHH
Confidence            27889999633   34543 3222211 1246678888876432110        1122367899999999999999866


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      +.... -.--+++..-|++.+.|..-.+..+-..
T Consensus       179 a~~~~-~~l~~ev~~~L~~~~~~d~r~l~~~l~~  211 (234)
T PRK05642        179 ASRRG-LHLTDEVGHFILTRGTRSMSALFDLLER  211 (234)
T ss_pred             HHHcC-CCCCHHHHHHHHHhcCCCHHHHHHHHHH
Confidence            54221 1111467778888888776555444433

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.41  E-value=4.1e-06  Score=89.17  Aligned_cols=158  Identities=15%  Similarity=0.259  Sum_probs=94.2

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc---c-ceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL---F-EKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~---f-~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ...+++||+++++.+++.|.......+.++|++|+|||++|+.++......+.   . ...+|. +    +...++.   
T Consensus       177 ~~~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~-l----~~~~l~a---  248 (821)
T CHL00095        177 NLDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT-L----DIGLLLA---  248 (821)
T ss_pred             CCCCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE-e----eHHHHhc---
Confidence            34678999999999999998665566789999999999999999887643211   1 233442 1    2222111   


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc---------ChhhhcCCCCCCCCCeEEEEeecchhh----
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL---------DLEAIGIPLADDNGGCKVLLTARSQDV----  291 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~---------~~~~l~~~l~~~~~~s~iivTtr~~~v----  291 (426)
                         +... .......+..+++.+...++.+|++|+++...         +...+..+... ...-++|.+|..+..    
T Consensus       249 ---g~~~-~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~-rg~l~~IgaTt~~ey~~~i  323 (821)
T CHL00095        249 ---GTKY-RGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALA-RGELQCIGATTLDEYRKHI  323 (821)
T ss_pred             ---cCCC-ccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHh-CCCcEEEEeCCHHHHHHHH
Confidence               1111 11122345556666655578999999996331         11222222211 123455555554432    


Q ss_pred             h--hccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          292 L--SCEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       292 a--~~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      .  .........+.+...+.++...++...
T Consensus       324 e~D~aL~rRf~~I~v~ep~~~e~~aILr~l  353 (821)
T CHL00095        324 EKDPALERRFQPVYVGEPSVEETIEILFGL  353 (821)
T ss_pred             hcCHHHHhcceEEecCCCCHHHHHHHHHHH
Confidence            1  112234567889999999988888754

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.38  E-value=3.1e-06  Score=77.82  Aligned_cols=135  Identities=15%  Similarity=0.222  Sum_probs=70.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ....+.++|++|+||||+|+.+++.......-....++.++.    .++....   .+     .. ......+++..   
T Consensus        41 ~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~----~~l~~~~---~g-----~~-~~~~~~~~~~a---  104 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVER----ADLVGEY---IG-----HT-AQKTREVIKKA---  104 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecH----HHhhhhh---cc-----ch-HHHHHHHHHhc---
Confidence            345678999999999999999987653221111112233322    1111110   00     00 11122222222   


Q ss_pred             CeEEEEEeCCCCcc----------ChhhhcCCCCCCCCCeEEEEeecchhhh-------hccCCceeeEEccCCCHHHHH
Q 044858          251 TKILIILDDIWGSL----------DLEAIGIPLADDNGGCKVLLTARSQDVL-------SCEMDCQQNFVVDVLNDKEAW  313 (426)
Q Consensus       251 k~~LlVlDdv~~~~----------~~~~l~~~l~~~~~~s~iivTtr~~~va-------~~~~~~~~~~~l~~L~~~e~~  313 (426)
                      ...+|+||+++...          ....+...+........+|+++......       .........+++++++.++-.
T Consensus       105 ~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~  184 (261)
T TIGR02881       105 LGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELM  184 (261)
T ss_pred             cCCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHH
Confidence            23589999997532          1222333332333344556665443210       001122357899999999999


Q ss_pred             HHHHHhhC
Q 044858          314 SLFKKMTG  321 (426)
Q Consensus       314 ~Lf~~~~~  321 (426)
                      +++.+.+.
T Consensus       185 ~Il~~~~~  192 (261)
T TIGR02881       185 EIAERMVK  192 (261)
T ss_pred             HHHHHHHH
Confidence            99998875

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.37  E-value=1.9e-05  Score=77.98  Aligned_cols=183  Identities=14%  Similarity=0.151  Sum_probs=106.1

Q ss_pred             CcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC---------------------ccceEE
Q 044858          149 DFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENN---------------------LFEKVI  206 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~---------------------~f~~~~  206 (426)
                      .+..++|.+..+..+...+..++. +.+.++|+.|+||||+|+.+.+......                     +++ .+
T Consensus        15 ~~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d-~~   93 (451)
T PRK06305         15 TFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLD-VL   93 (451)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCc-eE
Confidence            566788999999999988887665 5678999999999999999987653211                     111 11


Q ss_pred             EEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEE
Q 044858          207 SSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLL  284 (426)
Q Consensus       207 wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iiv  284 (426)
                      ++.........++ +++.+.+.                ..-..+++-++|+|+++..  ...+.+...+.....++.+|+
T Consensus        94 ~i~g~~~~gid~i-r~i~~~l~----------------~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il  156 (451)
T PRK06305         94 EIDGASHRGIEDI-RQINETVL----------------FTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFL  156 (451)
T ss_pred             EeeccccCCHHHH-HHHHHHHH----------------hhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEE
Confidence            1111111111111 11111110                0001245678999998644  233334333333233556666


Q ss_pred             eecc-hhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHH
Q 044858          285 TARS-QDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPI  350 (426)
Q Consensus       285 Ttr~-~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~  350 (426)
                      +|.. ..+..........+++.++++++....+.+.+...... --.+.+..|++.++|.+- |+..+
T Consensus       157 ~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~-i~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        157 ATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIE-TSREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             EeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            6533 32222122345689999999999998888776422111 124567889999999765 44443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.37  E-value=1.4e-05  Score=81.86  Aligned_cols=178  Identities=13%  Similarity=0.117  Sum_probs=106.0

Q ss_pred             CcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCcc----ce------------EEEEEec
Q 044858          149 DFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLF----EK------------VISSRVS  211 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----~~------------~~wv~v~  211 (426)
                      .+..++|.+..+..|...+..++. +.+.++|+.|+||||+|+.+....-.....    .|            ++++...
T Consensus        16 ~f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaa   95 (725)
T PRK07133         16 TFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMDAA   95 (725)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEEEEecc
Confidence            566788999999999998887654 466899999999999999998764321100    00            0111110


Q ss_pred             CCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEE-E
Q 044858          212 QTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVL-L  284 (426)
Q Consensus       212 ~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~ii-v  284 (426)
                      ...                     ....+..+.+.+.    .+++-++|+|+++..  ..+..+...+-.-...+.+| +
T Consensus        96 sn~---------------------~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILa  154 (725)
T PRK07133         96 SNN---------------------GVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILA  154 (725)
T ss_pred             ccC---------------------CHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEE
Confidence            001                     1122333333332    245669999999754  34555443332222344444 5


Q ss_pred             eecchhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHH
Q 044858          285 TARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       285 Ttr~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                      |+....+..........+.+.+++.++....+...+......- -.+.+..|++.++|.+.-+.
T Consensus       155 Tte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~i-d~eAl~~LA~lS~GslR~Al  217 (725)
T PRK07133        155 TTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISY-EKNALKLIAKLSSGSLRDAL  217 (725)
T ss_pred             cCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHH
Confidence            5554444322233456899999999999988887654221111 13457789999999765333

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

Probab=98.37  E-value=8.1e-06  Score=79.37  Aligned_cols=136  Identities=24%  Similarity=0.241  Sum_probs=86.2

Q ss_pred             hHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccC
Q 044858          156 RKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQES  235 (426)
Q Consensus       156 R~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~  235 (426)
                      |...+.++++.+..... ++.|.|+.++||||+++.+.......     .+++..........-+.+...          
T Consensus        22 ~~~~~~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~~-----~iy~~~~d~~~~~~~l~d~~~----------   85 (398)
T COG1373          22 RRKLLPRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLEE-----IIYINFDDLRLDRIELLDLLR----------   85 (398)
T ss_pred             HHhhhHHHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCCcc-----eEEEEecchhcchhhHHHHHH----------
Confidence            44455666666554433 99999999999999997666554432     455543322211111111111          


Q ss_pred             cHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhh-----hccCCceeeEEccCCCHH
Q 044858          236 ESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVL-----SCEMDCQQNFVVDVLNDK  310 (426)
Q Consensus       236 ~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va-----~~~~~~~~~~~l~~L~~~  310 (426)
                            .+...- ..++..++||.|+....|......+.+..+. +|++|+.+....     ....+....+++-|||..
T Consensus        86 ------~~~~~~-~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~  157 (398)
T COG1373          86 ------AYIELK-EREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFR  157 (398)
T ss_pred             ------HHHHhh-ccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHH
Confidence                  111111 1267899999999999999876666665555 889988887553     223455678999999999


Q ss_pred             HHHHH
Q 044858          311 EAWSL  315 (426)
Q Consensus       311 e~~~L  315 (426)
                      |...+
T Consensus       158 Efl~~  162 (398)
T COG1373         158 EFLKL  162 (398)
T ss_pred             HHHhh
Confidence            98764

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.34  E-value=2.4e-05  Score=79.14  Aligned_cols=195  Identities=12%  Similarity=0.116  Sum_probs=109.6

Q ss_pred             CCcccccchHHHHHHHHHHhccCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ..+..++|.+..+..|...+.+++.+ .+.++|+.|+||||+|+.+.+..........       .++......+.|...
T Consensus        13 ~~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~-------~pC~~C~~C~~i~~~   85 (563)
T PRK06647         13 RDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP-------MPCGECSSCKSIDND   85 (563)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCC-------CCCccchHHHHHHcC
Confidence            35667889999999999988876554 5889999999999999999887542110000       000000000111100


Q ss_pred             hCCC---ccc--cCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecc-hhhhhc
Q 044858          227 LGLK---IDQ--ESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARS-QDVLSC  294 (426)
Q Consensus       227 l~~~---~~~--~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~-~~va~~  294 (426)
                      -...   .+.  ....+.+..+.+.+.    .+++-++|+|+++...  .++.+...+..-...+.+|++|.. ..+...
T Consensus        86 ~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~t  165 (563)
T PRK06647         86 NSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPAT  165 (563)
T ss_pred             CCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHH
Confidence            0000   000  011112222222211    2456689999997553  355554444333345666655543 333221


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      .......+++.+++.++....+.+.+..... +--.+....|++.++|.+..+..+
T Consensus       166 I~SRc~~~~f~~l~~~el~~~L~~i~~~egi-~id~eAl~lLa~~s~GdlR~alsl  220 (563)
T PRK06647        166 IKSRCQHFNFRLLSLEKIYNMLKKVCLEDQI-KYEDEALKWIAYKSTGSVRDAYTL  220 (563)
T ss_pred             HHHhceEEEecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            2234567899999999999888887642221 122456778999999988654443

>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=98.33  E-value=4.7e-06  Score=74.29  Aligned_cols=163  Identities=17%  Similarity=0.183  Sum_probs=93.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      ...+.|+|+.|+|||.|.+.+++.......-..++|++      ..++...+...+...        ....+.+.+.  .
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~------~~~f~~~~~~~~~~~--------~~~~~~~~~~--~   97 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS------AEEFIREFADALRDG--------EIEEFKDRLR--S   97 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE------HHHHHHHHHHHHHTT--------SHHHHHHHHC--T
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec------HHHHHHHHHHHHHcc--------cchhhhhhhh--c
Confidence            34688999999999999999999876532222455654      345555555544321        1223445554  2


Q ss_pred             eEEEEEeCCCCccC---hhh-hcCCCC-CCCCCeEEEEeecchhhhh--------ccCCceeeEEccCCCHHHHHHHHHH
Q 044858          252 KILIILDDIWGSLD---LEA-IGIPLA-DDNGGCKVLLTARSQDVLS--------CEMDCQQNFVVDVLNDKEAWSLFKK  318 (426)
Q Consensus       252 ~~LlVlDdv~~~~~---~~~-l~~~l~-~~~~~s~iivTtr~~~va~--------~~~~~~~~~~l~~L~~~e~~~Lf~~  318 (426)
                      -=+|+|||++....   |+. +...+. ....|-+||+|+......-        ......-.+++++.+.++-.+++.+
T Consensus        98 ~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~  177 (219)
T PF00308_consen   98 ADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQK  177 (219)
T ss_dssp             SSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHH
T ss_pred             CCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHH
Confidence            35899999976522   332 111111 0124668999997653220        1122345899999999999999998


Q ss_pred             hhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          319 MTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       319 ~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      .+...... --+++.+-|++.+.+..-.+..+-
T Consensus       178 ~a~~~~~~-l~~~v~~~l~~~~~~~~r~L~~~l  209 (219)
T PF00308_consen  178 KAKERGIE-LPEEVIEYLARRFRRDVRELEGAL  209 (219)
T ss_dssp             HHHHTT---S-HHHHHHHHHHTTSSHHHHHHHH
T ss_pred             HHHHhCCC-CcHHHHHHHHHhhcCCHHHHHHHH
Confidence            88522211 224567777777776655554443

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.

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

Probab=98.33  E-value=9e-06  Score=73.40  Aligned_cols=189  Identities=17%  Similarity=0.180  Sum_probs=118.6

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEE-EEEecCCcCHHHHHHHHH--
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVI-SSRVSQTPQIKEIQREIA--  224 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~-wv~v~~~~~~~~il~~i~--  224 (426)
                      .....+.|.+..+..|.+.+.....++...+||+|.|||+-|..+....-..+.|.+.+ -.++|......-+-..+-  
T Consensus        33 kt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~f  112 (346)
T KOG0989|consen   33 KTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNF  112 (346)
T ss_pred             CcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCH
Confidence            45677889999999999988887788999999999999999999988776666777654 345554433221111110  


Q ss_pred             HHhCCCccccCcHHHHHHHHHHH-hcCCe-EEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhccCCce
Q 044858          225 EKLGLKIDQESESVRAWRLLEQL-KKETK-ILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSCEMDCQ  299 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l-~~~k~-~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~~~~~  299 (426)
                      .++.....            ... ..-++ -++|||+++..  +.|..+...+......++.|+.+.. ..+........
T Consensus       113 akl~~~~~------------~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC  180 (346)
T KOG0989|consen  113 AKLTVLLK------------RSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRC  180 (346)
T ss_pred             HHHhhccc------------cccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhH
Confidence            00000000            000 01123 48889999865  6788776655544555665544433 33322223345


Q ss_pred             eeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHH
Q 044858          300 QNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVP  349 (426)
Q Consensus       300 ~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~  349 (426)
                      ..+..++|.+++...-+...+..+..+-+ .+..+.|++.++|----..+
T Consensus       181 ~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d-~~al~~I~~~S~GdLR~Ait  229 (346)
T KOG0989|consen  181 QKFRFKKLKDEDIVDRLEKIASKEGVDID-DDALKLIAKISDGDLRRAIT  229 (346)
T ss_pred             HHhcCCCcchHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHcCCcHHHHHH
Confidence            67899999999999888888753332222 45678899999996443333

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.32  E-value=1.2e-05  Score=81.82  Aligned_cols=197  Identities=14%  Similarity=0.151  Sum_probs=108.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ..+..++|.++....|...+..++. +.+.++|+.|+||||+|+.+.+..........       ..++.......|...
T Consensus        13 ~~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~-------~~c~~c~~c~~i~~g   85 (576)
T PRK14965         13 QTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTA-------EPCNVCPPCVEITEG   85 (576)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC-------CCCCccHHHHHHhcC
Confidence            3567789999999999998887665 45689999999999999999877532111100       000000111111000


Q ss_pred             hCCC---ccc--cCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEE-eecchhhhhc
Q 044858          227 LGLK---IDQ--ESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLL-TARSQDVLSC  294 (426)
Q Consensus       227 l~~~---~~~--~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iiv-Ttr~~~va~~  294 (426)
                      -...   .+.  ....+.+..+.+.+.    .+++-++|||+++...  ..+.+...+-.-...+.+|+ ||....+...
T Consensus        86 ~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~t  165 (576)
T PRK14965         86 RSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPIT  165 (576)
T ss_pred             CCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHH
Confidence            0000   000  001112222332221    2345689999997542  34444433322233555555 4444444322


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch-HHHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP-IAIVPIAK  352 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP-lai~~~~~  352 (426)
                      ..+....+++.+++.++....+...+......- -.+....|++.++|.. .|+..+-.
T Consensus       166 I~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i-~~~al~~la~~a~G~lr~al~~Ldq  223 (576)
T PRK14965        166 ILSRCQRFDFRRIPLQKIVDRLRYIADQEGISI-SDAALALVARKGDGSMRDSLSTLDQ  223 (576)
T ss_pred             HHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            233456889999999999888887664222111 1456778889999866 44444433

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.31  E-value=1.1e-06  Score=82.67  Aligned_cols=226  Identities=22%  Similarity=0.260  Sum_probs=146.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .+.+.++|.||+||||++-++.. ...  .|. .+.++...+-.+...+.-.....++......  ......+...+. +
T Consensus        14 ~RlvtL~g~ggvgkttl~~~~a~-~~~--~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~g--~~~~~~~~~~~~-~   87 (414)
T COG3903          14 LRLVTLTGAGGVGKTTLALQAAH-AAS--EYADGVAFVDLAPITDPALVFPTLAGALGLHVQPG--DSAVDTLVRRIG-D   87 (414)
T ss_pred             hheeeeeccCccceehhhhhhHh-Hhh--hcccceeeeeccccCchhHhHHHHHhhcccccccc--hHHHHHHHHHHh-h
Confidence            47799999999999999999988 332  365 5666666666666666666666676654321  123334455554 5


Q ss_pred             CeEEEEEeCCCCcc-ChhhhcCCCCCCCCCeEEEEeecchhhhhccCCceeeEEccCCCHH-HHHHHHHHhhCCCC----
Q 044858          251 TKILIILDDIWGSL-DLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDK-EAWSLFKKMTGDCI----  324 (426)
Q Consensus       251 k~~LlVlDdv~~~~-~~~~l~~~l~~~~~~s~iivTtr~~~va~~~~~~~~~~~l~~L~~~-e~~~Lf~~~~~~~~----  324 (426)
                      +|.++|+||..+.. .-..+...+..+.+.-.|+.|+|....    ........+.+|+.. ++.++|...+....    
T Consensus        88 rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l----~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~  163 (414)
T COG3903          88 RRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAIL----VAGEVHRRVPSLSLFDEAIELFVCRAVLVALSFW  163 (414)
T ss_pred             hhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhc----ccccccccCCccccCCchhHHHHHHHHHhcccee
Confidence            89999999986542 222222233334455678888887653    233456777777755 78899887763111    


Q ss_pred             CCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHH----HhhccccCCCCcchhhhhhhHHhhhcCCCCCh
Q 044858          325 ENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQ----LKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEE  400 (426)
Q Consensus       325 ~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~----l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~  400 (426)
                      -.......+..|.++.+|.|++|...++..++....+-...++.    +..- ... ...........+.+||.-|... 
T Consensus       164 l~~~~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~-~r~-a~~~~qtl~asl~ws~~lLtgw-  240 (414)
T COG3903         164 LTDDNAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGG-ARL-AVLRQQTLRASLDWSYALLTGW-  240 (414)
T ss_pred             ecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcc-ccc-chhHHHhccchhhhhhHhhhhH-
Confidence            12233567889999999999999999999987755554443332    2111 111 1111267788999999999886 


Q ss_pred             hHHHHHHhhc
Q 044858          401 LRKTFLLIGY  410 (426)
Q Consensus       401 lk~cfl~~s~  410 (426)
                      .+--|--++.
T Consensus       241 e~~~~~rLa~  250 (414)
T COG3903         241 ERALFGRLAV  250 (414)
T ss_pred             HHHHhcchhh
Confidence            7777766666

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.29  E-value=3.9e-05  Score=78.59  Aligned_cols=197  Identities=15%  Similarity=0.108  Sum_probs=111.6

Q ss_pred             CcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .+..++|.+..+..|..++..++. +.+.++|+.|+||||+|+.+.+..........     ....+...+..+.+....
T Consensus        14 ~f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~-----~~~~Cg~C~~C~~i~~g~   88 (620)
T PRK14948         14 RFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKP-----TPEPCGKCELCRAIAAGN   88 (620)
T ss_pred             cHhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCC-----CCCCCcccHHHHHHhcCC
Confidence            456788999999998888886653 57889999999999999999887643211100     001111222233332221


Q ss_pred             CCCc---c--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhcc
Q 044858          228 GLKI---D--QESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSCE  295 (426)
Q Consensus       228 ~~~~---~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~  295 (426)
                      ....   +  .....+.+..+.+.+.    .+++-++|||+++..  ...+.+...+..-...+.+|++|.+ ..+....
T Consensus        89 h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTI  168 (620)
T PRK14948         89 ALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTI  168 (620)
T ss_pred             CccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHH
Confidence            1110   0  0111223333333322    245568999999755  3355554444332334555555543 3332222


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      ......+.+.+++.++....+...+...... --.+....|++.++|.+..+..+.
T Consensus       169 rSRc~~~~f~~l~~~ei~~~L~~ia~kegi~-is~~al~~La~~s~G~lr~A~~lL  223 (620)
T PRK14948        169 ISRCQRFDFRRIPLEAMVQHLSEIAEKESIE-IEPEALTLVAQRSQGGLRDAESLL  223 (620)
T ss_pred             HhheeEEEecCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            3345678899999999888887766432111 113457889999999886554443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.29  E-value=4.6e-05  Score=77.35  Aligned_cols=195  Identities=14%  Similarity=0.122  Sum_probs=109.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ..+..++|.+.....+..++..++. +.+.++|+.|+||||+|+.+.+.......-+       ..+++.....+.|...
T Consensus        13 ~~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~-------~~pC~~C~~C~~i~~g   85 (559)
T PRK05563         13 QTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPD-------GEPCNECEICKAITNG   85 (559)
T ss_pred             CcHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCccHHHHHHhcC
Confidence            3567789999999999998886654 4577899999999999999987653211000       0011111111111111


Q ss_pred             hCCCc---c--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEE-eecchhhhhc
Q 044858          227 LGLKI---D--QESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLL-TARSQDVLSC  294 (426)
Q Consensus       227 l~~~~---~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iiv-Ttr~~~va~~  294 (426)
                      ...+.   +  .....+.+..+.+...    .+++-++|+|+++..  ..++.+...+..-...+.+|+ ||....+...
T Consensus        86 ~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~t  165 (559)
T PRK05563         86 SLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPAT  165 (559)
T ss_pred             CCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHH
Confidence            00000   0  0011222333333322    245678899999755  345555443332223444454 4444433322


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      ..+....+.+.+++.++....+...+......- -.+....|++.++|.+.-+...
T Consensus       166 I~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i-~~~al~~ia~~s~G~~R~al~~  220 (559)
T PRK05563        166 ILSRCQRFDFKRISVEDIVERLKYILDKEGIEY-EDEALRLIARAAEGGMRDALSI  220 (559)
T ss_pred             HHhHheEEecCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            233456789999999999999888764222111 1356778888999877644433

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

Probab=98.29  E-value=2.6e-05  Score=75.55  Aligned_cols=176  Identities=16%  Similarity=0.239  Sum_probs=99.2

Q ss_pred             cCCcccccchHHHHHHHHHHhc----c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC
Q 044858          147 TQDFMHFESRKSTLKGILDALS----N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT  213 (426)
Q Consensus       147 ~~~~~~~~gR~~~~~~l~~~l~----~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  213 (426)
                      ...+.++.|-+..+++|.+.+.    .         ..++-+.++|++|+|||+||+.+++.....  |     +.+.. 
T Consensus       141 ~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~--f-----i~i~~-  212 (398)
T PTZ00454        141 DVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTAT--F-----IRVVG-  212 (398)
T ss_pred             CCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCC--E-----EEEeh-
Confidence            3445667788777777666543    1         235678999999999999999999875432  2     22211 


Q ss_pred             cCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------C----hhhhcCCCC--C
Q 044858          214 PQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------D----LEAIGIPLA--D  275 (426)
Q Consensus       214 ~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~----~~~l~~~l~--~  275 (426)
                         ..+....   ++      .....+..++.......+++|+||+++...            .    +..+...+.  .
T Consensus       213 ---s~l~~k~---~g------e~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~  280 (398)
T PTZ00454        213 ---SEFVQKY---LG------EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFD  280 (398)
T ss_pred             ---HHHHHHh---cc------hhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccC
Confidence               1111111   11      011234455555555678999999986421            0    111111111  1


Q ss_pred             CCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          276 DNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       276 ~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      ...+..||.||.......    ....-...++++..+.++-..+|..........++.  ....+++.+.|+-
T Consensus       281 ~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dv--d~~~la~~t~g~s  351 (398)
T PTZ00454        281 QTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEV--DLEDFVSRPEKIS  351 (398)
T ss_pred             CCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCccc--CHHHHHHHcCCCC
Confidence            234667888887654321    111234578898889998888888776532222211  1345666676653

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.28  E-value=4.7e-05  Score=74.73  Aligned_cols=180  Identities=17%  Similarity=0.180  Sum_probs=105.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.|+|+.|+|||+|++.+++.......-..+++++.      .++..++...+...        ....+.+.+.+  .
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~------~~~~~~~~~~~~~~--------~~~~~~~~~~~--~  200 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS------EKFTNDFVNALRNN--------KMEEFKEKYRS--V  200 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH------HHHHHHHHHHHHcC--------CHHHHHHHHHh--C
Confidence            46889999999999999999998765321123555543      34444555444321        12233334432  3


Q ss_pred             EEEEEeCCCCccC---hh-hhcCCCCC-CCCCeEEEEeecchhhh-----h---ccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGSLD---LE-AIGIPLAD-DNGGCKVLLTARSQDVL-----S---CEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~~~---~~-~l~~~l~~-~~~~s~iivTtr~~~va-----~---~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      -+|+|||++....   +. .+...+.. ...+..+|+||....-.     .   ........+.+++.+.++-..++.+.
T Consensus       201 dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~  280 (405)
T TIGR00362       201 DLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKK  280 (405)
T ss_pred             CEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHH
Confidence            4899999975421   11 12211110 12345688887653211     0   11222357899999999999999998


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh------hcC--CHHHHHHHHHHH
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL------KNK--SPYEWRNALRQL  369 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l------~~~--~~~~w~~~l~~l  369 (426)
                      +..... .--+++...|++.+.|.+-.+.-+-..|      .++  +....+.++...
T Consensus       281 ~~~~~~-~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~~it~~~~~~~L~~~  337 (405)
T TIGR00362       281 AEEEGL-ELPDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGKPITLELAKEALKDL  337 (405)
T ss_pred             HHHcCC-CCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence            853221 1125678889999998777544332222      122  667777777764

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).

>CHL00181 cbbX CbbX; Provisional

Probab=98.27  E-value=2.5e-05  Score=72.46  Aligned_cols=133  Identities=12%  Similarity=0.108  Sum_probs=73.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.++|++|+||||+|+.+++.....+.-...-|+.++    ..++.....   +.     .. .....+++..   ..
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~----~~~l~~~~~---g~-----~~-~~~~~~l~~a---~g  123 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVT----RDDLVGQYI---GH-----TA-PKTKEVLKKA---MG  123 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEec----HHHHHHHHh---cc-----ch-HHHHHHHHHc---cC
Confidence            357899999999999999998865432211111244443    122222211   11     00 1112223222   23


Q ss_pred             EEEEEeCCCCc-----------cChhhhcCCCCCCCCCeEEEEeecchhhh-------hccCCceeeEEccCCCHHHHHH
Q 044858          253 ILIILDDIWGS-----------LDLEAIGIPLADDNGGCKVLLTARSQDVL-------SCEMDCQQNFVVDVLNDKEAWS  314 (426)
Q Consensus       253 ~LlVlDdv~~~-----------~~~~~l~~~l~~~~~~s~iivTtr~~~va-------~~~~~~~~~~~l~~L~~~e~~~  314 (426)
                      -+|+||++...           +....+...+.....+.+||+++......       .........+.+++++.+|..+
T Consensus       124 gVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~  203 (287)
T CHL00181        124 GVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQ  203 (287)
T ss_pred             CEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHH
Confidence            59999999642           11122333333334567777777643321       0112234589999999999999


Q ss_pred             HHHHhhC
Q 044858          315 LFKKMTG  321 (426)
Q Consensus       315 Lf~~~~~  321 (426)
                      ++...+.
T Consensus       204 I~~~~l~  210 (287)
T CHL00181        204 IAKIMLE  210 (287)
T ss_pred             HHHHHHH
Confidence            9988874

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.25  E-value=5.3e-05  Score=75.33  Aligned_cols=202  Identities=16%  Similarity=0.156  Sum_probs=114.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.|+|+.|+|||+|++.+.+.......-..+++++.      .++..++...+...        ....+.+.+.  +.
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~------~~~~~~~~~~~~~~--------~~~~~~~~~~--~~  212 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTS------EKFTNDFVNALRNN--------TMEEFKEKYR--SV  212 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHHcC--------cHHHHHHHHh--cC
Confidence            46889999999999999999998765422223455543      23344444443211        1123334443  24


Q ss_pred             EEEEEeCCCCccC---h-hhhcCCCCC-CCCCeEEEEeecchhhh--------hccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGSLD---L-EAIGIPLAD-DNGGCKVLLTARSQDVL--------SCEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~~~---~-~~l~~~l~~-~~~~s~iivTtr~~~va--------~~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      -+|+|||++....   + +.+...+.. ...|..||+||....-.        .........+++++.+.++-..++.+.
T Consensus       213 dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~  292 (450)
T PRK00149        213 DVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKK  292 (450)
T ss_pred             CEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHH
Confidence            5899999975421   1 122221110 11245688887654211        112223457999999999999999998


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh------hcC--CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHh
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL------KNK--SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQL  391 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l------~~~--~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~  391 (426)
                      +.... ..--+++..-|++.++|..-.+.-+-..|      .++  +....+.+++.+........   +.+.+.....-
T Consensus       293 ~~~~~-~~l~~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~~~~it~~~~~~~l~~~~~~~~~~~---~~~~i~~~v~~  368 (450)
T PRK00149        293 AEEEG-IDLPDEVLEFIAKNITSNVRELEGALNRLIAYASLTGKPITLELAKEALKDLLAAQKKKI---TIENIQKVVAE  368 (450)
T ss_pred             HHHcC-CCCCHHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCC---CHHHHHHHHHH
Confidence            85321 11224678889999998877544332222      122  77777777776532111111   23555555554


Q ss_pred             hhc
Q 044858          392 SYN  394 (426)
Q Consensus       392 sy~  394 (426)
                      .|.
T Consensus       369 ~~~  371 (450)
T PRK00149        369 YYN  371 (450)
T ss_pred             HcC
Confidence            443

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.25  E-value=2.7e-05  Score=72.34  Aligned_cols=132  Identities=14%  Similarity=0.162  Sum_probs=73.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeE
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKI  253 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~  253 (426)
                      -+.++|++|+|||++|+.+.+...........-++.++.    .++...+   .+.     +. .....+++..   ..-
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~----~~l~~~~---~g~-----~~-~~~~~~~~~a---~~g  123 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR----DDLVGQY---IGH-----TA-PKTKEILKRA---MGG  123 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH----HHHhHhh---ccc-----ch-HHHHHHHHHc---cCc
Confidence            588999999999999988877654322222112444432    2222211   111     11 1122233332   346


Q ss_pred             EEEEeCCCCc------cC-----hhhhcCCCCCCCCCeEEEEeecchhhhh-------ccCCceeeEEccCCCHHHHHHH
Q 044858          254 LIILDDIWGS------LD-----LEAIGIPLADDNGGCKVLLTARSQDVLS-------CEMDCQQNFVVDVLNDKEAWSL  315 (426)
Q Consensus       254 LlVlDdv~~~------~~-----~~~l~~~l~~~~~~s~iivTtr~~~va~-------~~~~~~~~~~l~~L~~~e~~~L  315 (426)
                      +|+||++...      ..     ...+...+.....+.+||+++.......       ........+++++++.+|..++
T Consensus       124 vL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I  203 (284)
T TIGR02880       124 VLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVI  203 (284)
T ss_pred             EEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHH
Confidence            9999999632      11     2233333333345667777765432210       0111246799999999999999


Q ss_pred             HHHhhC
Q 044858          316 FKKMTG  321 (426)
Q Consensus       316 f~~~~~  321 (426)
                      +.+.+.
T Consensus       204 ~~~~l~  209 (284)
T TIGR02880       204 AGLMLK  209 (284)
T ss_pred             HHHHHH
Confidence            988874

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.25  E-value=1.6e-05  Score=78.89  Aligned_cols=162  Identities=15%  Similarity=0.191  Sum_probs=90.8

Q ss_pred             CCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC---ccceEEEEEec
Q 044858          148 QDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN---LFEKVISSRVS  211 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~---~f~~~~wv~v~  211 (426)
                      ..+.++.|.+..++++.+.+.             -..++-+.++|++|+|||++|+.+++.....-   .+....++.+.
T Consensus       179 v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~  258 (512)
T TIGR03689       179 VTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIK  258 (512)
T ss_pred             CCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEecc
Confidence            345667788888888777653             12345689999999999999999999865321   01223344443


Q ss_pred             CCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHH----hcCCeEEEEEeCCCCcc---------Ch-----hhhcCCC
Q 044858          212 QTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL----KKETKILIILDDIWGSL---------DL-----EAIGIPL  273 (426)
Q Consensus       212 ~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l----~~~k~~LlVlDdv~~~~---------~~-----~~l~~~l  273 (426)
                      ..    +++...        ... ....+..+++..    ..+++++|+||+++...         +.     ..+...+
T Consensus       259 ~~----eLl~ky--------vGe-te~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~L  325 (512)
T TIGR03689       259 GP----ELLNKY--------VGE-TERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSEL  325 (512)
T ss_pred             ch----hhcccc--------cch-HHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHh
Confidence            21    111110        000 011122222222    23578999999997431         11     1222222


Q ss_pred             CC--CCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCC
Q 044858          274 AD--DNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGD  322 (426)
Q Consensus       274 ~~--~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~  322 (426)
                      ..  ...+..||.||.......    +...-...|++++.+.++..++|..++..
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            11  123445566665443321    11123457999999999999999998753

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.

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=98.23  E-value=0.00012  Score=64.66  Aligned_cols=188  Identities=16%  Similarity=0.142  Sum_probs=109.3

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe-cCCcCHHHHHHHHHHHhCCCcccc--Cc
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV-SQTPQIKEIQREIAEKLGLKIDQE--SE  236 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v-~~~~~~~~il~~i~~~l~~~~~~~--~~  236 (426)
                      +..+...+. .+.+++.++|.-|+|||.+.+.+.......+    ++-+.+ .+..+...+...|+..+..+....  ..
T Consensus        40 l~~l~~~i~-d~qg~~~vtGevGsGKTv~~Ral~~s~~~d~----~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~  114 (269)
T COG3267          40 LLMLHAAIA-DGQGILAVTGEVGSGKTVLRRALLASLNEDQ----VAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAV  114 (269)
T ss_pred             HHHHHHHHh-cCCceEEEEecCCCchhHHHHHHHHhcCCCc----eEEEEecCcchhHHHHHHHHHHHhccCccchhHHH
Confidence            333333333 3456899999999999999995555444321    122333 345577788888888877622111  11


Q ss_pred             HH-HHHHHHHHHhcCCe-EEEEEeCCCCc--cChhhhcC---CCCCCCCCeEEEEeecchh-------hhhccCCceee-
Q 044858          237 SV-RAWRLLEQLKKETK-ILIILDDIWGS--LDLEAIGI---PLADDNGGCKVLLTARSQD-------VLSCEMDCQQN-  301 (426)
Q Consensus       237 ~~-~~~~l~~~l~~~k~-~LlVlDdv~~~--~~~~~l~~---~l~~~~~~s~iivTtr~~~-------va~~~~~~~~~-  301 (426)
                      .. ....+.....+++| ..+++||..+.  ...+.++.   .-.....--+|+.....+-       +.......... 
T Consensus       115 ~e~~~~~L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir  194 (269)
T COG3267         115 LEQIDRELAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIR  194 (269)
T ss_pred             HHHHHHHHHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEE
Confidence            11 22234444456777 99999999765  22333221   1111111123444333221       00111122334 


Q ss_pred             EEccCCCHHHHHHHHHHhhCCCCCCC--chHHHHHHHHHHcCCchHHHHHHHH
Q 044858          302 FVVDVLNDKEAWSLFKKMTGDCIENG--ELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       302 ~~l~~L~~~e~~~Lf~~~~~~~~~~~--~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      |++.|++.++...++...+.....++  --.+....|.....|.|.+|..++.
T Consensus       195 ~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         195 IELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             EecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            99999999999999998886332222  2245678899999999999988764

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

Probab=98.22  E-value=4.9e-05  Score=74.32  Aligned_cols=200  Identities=19%  Similarity=0.268  Sum_probs=109.6

Q ss_pred             CCcccccchHHHHHHHHHHhc----c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALS----N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~----~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..+.++.|.+..++++.+.+.    .         ..+.-+.++|++|+|||++|+.+++.....  |     +.+... 
T Consensus       180 ~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~--f-----i~V~~s-  251 (438)
T PTZ00361        180 ESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSAT--F-----LRVVGS-  251 (438)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCC--E-----EEEecc-
Confidence            345567788888877776653    1         234568899999999999999999976532  3     222111 


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------C------hhhhcCCCC--CC
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL----------D------LEAIGIPLA--DD  276 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~----------~------~~~l~~~l~--~~  276 (426)
                         ++....   .+      .....+..+++......+++|+||+++...          +      +..+...+.  ..
T Consensus       252 ---eL~~k~---~G------e~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~  319 (438)
T PTZ00361        252 ---ELIQKY---LG------DGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDS  319 (438)
T ss_pred             ---hhhhhh---cc------hHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcc
Confidence               111110   00      011234445555555678999999975321          0      011111111  12


Q ss_pred             CCCeEEEEeecchhhhhc----cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH----HHH
Q 044858          277 NGGCKVLLTARSQDVLSC----EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI----AIV  348 (426)
Q Consensus       277 ~~~s~iivTtr~~~va~~----~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl----ai~  348 (426)
                      ..+..||.||........    ...-...+++.+.+.++-.++|..++......++.  ....++..+.|+--    ++.
T Consensus       320 ~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dv--dl~~la~~t~g~sgAdI~~i~  397 (438)
T PTZ00361        320 RGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDV--DLEEFIMAKDELSGADIKAIC  397 (438)
T ss_pred             cCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCc--CHHHHHHhcCCCCHHHHHHHH
Confidence            335678888876543311    12234688999999999999999877533222211  12345555555432    222


Q ss_pred             HHHHHhh---cC---CHHHHHHHHHHH
Q 044858          349 PIAKALK---NK---SPYEWRNALRQL  369 (426)
Q Consensus       349 ~~~~~l~---~~---~~~~w~~~l~~l  369 (426)
                      .-|+.++   +.   +.+++..+.+..
T Consensus       398 ~eA~~~Alr~~r~~Vt~~D~~~A~~~v  424 (438)
T PTZ00361        398 TEAGLLALRERRMKVTQADFRKAKEKV  424 (438)
T ss_pred             HHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence            2233332   21   566666666554

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

Probab=98.22  E-value=8.7e-05  Score=69.11  Aligned_cols=196  Identities=15%  Similarity=0.161  Sum_probs=117.8

Q ss_pred             cccchHHHHHHHHHHhccCC---ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC
Q 044858          152 HFESRKSTLKGILDALSNRN---FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG  228 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~~~---~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~  228 (426)
                      .|.+|+.++..+...+.+..   +..|.|.|..|.|||.+.+++.+....     ..+|+++-..++...++..|+.+.+
T Consensus         7 ~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~IL~~~~   81 (438)
T KOG2543|consen    7 NVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKILNKSQ   81 (438)
T ss_pred             CccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHHHHHhc
Confidence            46789999999998887443   345689999999999999999988743     2579999999999999999999985


Q ss_pred             -CCccccC---cHHHHHHHHHHHh-------cCCeEEEEEeCCCCccChhhhcCC----C--CCCCCCeEEEEeecchhh
Q 044858          229 -LKIDQES---ESVRAWRLLEQLK-------KETKILIILDDIWGSLDLEAIGIP----L--ADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       229 -~~~~~~~---~~~~~~~l~~~l~-------~~k~~LlVlDdv~~~~~~~~l~~~----l--~~~~~~s~iivTtr~~~v  291 (426)
                       .+.+...   +.+........+.       .++.++||||+++...+.+.+..+    +  .-+.+.. .|+++-....
T Consensus        82 ~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i-~iils~~~~e  160 (438)
T KOG2543|consen   82 LADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTI-VIILSAPSCE  160 (438)
T ss_pred             cCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCce-EEEEeccccH
Confidence             2222211   1122222222221       246899999999866443332100    0  0112233 3333333222


Q ss_pred             h--hccCCc--eeeEEccCCCHHHHHHHHHHhhCCCCC----CCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          292 L--SCEMDC--QQNFVVDVLNDKEAWSLFKKMTGDCIE----NGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       292 a--~~~~~~--~~~~~l~~L~~~e~~~Lf~~~~~~~~~----~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      .  ...+++  ..++..+.-+.+|...++.+.-.+...    ..-+.-+..-....|+ -|-.+..+....
T Consensus       161 ~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~r~~~~ya~fl~v~l~vF~~~cr-d~~eL~~~~~~~  230 (438)
T KOG2543|consen  161 KQYLINTGTLEIVVLHFPQYSVEETQVILSRDNPGKRKLDVYAQFLHVLLQVFYMACR-DVNELRSLISLA  230 (438)
T ss_pred             HHhhcccCCCCceEEecCCCCHHHHHHHHhcCCccccchHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHH
Confidence            1  111233  346777888999999998765432111    0111223445566777 555666555443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=98.20  E-value=7.6e-05  Score=70.14  Aligned_cols=199  Identities=15%  Similarity=0.154  Sum_probs=111.2

Q ss_pred             cccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------ccceEEEEEecCCcC
Q 044858          150 FMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENN-------------LFEKVISSRVSQTPQ  215 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~-------------~f~~~~wv~v~~~~~  215 (426)
                      +..++|.+...+.+...+..++. +...++|+.|+||+++|..+.+..-...             ..+...|+.-....+
T Consensus         3 f~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~   82 (314)
T PRK07399          3 FANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQ   82 (314)
T ss_pred             HHHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEecccccc
Confidence            34678999999999998887764 7899999999999999998877643211             111223332110000


Q ss_pred             HHHHHHHHHHHhCC--CccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeec
Q 044858          216 IKEIQREIAEKLGL--KIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTAR  287 (426)
Q Consensus       216 ~~~il~~i~~~l~~--~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr  287 (426)
                      -..+-..-+...+.  .....-..+.+..+.+.+.    .+.+-++|+|+++..  ...+.+...+-.-.+..-|++|+.
T Consensus        83 g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp~~~fILi~~~  162 (314)
T PRK07399         83 GKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPGNGTLILIAPS  162 (314)
T ss_pred             ccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCCCCeEEEEECC
Confidence            00000001111110  0001111223444555443    256679999998754  233444333321112333444444


Q ss_pred             chhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHH
Q 044858          288 SQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       288 ~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      .+.+.....+....+++.++++++..+.+.+......    .......++..++|.|..+.....
T Consensus       163 ~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~----~~~~~~~l~~~a~Gs~~~al~~l~  223 (314)
T PRK07399        163 PESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEI----LNINFPELLALAQGSPGAAIANIE  223 (314)
T ss_pred             hHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhcccc----chhHHHHHHHHcCCCHHHHHHHHH
Confidence            4444333345568999999999999999988643211    111135789999999976655433

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.19  E-value=4e-05  Score=81.97  Aligned_cols=159  Identities=16%  Similarity=0.222  Sum_probs=92.7

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCcc----ceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLF----EKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ...+++||+++++.++..|.......+.++|++|+|||++|+.+.+........    ...+|..     ++..++.   
T Consensus       171 ~~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l-----~~~~l~a---  242 (852)
T TIGR03346       171 KLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLAL-----DMGALIA---  242 (852)
T ss_pred             CCCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEe-----eHHHHhh---
Confidence            456799999999999999886665667799999999999999998876432111    2222221     1111110   


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhc-CCeEEEEEeCCCCccC---------hhhhcCCCCCCCCCeEEEEeecchhh---
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKK-ETKILIILDDIWGSLD---------LEAIGIPLADDNGGCKVLLTARSQDV---  291 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~~---------~~~l~~~l~~~~~~s~iivTtr~~~v---  291 (426)
                         +.... ......+..+++.+.. +++.+|++|+++....         ...+..+... ...-++|-+|..+..   
T Consensus       243 ---~~~~~-g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~-~g~i~~IgaTt~~e~r~~  317 (852)
T TIGR03346       243 ---GAKYR-GEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALA-RGELHCIGATTLDEYRKY  317 (852)
T ss_pred             ---cchhh-hhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhh-cCceEEEEeCcHHHHHHH
Confidence               00000 1112234455555532 4689999999974421         1122222222 223455555544422   


Q ss_pred             -h--hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          292 -L--SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       292 -a--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                       .  .........+.++..+.++...++....
T Consensus       318 ~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~  349 (852)
T TIGR03346       318 IEKDAALERRFQPVFVDEPTVEDTISILRGLK  349 (852)
T ss_pred             hhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHH
Confidence             1  1112344678899899999999987654

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.16  E-value=5.1e-05  Score=76.42  Aligned_cols=201  Identities=21%  Similarity=0.245  Sum_probs=108.2

Q ss_pred             CCcccccchHHHHHHHH---HHhcc---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGIL---DALSN---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~---~~l~~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+.++.|-+..++++.   .++..         ..++-+.++|++|+|||+||+.+.+.....       ++.++.   
T Consensus        52 ~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~-------~~~i~~---  121 (495)
T TIGR01241        52 VTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP-------FFSISG---  121 (495)
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCC-------eeeccH---
Confidence            34566777766554444   33321         224468899999999999999998875432       222221   


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------Chh----hhcCCCC--CCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------DLE----AIGIPLA--DDN  277 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~~~----~l~~~l~--~~~  277 (426)
                       .++....   .+      .....+..+++......+++|+|||++...            .+.    .+...+.  ...
T Consensus       122 -~~~~~~~---~g------~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~  191 (495)
T TIGR01241       122 -SDFVEMF---VG------VGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTN  191 (495)
T ss_pred             -HHHHHHH---hc------ccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCC
Confidence             1111111   01      011233445555555568999999996431            011    1111111  122


Q ss_pred             CCeEEEEeecchhhh----hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc-hHHHHHHHH
Q 044858          278 GGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL-PIAIVPIAK  352 (426)
Q Consensus       278 ~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl-Plai~~~~~  352 (426)
                      .+..||.||......    .....-...++++..+.++-.++|...+......++  .....+++.+.|. |--|..+..
T Consensus       192 ~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~--~~l~~la~~t~G~sgadl~~l~~  269 (495)
T TIGR01241       192 TGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPD--VDLKAVARRTPGFSGADLANLLN  269 (495)
T ss_pred             CCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcc--hhHHHHHHhCCCCCHHHHHHHHH
Confidence            345566666554321    111223467889988999999999887754322222  1245788888874 344444432


Q ss_pred             ---Hh--h-cC---CHHHHHHHHHHHh
Q 044858          353 ---AL--K-NK---SPYEWRNALRQLK  370 (426)
Q Consensus       353 ---~l--~-~~---~~~~w~~~l~~l~  370 (426)
                         ..  + ++   +...++.+++...
T Consensus       270 eA~~~a~~~~~~~i~~~~l~~a~~~~~  296 (495)
T TIGR01241       270 EAALLAARKNKTEITMNDIEEAIDRVI  296 (495)
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence               11  1 22   6666766666543

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.

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

Probab=98.15  E-value=0.00015  Score=64.36  Aligned_cols=53  Identities=15%  Similarity=0.241  Sum_probs=41.1

Q ss_pred             CCcccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC
Q 044858          148 QDFMHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN  200 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~  200 (426)
                      .....++|-+.+.+.|++.-.    ......+.++|..|+|||+|++.+.+....++
T Consensus        24 ~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~G   80 (249)
T PF05673_consen   24 IRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQG   80 (249)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC
Confidence            456678898888887776543    33445688999999999999999999887653

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.12  E-value=5e-05  Score=80.98  Aligned_cols=158  Identities=14%  Similarity=0.210  Sum_probs=90.3

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceE-EEEEecCCcCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKV-ISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~-~wv~v~~~~~~~~il~~i  223 (426)
                      ...+++||+.+++.++..|.......+.++|++|+|||+||+.+.........    .... +++.++.      +..  
T Consensus       176 ~l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~------l~a--  247 (857)
T PRK10865        176 KLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA------LVA--  247 (857)
T ss_pred             CCCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhh------hhh--
Confidence            45679999999999999988666667789999999999999999987643211    1222 2222221      110  


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHh-cCCeEEEEEeCCCCcc---------ChhhhcCCCCCCCCCeEEEEeecchhh--
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLK-KETKILIILDDIWGSL---------DLEAIGIPLADDNGGCKVLLTARSQDV--  291 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~---------~~~~l~~~l~~~~~~s~iivTtr~~~v--  291 (426)
                          +.. ........+..+++.+. .+++.+|++|+++...         +-..+..+... ...-++|-+|..+..  
T Consensus       248 ----g~~-~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~-~g~l~~IgaTt~~e~r~  321 (857)
T PRK10865        248 ----GAK-YRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA-RGELHCVGATTLDEYRQ  321 (857)
T ss_pred             ----ccc-hhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchhh-cCCCeEEEcCCCHHHHH
Confidence                000 00111223444444442 3568999999997542         12223223222 223456655554432  


Q ss_pred             --h--hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          292 --L--SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       292 --a--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                        .  .........+.+..-+.++...+++...
T Consensus       322 ~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~  354 (857)
T PRK10865        322 YIEKDAALERRFQKVFVAEPSVEDTIAILRGLK  354 (857)
T ss_pred             HhhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHh
Confidence              0  1111233456666668888888887654

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

Probab=98.11  E-value=2.7e-05  Score=75.32  Aligned_cols=109  Identities=18%  Similarity=0.257  Sum_probs=72.7

Q ss_pred             cccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCC
Q 044858          150 FMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGL  229 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~  229 (426)
                      ...++..+..++.+...+...  +.+.++|++|+|||++|+.+++.......|+.+.||.+++..+..+++..+.-. +.
T Consensus       174 l~d~~i~e~~le~l~~~L~~~--~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~-~v  250 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTIK--KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPN-GV  250 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhcC--CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCC-CC
Confidence            344667788899999888754  458889999999999999999887665668888999999988877766433110 00


Q ss_pred             CccccCcHHHHHHHHHHHh--cCCeEEEEEeCCCCc
Q 044858          230 KIDQESESVRAWRLLEQLK--KETKILIILDDIWGS  263 (426)
Q Consensus       230 ~~~~~~~~~~~~~l~~~l~--~~k~~LlVlDdv~~~  263 (426)
                      ..... . ....++.....  .+++++||||++...
T Consensus       251 gy~~~-~-G~f~~~~~~A~~~p~~~~vliIDEINRa  284 (459)
T PRK11331        251 GFRRK-D-GIFYNFCQQAKEQPEKKYVFIIDEINRA  284 (459)
T ss_pred             CeEec-C-chHHHHHHHHHhcccCCcEEEEehhhcc
Confidence            00000 0 11112222221  246899999999644

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.10  E-value=0.00014  Score=68.77  Aligned_cols=155  Identities=12%  Similarity=0.138  Sum_probs=89.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------ccceEEEEEecCCcCHHHHHHHHHHHhCCCc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENN--------------------LFEKVISSRVSQTPQIKEIQREIAEKLGLKI  231 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~  231 (426)
                      .+.+.++|+.|+|||++|..+....--..                    |.| ..|+.-...                  
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~~~~~------------------   82 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPD-NFVLEPEEA------------------   82 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccCC------------------
Confidence            45688999999999999999887654221                    111 112211000                  


Q ss_pred             cccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecch-hhhhccCCceeeEEc
Q 044858          232 DQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMDCQQNFVV  304 (426)
Q Consensus       232 ~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~~~~~~~l  304 (426)
                      ...-..+.+..+.+.+.    .+++-++|||+++..  ...+.+...+..-..++.+|+||.+. .+.....+....+.+
T Consensus        83 ~~~i~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~  162 (328)
T PRK05707         83 DKTIKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQAC  162 (328)
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeC
Confidence            00011123333333332    234456678999754  33444443332223466777777665 333323445578999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      .+++.+++.+.+.......     ..+.+..++..++|.|+....+
T Consensus       163 ~~~~~~~~~~~L~~~~~~~-----~~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        163 PLPSNEESLQWLQQALPES-----DERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             CCcCHHHHHHHHHHhcccC-----ChHHHHHHHHHcCCCHHHHHHH
Confidence            9999999999988754211     1234567789999999855443

>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=98.10  E-value=1.2e-05  Score=65.46  Aligned_cols=69  Identities=20%  Similarity=0.194  Sum_probs=41.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC-eE
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET-KI  253 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k-~~  253 (426)
                      |.|+|++|+|||++|+.+.+.....     .+.++.+.-.+.               ........+..+++...... +.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~-----~~~i~~~~~~~~---------------~~~~~~~~i~~~~~~~~~~~~~~   60 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFP-----FIEIDGSELISS---------------YAGDSEQKIRDFFKKAKKSAKPC   60 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSE-----EEEEETTHHHTS---------------STTHHHHHHHHHHHHHHHTSTSE
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccc-----cccccccccccc---------------cccccccccccccccccccccce
Confidence            5799999999999999999987522     233433221100               11111223334444443334 89


Q ss_pred             EEEEeCCCCc
Q 044858          254 LIILDDIWGS  263 (426)
Q Consensus       254 LlVlDdv~~~  263 (426)
                      +|+|||++..
T Consensus        61 vl~iDe~d~l   70 (132)
T PF00004_consen   61 VLFIDEIDKL   70 (132)
T ss_dssp             EEEEETGGGT
T ss_pred             eeeeccchhc
Confidence            9999999644

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 ....

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.10  E-value=1.8e-05  Score=64.74  Aligned_cols=91  Identities=26%  Similarity=0.184  Sum_probs=51.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.|+|++|+||||+++.+........  ..++++..+........... ...................+.......+.
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDILEEVLDQLL-LIIVGGKKASGSGELRLRLALALARKLKP   79 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC--CCEEEECCEEccccCHHHHH-hhhhhccCCCCCHHHHHHHHHHHHHhcCC
Confidence            5789999999999999999998876532  23455554433322211111 11111111122222334445555544345


Q ss_pred             EEEEEeCCCCccCh
Q 044858          253 ILIILDDIWGSLDL  266 (426)
Q Consensus       253 ~LlVlDdv~~~~~~  266 (426)
                      .++++|++......
T Consensus        80 ~viiiDei~~~~~~   93 (148)
T smart00382       80 DVLILDEITSLLDA   93 (148)
T ss_pred             CEEEEECCcccCCH
Confidence            89999999876443

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.

>CHL00176 ftsH cell division protein; Validated

Probab=98.10  E-value=0.00016  Score=74.31  Aligned_cols=199  Identities=16%  Similarity=0.219  Sum_probs=108.6

Q ss_pred             CcccccchHH---HHHHHHHHhccC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          149 DFMHFESRKS---TLKGILDALSNR---------NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       149 ~~~~~~gR~~---~~~~l~~~l~~~---------~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .+.++.|.++   ++.+++..+.++         .++-+.++|++|+|||+||+.++......       ++.++.    
T Consensus       181 ~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p-------~i~is~----  249 (638)
T CHL00176        181 TFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVP-------FFSISG----  249 (638)
T ss_pred             CHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCC-------eeeccH----
Confidence            3445566554   444455554422         24568999999999999999998865432       233321    


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------C----hhhhcCCCC--CCCC
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------D----LEAIGIPLA--DDNG  278 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~----~~~l~~~l~--~~~~  278 (426)
                      .++....   .+      .....+..+++......+++|+|||++...            .    +..+...+.  ....
T Consensus       250 s~f~~~~---~g------~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~  320 (638)
T CHL00176        250 SEFVEMF---VG------VGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNK  320 (638)
T ss_pred             HHHHHHh---hh------hhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCC
Confidence            1111100   00      011234445555556678999999996431            1    112221111  1234


Q ss_pred             CeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-chHHHHHHHH-
Q 044858          279 GCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAG-LPIAIVPIAK-  352 (426)
Q Consensus       279 ~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G-lPlai~~~~~-  352 (426)
                      +..||.||.......    ....-...+.+...+.++-.++++.++......+  ......+++.+.| .+--|..+.. 
T Consensus       321 ~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~--d~~l~~lA~~t~G~sgaDL~~lvne  398 (638)
T CHL00176        321 GVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSP--DVSLELIARRTPGFSGADLANLLNE  398 (638)
T ss_pred             CeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccch--hHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            556666776543221    1112346788888899999999988876422222  2345678888887 3333333322 


Q ss_pred             --Hhh---cC---CHHHHHHHHHHH
Q 044858          353 --ALK---NK---SPYEWRNALRQL  369 (426)
Q Consensus       353 --~l~---~~---~~~~w~~~l~~l  369 (426)
                        +.+   ++   +.++.+.+++..
T Consensus       399 Aal~a~r~~~~~It~~dl~~Ai~rv  423 (638)
T CHL00176        399 AAILTARRKKATITMKEIDTAIDRV  423 (638)
T ss_pred             HHHHHHHhCCCCcCHHHHHHHHHHH
Confidence              111   21   566676666654

>PRK06620 hypothetical protein; Validated

Probab=98.08  E-value=2.1e-05  Score=69.80  Aligned_cols=136  Identities=15%  Similarity=0.045  Sum_probs=78.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      +.+.|+|++|+|||+|++.+.+....       .++.  ..+..                   .        +...  ..
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~-------~~~~--~~~~~-------------------~--------~~~~--~~   86 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNA-------YIIK--DIFFN-------------------E--------EILE--KY   86 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCC-------EEcc--hhhhc-------------------h--------hHHh--cC
Confidence            56899999999999999987765421       1111  00000                   0        0111  23


Q ss_pred             EEEEEeCCCCccChhhhcCCCC-CCCCCeEEEEeecchhhh------hccCCceeeEEccCCCHHHHHHHHHHhhCCCCC
Q 044858          253 ILIILDDIWGSLDLEAIGIPLA-DDNGGCKVLLTARSQDVL------SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIE  325 (426)
Q Consensus       253 ~LlVlDdv~~~~~~~~l~~~l~-~~~~~s~iivTtr~~~va------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~  325 (426)
                      -+|++||++...+ ..+...+. -...|..||+|++.....      .......-+++++++++++-..++.+.+.... 
T Consensus        87 d~lliDdi~~~~~-~~lf~l~N~~~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~-  164 (214)
T PRK06620         87 NAFIIEDIENWQE-PALLHIFNIINEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS-  164 (214)
T ss_pred             CEEEEeccccchH-HHHHHHHHHHHhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC-
Confidence            5788999974321 11211110 013466899998865432      01122334899999999998888887764221 


Q ss_pred             CCchHHHHHHHHHHcCCchHHHH
Q 044858          326 NGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       326 ~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                      -.--+++.+-|++.+.|.--.+.
T Consensus       165 l~l~~ev~~~L~~~~~~d~r~l~  187 (214)
T PRK06620        165 VTISRQIIDFLLVNLPREYSKII  187 (214)
T ss_pred             CCCCHHHHHHHHHHccCCHHHHH
Confidence            11124567778887777654443

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

Probab=98.08  E-value=1.5e-05  Score=83.04  Aligned_cols=159  Identities=19%  Similarity=0.223  Sum_probs=94.0

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-c---cceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN-L---FEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~-~---f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ...+++||+.+++.+++.|.......+.++|++|+|||++|+.+++.....+ .   .++.+|..     +...++.   
T Consensus       184 ~~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l-----~~~~lla---  255 (758)
T PRK11034        184 GIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL-----DIGSLLA---  255 (758)
T ss_pred             CCCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEec-----cHHHHhc---
Confidence            3467899999999999988865555667999999999999999987653321 1   13344421     1111110   


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--------c--ChhhhcCCCCCCCCCeEEEEeecchhhh--
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--------L--DLEAIGIPLADDNGGCKVLLTARSQDVL--  292 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--------~--~~~~l~~~l~~~~~~s~iivTtr~~~va--  292 (426)
                         +.. ........+..+++.+.+..+.+|+||+++..        .  +...+..++.. ...-++|-+|..+...  
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 01112233445556565556789999999743        1  11112222222 2234555555543321  


Q ss_pred             ----hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          293 ----SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       293 ----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                          .........+.+++.+.++..+++....
T Consensus       331 ~~~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        331 FEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             hhccHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence                1112345689999999999999998654

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

Probab=98.05  E-value=9.2e-05  Score=64.32  Aligned_cols=101  Identities=19%  Similarity=0.172  Sum_probs=67.3

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG  228 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~  228 (426)
                      ...+++|.++.++.+--...+++.+.+.|.||+|+||||-+..+.+..-....-+.+.-.++|....+.-+-..|-.-. 
T Consensus        25 ~l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~FA-  103 (333)
T KOG0991|consen   25 VLQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFA-  103 (333)
T ss_pred             HHHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHHHH-
Confidence            3567899999888877777788899999999999999999988888765433333455555555554444433332100 


Q ss_pred             CCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          229 LKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       229 ~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                                   +-.-.+..++.-+++||+.++.
T Consensus       104 -------------Q~kv~lp~grhKIiILDEADSM  125 (333)
T KOG0991|consen  104 -------------QKKVTLPPGRHKIIILDEADSM  125 (333)
T ss_pred             -------------HhhccCCCCceeEEEeeccchh
Confidence                         0001112367779999999876

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.03  E-value=0.0003  Score=70.98  Aligned_cols=181  Identities=14%  Similarity=0.090  Sum_probs=104.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.|+|..|+|||.|++.+++.......-..++|++.      .++..++...+...        ....+.+.+.  +.
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yita------eef~~el~~al~~~--------~~~~f~~~y~--~~  378 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSS------EEFTNEFINSIRDG--------KGDSFRRRYR--EM  378 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH------HHHHHHHHHHHHhc--------cHHHHHHHhh--cC
Confidence            35899999999999999999998754211223455543      44454554433211        1122333333  23


Q ss_pred             EEEEEeCCCCc---cChhh-hcCCCCC-CCCCeEEEEeecchhhh--------hccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGS---LDLEA-IGIPLAD-DNGGCKVLLTARSQDVL--------SCEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~---~~~~~-l~~~l~~-~~~~s~iivTtr~~~va--------~~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      =+|+|||+...   ..|.. +...+.. ...+..|||||....-.        .......-++.|++.+.+.-..++.+.
T Consensus       379 DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kk  458 (617)
T PRK14086        379 DILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKK  458 (617)
T ss_pred             CEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHH
Confidence            58999999754   22322 2222211 12355688888764211        112334568899999999999999988


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh------hcC--CHHHHHHHHHHHh
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL------KNK--SPYEWRNALRQLK  370 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l------~~~--~~~~w~~~l~~l~  370 (426)
                      +...... --.++..-|++.+.+..-.|.-+...|      .++  +...-+.+++.+.
T Consensus       459 a~~r~l~-l~~eVi~yLa~r~~rnvR~LegaL~rL~a~a~~~~~~itl~la~~vL~~~~  516 (617)
T PRK14086        459 AVQEQLN-APPEVLEFIASRISRNIRELEGALIRVTAFASLNRQPVDLGLTEIVLRDLI  516 (617)
T ss_pred             HHhcCCC-CCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhh
Confidence            8533211 125677788888777655444333222      122  5666666776553

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.03  E-value=9.6e-05  Score=72.96  Aligned_cols=181  Identities=12%  Similarity=0.138  Sum_probs=105.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .-+.|+|++|+|||+|++.+++.......-..++|++.      .++..++...+...        ......+.+. .+.
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~------~~f~~~~~~~~~~~--------~~~~f~~~~~-~~~  195 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS------EKFLNDLVDSMKEG--------KLNEFREKYR-KKV  195 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHhcc--------cHHHHHHHHH-hcC
Confidence            45899999999999999999998764321124556643      45566665554321        1112333332 235


Q ss_pred             EEEEEeCCCCcc---Ch-hhhcCCCCC-CCCCeEEEEeecchh-h----hhc---cCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGSL---DL-EAIGIPLAD-DNGGCKVLLTARSQD-V----LSC---EMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~~---~~-~~l~~~l~~-~~~~s~iivTtr~~~-v----a~~---~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      -+|+|||++...   .+ ..+...+.. ...|..||+||.... -    ...   .......+.+++.+.+.-..++.+.
T Consensus       196 dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~  275 (440)
T PRK14088        196 DVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKM  275 (440)
T ss_pred             CEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHH
Confidence            589999997441   11 122221110 123456888875321 1    111   1223357899999999999999988


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh------hcC--CHHHHHHHHHHH
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL------KNK--SPYEWRNALRQL  369 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l------~~~--~~~~w~~~l~~l  369 (426)
                      +..... .--+++..-|++.+.|..-.+.-+-..|      .++  +...-+.++..+
T Consensus       276 ~~~~~~-~l~~ev~~~Ia~~~~~~~R~L~g~l~~l~~~~~~~~~~it~~~a~~~L~~~  332 (440)
T PRK14088        276 LEIEHG-ELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGEEVDLKEAILLLKDF  332 (440)
T ss_pred             HHhcCC-CCCHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence            753211 1125678889998888655444333222      122  667777777665

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

Probab=98.02  E-value=0.00046  Score=63.94  Aligned_cols=201  Identities=18%  Similarity=0.250  Sum_probs=119.0

Q ss_pred             ccCCcccccchHHHHHHHHHHhc----c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          146 STQDFMHFESRKSTLKGILDALS----N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       146 ~~~~~~~~~gR~~~~~~l~~~l~----~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      |...+.++-|-++.+++|.+...    +         ..++=|.++|++|.|||-||+.|++.....       |+.+..
T Consensus       146 PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~At-------FIrvvg  218 (406)
T COG1222         146 PDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDAT-------FIRVVG  218 (406)
T ss_pred             CCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCce-------EEEecc
Confidence            34456667788888888777654    1         346678899999999999999999987654       444432


Q ss_pred             CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------C----hhhhcCCCC--
Q 044858          213 TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------D----LEAIGIPLA--  274 (426)
Q Consensus       213 ~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~----~~~l~~~l~--  274 (426)
                      +    ++.+..+   |      .....+..+++......+++|++|.++...            +    .-.+...+-  
T Consensus       219 S----ElVqKYi---G------EGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGF  285 (406)
T COG1222         219 S----ELVQKYI---G------EGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGF  285 (406)
T ss_pred             H----HHHHHHh---c------cchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCC
Confidence            2    2222221   1      113456677777777889999999986330            0    111111221  


Q ss_pred             CCCCCeEEEEeecchhhh----hccCCceeeEEccCCCHHHHHHHHHHhhCCC--CCCCchHHHHHHHHHHcCCch----
Q 044858          275 DDNGGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDC--IENGELKSVVTEVVKECAGLP----  344 (426)
Q Consensus       275 ~~~~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~--~~~~~~~~~~~~i~~~c~GlP----  344 (426)
                      +.....+||..|...++.    -+...-...|+++.=+.+.-.++|+-+....  ...-++    +.|++.|.|.-    
T Consensus       286 D~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~----e~la~~~~g~sGAdl  361 (406)
T COG1222         286 DPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDL----ELLARLTEGFSGADL  361 (406)
T ss_pred             CCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCH----HHHHHhcCCCchHHH
Confidence            224567899888776554    1122334567777444445555666555432  223343    34666666653    


Q ss_pred             HHHHHHHHHhh---cC---CHHHHHHHHHHHh
Q 044858          345 IAIVPIAKALK---NK---SPYEWRNALRQLK  370 (426)
Q Consensus       345 lai~~~~~~l~---~~---~~~~w~~~l~~l~  370 (426)
                      .|+-+=|++++   .+   +.+++..+.+...
T Consensus       362 kaictEAGm~AiR~~R~~Vt~~DF~~Av~KV~  393 (406)
T COG1222         362 KAICTEAGMFAIRERRDEVTMEDFLKAVEKVV  393 (406)
T ss_pred             HHHHHHHhHHHHHhccCeecHHHHHHHHHHHH
Confidence            34555566665   22   6667766666544

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

Probab=97.98  E-value=0.00019  Score=64.35  Aligned_cols=231  Identities=12%  Similarity=0.111  Sum_probs=132.3

Q ss_pred             CCcccccchHHHHHHHHHHhc-----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALS-----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .....|+|.++..+++-=.+.     +..+--+.++|++|.||||||..+.+...+.  +    -++.++..        
T Consensus        23 ~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn--~----k~tsGp~l--------   88 (332)
T COG2255          23 KTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVN--L----KITSGPAL--------   88 (332)
T ss_pred             ccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCC--e----Eecccccc--------
Confidence            456789999888877665554     3456678999999999999999999998764  1    11111110        


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-C--------hhhhcCC-CCCCCCCeE-----------
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-D--------LEAIGIP-LADDNGGCK-----------  281 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-~--------~~~l~~~-l~~~~~~s~-----------  281 (426)
                                  .....+..++..+.  ..=++++|+++... .        .+++..- ....++++|           
T Consensus        89 ------------eK~gDlaaiLt~Le--~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTL  154 (332)
T COG2255          89 ------------EKPGDLAAILTNLE--EGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTL  154 (332)
T ss_pred             ------------cChhhHHHHHhcCC--cCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeE
Confidence                        01112223333333  23467778876441 1        1111100 011122222           


Q ss_pred             EEEeecchhhhh-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhc----
Q 044858          282 VLLTARSQDVLS-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKN----  356 (426)
Q Consensus       282 iivTtr~~~va~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~----  356 (426)
                      |=-|||.-.+.. ....-..+.+++--+.+|-.++..+.+..-. -+--++.+.+|++...|-|--..-+.+..+.    
T Consensus       155 IGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~-i~i~~~~a~eIA~rSRGTPRIAnRLLrRVRDfa~V  233 (332)
T COG2255         155 IGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILG-IEIDEEAALEIARRSRGTPRIANRLLRRVRDFAQV  233 (332)
T ss_pred             eeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhC-CCCChHHHHHHHHhccCCcHHHHHHHHHHHHHHHH
Confidence            335888765432 1222335778999999999999998874211 1112456889999999999877666655541    


Q ss_pred             --C---CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHHHhhc
Q 044858          357 --K---SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGY  410 (426)
Q Consensus       357 --~---~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s~  410 (426)
                        .   +..--..+++.|.-... .+...+ ..++.++.-.|+.=|-- ++..-..++.
T Consensus       234 ~~~~~I~~~ia~~aL~~L~Vd~~-GLd~~D-~k~L~~li~~f~GgPVG-l~tia~~lge  289 (332)
T COG2255         234 KGDGDIDRDIADKALKMLDVDEL-GLDEID-RKYLRALIEQFGGGPVG-LDTIAAALGE  289 (332)
T ss_pred             hcCCcccHHHHHHHHHHhCcccc-cccHHH-HHHHHHHHHHhCCCCcc-HHHHHHHhcC
Confidence              1   33333445554432111 111123 56677777777777765 6665555554

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.94  E-value=0.00011  Score=75.08  Aligned_cols=201  Identities=11%  Similarity=0.055  Sum_probs=104.1

Q ss_pred             cCCcccccchHHHHHHHHHHhccC-----CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC---CcCHHH
Q 044858          147 TQDFMHFESRKSTLKGILDALSNR-----NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ---TPQIKE  218 (426)
Q Consensus       147 ~~~~~~~~gR~~~~~~l~~~l~~~-----~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~---~~~~~~  218 (426)
                      |.....+++.++.+.++..++...     ...++.|+|++|+||||+++.+......    +..-|.+-..   ..+...
T Consensus        80 P~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~----~~~Ew~npv~~~~~~~~~~  155 (637)
T TIGR00602        80 PETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGI----QVQEWSNPTLPDFQKNDHK  155 (637)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhh----HHHHHhhhhhhcccccccc
Confidence            345677889999999888888632     3356999999999999999999876542    2222321100   000011


Q ss_pred             HHHHHHHHhCCCccccCcHHHHHHHHHHH----------hcCCeEEEEEeCCCCcc-----ChhhhcC-CCCCCCCCeEE
Q 044858          219 IQREIAEKLGLKIDQESESVRAWRLLEQL----------KKETKILIILDDIWGSL-----DLEAIGI-PLADDNGGCKV  282 (426)
Q Consensus       219 il~~i~~~l~~~~~~~~~~~~~~~l~~~l----------~~~k~~LlVlDdv~~~~-----~~~~l~~-~l~~~~~~s~i  282 (426)
                      +...+..++....   +.......+....          ..+++.+|+||++....     .+..+.. .+.....-.-|
T Consensus       156 ~~~s~~~~~~~~~---s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~~~~lq~lLr~~~~e~~~~pLI  232 (637)
T TIGR00602       156 VTLSLESCFSNFQ---SQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLV  232 (637)
T ss_pred             cchhhhhcccccc---chHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhhHHHHHHHHHHHhhcCCCceEE
Confidence            1112222221111   1111111111111          12467899999995431     2333333 22222222334


Q ss_pred             EEeecchh----------hh-----hcc--CCceeeEEccCCCHHHHHHHHHHhhCCCC---CCC---chHHHHHHHHHH
Q 044858          283 LLTARSQD----------VL-----SCE--MDCQQNFVVDVLNDKEAWSLFKKMTGDCI---ENG---ELKSVVTEVVKE  339 (426)
Q Consensus       283 ivTtr~~~----------va-----~~~--~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~---~~~---~~~~~~~~i~~~  339 (426)
                      ++||-+..          .+     ...  ......|.+.|++..+....+.+.+....   ...   .-.+....|+..
T Consensus       233 ~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~  312 (637)
T TIGR00602       233 FIITESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQG  312 (637)
T ss_pred             EEecCCccccccccccccchhcccCHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHh
Confidence            44552211          00     001  12345799999999998888877764211   011   013567778888


Q ss_pred             cCCchHHHHHHHHHh
Q 044858          340 CAGLPIAIVPIAKAL  354 (426)
Q Consensus       340 c~GlPlai~~~~~~l  354 (426)
                      ++|---.+.....++
T Consensus       313 s~GDiRsAIn~LQf~  327 (637)
T TIGR00602       313 CSGDIRSAINSLQFS  327 (637)
T ss_pred             CCChHHHHHHHHHHH
Confidence            888655554444444

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

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.91  E-value=0.00019  Score=71.27  Aligned_cols=176  Identities=14%  Similarity=0.113  Sum_probs=93.1

Q ss_pred             CcccccchHHHHHHHHHHh---c-------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHH
Q 044858          149 DFMHFESRKSTLKGILDAL---S-------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKE  218 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l---~-------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  218 (426)
                      .+.++.|.+..++.+....   .       -..++-|.++|++|+|||.+|+.+.+.....  |   +-+..+      .
T Consensus       226 ~~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~--~---~~l~~~------~  294 (489)
T CHL00195        226 KISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLP--L---LRLDVG------K  294 (489)
T ss_pred             CHHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC--E---EEEEhH------H
Confidence            3445667665555444321   1       1235678999999999999999999876532  2   122211      1


Q ss_pred             HHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC----------h----hhhcCCCCCCCCCeEEEE
Q 044858          219 IQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD----------L----EAIGIPLADDNGGCKVLL  284 (426)
Q Consensus       219 il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~----------~----~~l~~~l~~~~~~s~iiv  284 (426)
                      +..        ..-.. ....+.++++......+++|+||+++....          -    ..+...+.....+.-||.
T Consensus       295 l~~--------~~vGe-se~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIa  365 (489)
T CHL00195        295 LFG--------GIVGE-SESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVA  365 (489)
T ss_pred             hcc--------cccCh-HHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEE
Confidence            110        00111 122344455544456799999999964210          0    011111112223444555


Q ss_pred             eecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          285 TARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       285 Ttr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      ||.......    +...-...+.++.-+.++-.++|..++........-......+++.+.|.-
T Consensus       366 TTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfS  429 (489)
T CHL00195        366 TANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFS  429 (489)
T ss_pred             ecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCC
Confidence            665543211    112234578888888899999998887532211100112456677776653

>PRK10536 hypothetical protein; Provisional

Probab=97.90  E-value=0.00018  Score=64.58  Aligned_cols=56  Identities=21%  Similarity=0.266  Sum_probs=40.9

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEE
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVI  206 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~  206 (426)
                      +...+.+|......++.++.+.  .++.+.|++|+|||+||..+..+.-..+.|+.++
T Consensus        53 ~~~~i~p~n~~Q~~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIi  108 (262)
T PRK10536         53 DTSPILARNEAQAHYLKAIESK--QLIFATGEAGCGKTWISAAKAAEALIHKDVDRII  108 (262)
T ss_pred             CCccccCCCHHHHHHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEE
Confidence            3445667888888888887764  4899999999999999999887643223355433

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

Probab=97.90  E-value=0.00031  Score=69.29  Aligned_cols=94  Identities=19%  Similarity=0.265  Sum_probs=63.4

Q ss_pred             CcccccchHHHHHHHHHHhc---c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          149 DFMHFESRKSTLKGILDALS---N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~---~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .+.++-|-+..+.++.+.+.   .         ..++=|.+||++|+|||.||+.+.+...+.       ++.++.+   
T Consensus       188 ~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vP-------f~~isAp---  257 (802)
T KOG0733|consen  188 SFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVP-------FLSISAP---  257 (802)
T ss_pred             chhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCc-------eEeecch---
Confidence            35567788887777666553   1         235568899999999999999999998865       3333322   


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWG  262 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~  262 (426)
                           +|...+.    . .....+..+++...+.-+|+++||+++-
T Consensus       258 -----eivSGvS----G-ESEkkiRelF~~A~~~aPcivFiDeIDA  293 (802)
T KOG0733|consen  258 -----EIVSGVS----G-ESEKKIRELFDQAKSNAPCIVFIDEIDA  293 (802)
T ss_pred             -----hhhcccC----c-ccHHHHHHHHHHHhccCCeEEEeecccc
Confidence                 1222211    1 1234566777777777899999999963

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.89  E-value=0.00068  Score=63.62  Aligned_cols=173  Identities=13%  Similarity=0.122  Sum_probs=96.1

Q ss_pred             HHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccc----------------eEEEEEecCCcCHHHHHH
Q 044858          159 TLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFE----------------KVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       159 ~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~----------------~~~wv~v~~~~~~~~il~  221 (426)
                      ..+.+...+..++. ..+.++|+.|+||+++|..+.+..-......                -..|+.......      
T Consensus        12 ~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~------   85 (319)
T PRK08769         12 AYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRT------   85 (319)
T ss_pred             HHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcc------
Confidence            34556666666554 4688999999999999999887653221111                111221000000      


Q ss_pred             HHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecc-hhhhhc
Q 044858          222 EIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARS-QDVLSC  294 (426)
Q Consensus       222 ~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~-~~va~~  294 (426)
                            +......-..+.+..+.+.+.    .+++-++|||+++...  .-+.+...+-.-..++.+|++|.+ ..+...
T Consensus        86 ------~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpT  159 (319)
T PRK08769         86 ------GDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPAT  159 (319)
T ss_pred             ------cccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchH
Confidence                  000000001223333333332    2456799999997542  223333333222346666666665 444333


Q ss_pred             cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          295 EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       295 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      ..+....+.+.+++.+++.+.+... +  . +   ...+..++..++|.|+....+
T Consensus       160 IrSRCq~i~~~~~~~~~~~~~L~~~-~--~-~---~~~a~~~~~l~~G~p~~A~~~  208 (319)
T PRK08769        160 IRSRCQRLEFKLPPAHEALAWLLAQ-G--V-S---ERAAQEALDAARGHPGLAAQW  208 (319)
T ss_pred             HHhhheEeeCCCcCHHHHHHHHHHc-C--C-C---hHHHHHHHHHcCCCHHHHHHH
Confidence            3445678999999999999888753 1  1 1   223667899999999866544

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

Probab=97.87  E-value=0.00014  Score=71.78  Aligned_cols=189  Identities=17%  Similarity=0.189  Sum_probs=113.3

Q ss_pred             CcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .+..++|.+.....|...+..++. ......|+.|+||||+|+.+....--.+      + ....++......+.|...-
T Consensus        14 ~F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~------~-~~~ePC~~C~~Ck~I~~g~   86 (515)
T COG2812          14 TFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCEN------G-PTAEPCGKCISCKEINEGS   86 (515)
T ss_pred             cHHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCC------C-CCCCcchhhhhhHhhhcCC
Confidence            566789999999999988886653 4567899999999999999987653221      0 1112222222223332220


Q ss_pred             CCC---cc--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCC--ccChhhhcCCCCCCCCCeEEEE-eecchhhhhcc
Q 044858          228 GLK---ID--QESESVRAWRLLEQLK----KETKILIILDDIWG--SLDLEAIGIPLADDNGGCKVLL-TARSQDVLSCE  295 (426)
Q Consensus       228 ~~~---~~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~s~iiv-Ttr~~~va~~~  295 (426)
                      ..+   .+  .....+.+..+.+...    .++.=+.++|+|+-  ...|+.+...+-.--.....|+ ||-...+....
T Consensus        87 ~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TI  166 (515)
T COG2812          87 LIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTI  166 (515)
T ss_pred             cccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhh
Confidence            000   01  1112334445555543    35556899999974  4667776655533333455444 55555554445


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI  345 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl  345 (426)
                      .+..+.|.++.++.++-...+...+....-.-+ .+...-|.+..+|...
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            566789999999999999988888753322222 3445566666666433

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.82  E-value=0.0024  Score=59.88  Aligned_cols=163  Identities=15%  Similarity=0.127  Sum_probs=94.4

Q ss_pred             HHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhc-------------------CccceEEEEEecCCcCHHHH
Q 044858          160 LKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKEN-------------------NLFEKVISSRVSQTPQIKEI  219 (426)
Q Consensus       160 ~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~-------------------~~f~~~~wv~v~~~~~~~~i  219 (426)
                      ...+...+..++ +..+.++|+.|+||+++|..+....--.                   .|.| ..|+.-...      
T Consensus        12 ~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~p~~~------   84 (319)
T PRK06090         12 WQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPD-LHVIKPEKE------   84 (319)
T ss_pred             HHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCC-EEEEecCcC------
Confidence            345555555555 4578999999999999999987654321                   1112 112211000      


Q ss_pred             HHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhh
Q 044858          220 QREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVL  292 (426)
Q Consensus       220 l~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va  292 (426)
                                  ...-..+.+..+.+.+.    .+++=++|+|+++..  ...+.+...+-.-..++.+|++|.+ ..+.
T Consensus        85 ------------~~~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lL  152 (319)
T PRK06090         85 ------------GKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLL  152 (319)
T ss_pred             ------------CCcCCHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhCh
Confidence                        00001122233333331    245568899999754  3444444444333345666666555 4444


Q ss_pred             hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          293 SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       293 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      ....+....+.+.++++++..+.+...-   .  +    ....+++.++|.|+....+
T Consensus       153 pTI~SRCq~~~~~~~~~~~~~~~L~~~~---~--~----~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        153 PTIVSRCQQWVVTPPSTAQAMQWLKGQG---I--T----VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             HHHHhcceeEeCCCCCHHHHHHHHHHcC---C--c----hHHHHHHHcCCCHHHHHHH
Confidence            3344556789999999999999887531   1  1    1356789999999977554

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.82  E-value=0.00068  Score=64.45  Aligned_cols=146  Identities=12%  Similarity=0.107  Sum_probs=85.1

Q ss_pred             ccc-hHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------ccceEEEEEe
Q 044858          153 FES-RKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENN--------------------LFEKVISSRV  210 (426)
Q Consensus       153 ~~g-R~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~v  210 (426)
                      ++| .+...+.+...+..++. +...++|+.|+||||+|..+.+..-...                    |.|..+....
T Consensus         7 i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~   86 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPD   86 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccc
Confidence            445 56667777777766654 4668999999999999999977653211                    1121111100


Q ss_pred             cCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEE
Q 044858          211 SQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLL  284 (426)
Q Consensus       211 ~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iiv  284 (426)
                      +...                     ..+.+..+.+.+.    .+.+-++|+|+++...  ..+.+...+..-..++.+|+
T Consensus        87 ~~~i---------------------~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il  145 (329)
T PRK08058         87 GQSI---------------------KKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAIL  145 (329)
T ss_pred             cccC---------------------CHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEE
Confidence            1111                     1122333333332    2445689999986542  33444444433334666777


Q ss_pred             eecch-hhhhccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          285 TARSQ-DVLSCEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       285 Ttr~~-~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      +|.+. .+.....+....+++.++++++..+.+.+.
T Consensus       146 ~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        146 LTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEE  181 (329)
T ss_pred             EeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHHc
Confidence            76553 333323445678999999999998888653

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.80  E-value=0.00058  Score=62.73  Aligned_cols=56  Identities=21%  Similarity=0.234  Sum_probs=36.0

Q ss_pred             HHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHH
Q 044858          158 STLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQ  220 (426)
Q Consensus       158 ~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il  220 (426)
                      +.++.+..++..+  .-+.+.|++|+|||+||+.+.+....     ..+.++.....+..+++
T Consensus         9 ~l~~~~l~~l~~g--~~vLL~G~~GtGKT~lA~~la~~lg~-----~~~~i~~~~~~~~~dll   64 (262)
T TIGR02640         9 RVTSRALRYLKSG--YPVHLRGPAGTGKTTLAMHVARKRDR-----PVMLINGDAELTTSDLV   64 (262)
T ss_pred             HHHHHHHHHHhcC--CeEEEEcCCCCCHHHHHHHHHHHhCC-----CEEEEeCCccCCHHHHh
Confidence            3445555555544  34679999999999999999874421     23455555555555554

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).

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.79  E-value=0.0015  Score=61.36  Aligned_cols=175  Identities=10%  Similarity=0.069  Sum_probs=95.6

Q ss_pred             HHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCC------C-c
Q 044858          160 LKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGL------K-I  231 (426)
Q Consensus       160 ~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~------~-~  231 (426)
                      -..+...+..++ ...+.++|+.|+||+++|..+....--......       ..+..-..-+.+...-..      + .
T Consensus        11 ~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~-------~~Cg~C~sC~~~~~g~HPD~~~i~p~~   83 (325)
T PRK06871         11 YQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGD-------QPCGQCHSCHLFQAGNHPDFHILEPID   83 (325)
T ss_pred             HHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCC-------CCCCCCHHHHHHhcCCCCCEEEEcccc
Confidence            345556665555 457889999999999999999876532111100       000000111111100000      0 0


Q ss_pred             cccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecch-hhhhccCCceeeEEc
Q 044858          232 DQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMDCQQNFVV  304 (426)
Q Consensus       232 ~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~~~~~~~l  304 (426)
                      ...-..+.+..+.+.+.    .+++-++|+|+++..  ...+.+...+-.-..++.+|++|.+. .+.....+....+.+
T Consensus        84 ~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~  163 (325)
T PRK06871         84 NKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLI  163 (325)
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeC
Confidence            00011233334444432    356668889999755  33444444443333466666666654 443323445678999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      .++++++..+.+......    +  ...+...++.++|.|+..
T Consensus       164 ~~~~~~~~~~~L~~~~~~----~--~~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        164 HPPEEQQALDWLQAQSSA----E--ISEILTALRINYGRPLLA  200 (325)
T ss_pred             CCCCHHHHHHHHHHHhcc----C--hHHHHHHHHHcCCCHHHH
Confidence            999999999888875421    1  123556788999999733

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.79  E-value=0.00051  Score=72.67  Aligned_cols=173  Identities=17%  Similarity=0.215  Sum_probs=95.9

Q ss_pred             cccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          150 FMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      ...+.|.+..++.|.+.+.             -..++-+.++|++|+|||+||+.+.+.....  |     +.+..    
T Consensus       452 ~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~--f-----i~v~~----  520 (733)
T TIGR01243       452 WSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGAN--F-----IAVRG----  520 (733)
T ss_pred             hhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCC--E-----EEEeh----
Confidence            4455676666655555432             1234568899999999999999999886532  2     22221    


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc---------C-----hhhhcCCCCC--CCCCe
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL---------D-----LEAIGIPLAD--DNGGC  280 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~---------~-----~~~l~~~l~~--~~~~s  280 (426)
                      .+++.    .    .-.. ....+..++.......+++|+||+++...         .     ...+...+..  ...+.
T Consensus       521 ~~l~~----~----~vGe-se~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v  591 (733)
T TIGR01243       521 PEILS----K----WVGE-SEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNV  591 (733)
T ss_pred             HHHhh----c----ccCc-HHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCE
Confidence            11111    1    1111 12234556666655678999999986431         0     1112111211  22344


Q ss_pred             EEEEeecchhhh-h---ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          281 KVLLTARSQDVL-S---CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       281 ~iivTtr~~~va-~---~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      -||.||...... .   ....-...+.++..+.++-.++|+.........++.  -...+++.|.|.-
T Consensus       592 ~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~--~l~~la~~t~g~s  657 (733)
T TIGR01243       592 VVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDV--DLEELAEMTEGYT  657 (733)
T ss_pred             EEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccC--CHHHHHHHcCCCC
Confidence            566666554332 1   112345678888889999999998766433222211  1355777777754

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.

>TIGR00763 lon ATP-dependent protease La

Probab=97.79  E-value=0.00091  Score=71.02  Aligned_cols=157  Identities=19%  Similarity=0.163  Sum_probs=81.9

Q ss_pred             cccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          152 HFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .++|.+..++.+.+++.      ..+.+++.++|++|+|||++|+.+.+.....  |-   -++.+...+..++...   
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~--~~---~i~~~~~~~~~~i~g~---  392 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRK--FV---RFSLGGVRDEAEIRGH---  392 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcCC--eE---EEeCCCcccHHHHcCC---
Confidence            36677777777777653      2234579999999999999999999887532  31   2223332233322110   


Q ss_pred             HhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC------hhhhcC--------CCCCC-------CCCeEEEE
Q 044858          226 KLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD------LEAIGI--------PLADD-------NGGCKVLL  284 (426)
Q Consensus       226 ~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~------~~~l~~--------~l~~~-------~~~s~iiv  284 (426)
                        ............. +.+..... ++-+++||+++....      ...+..        .|.+.       ..+..+|.
T Consensus       393 --~~~~~g~~~g~i~-~~l~~~~~-~~~villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~  468 (775)
T TIGR00763       393 --RRTYVGAMPGRII-QGLKKAKT-KNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIA  468 (775)
T ss_pred             --CCceeCCCCchHH-HHHHHhCc-CCCEEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEE
Confidence              0000011111111 22222222 334789999965421      011111        11111       12333444


Q ss_pred             eecchh-hhhccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          285 TARSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       285 Ttr~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      ||.... +..........+++.+++.++-.+++...+
T Consensus       469 TtN~~~~i~~~L~~R~~vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       469 TANSIDTIPRPLLDRMEVIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             ecCCchhCCHHHhCCeeEEecCCCCHHHHHHHHHHHH
Confidence            554332 112223445689999999999988887654

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.79  E-value=0.00047  Score=68.00  Aligned_cols=153  Identities=12%  Similarity=0.117  Sum_probs=87.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .-+.|+|+.|+|||+|++.+.+.....  ...+++++.      .++...+...+...        ........+.  +.
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~--~~~v~yi~~------~~f~~~~~~~l~~~--------~~~~f~~~~~--~~  203 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRES--GGKILYVRS------ELFTEHLVSAIRSG--------EMQRFRQFYR--NV  203 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHc--CCCEEEeeH------HHHHHHHHHHHhcc--------hHHHHHHHcc--cC
Confidence            458899999999999999999987643  223455542      34444554444211        1112222222  34


Q ss_pred             EEEEEeCCCCccC--h--hhhcCCCCC-CCCCeEEEEeecchhh-----hh---ccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGSLD--L--EAIGIPLAD-DNGGCKVLLTARSQDV-----LS---CEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~~~--~--~~l~~~l~~-~~~~s~iivTtr~~~v-----a~---~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      -+|++||+.....  +  +.+...+.. ...|..||+||.....     ..   ........+.+.+++.++-..++.+.
T Consensus       204 dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k  283 (445)
T PRK12422        204 DALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERK  283 (445)
T ss_pred             CEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHH
Confidence            5899999975422  1  122222110 1135578888855311     11   11223468899999999999999988


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCch
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      +.... ..--+++..-|++.+.|.-
T Consensus       284 ~~~~~-~~l~~evl~~la~~~~~di  307 (445)
T PRK12422        284 AEALS-IRIEETALDFLIEALSSNV  307 (445)
T ss_pred             HHHcC-CCCCHHHHHHHHHhcCCCH
Confidence            75322 1112456666777776543

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

Probab=97.78  E-value=0.00046  Score=66.24  Aligned_cols=178  Identities=17%  Similarity=0.194  Sum_probs=97.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      ...+.|+|+.|.|||.|++.+.+.....  ......++++    ..+...+.+..+..        .......+.. +  
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~--~~~a~v~y~~----se~f~~~~v~a~~~--------~~~~~Fk~~y-~--  175 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALAN--GPNARVVYLT----SEDFTNDFVKALRD--------NEMEKFKEKY-S--  175 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhh--CCCceEEecc----HHHHHHHHHHHHHh--------hhHHHHHHhh-c--
Confidence            5679999999999999999999988754  3322233332    23333333333211        1122333333 1  


Q ss_pred             eEEEEEeCCCCcc---Chhh-h---cCCCCCCCCCeEEEEeecchhhh--------hccCCceeeEEccCCCHHHHHHHH
Q 044858          252 KILIILDDIWGSL---DLEA-I---GIPLADDNGGCKVLLTARSQDVL--------SCEMDCQQNFVVDVLNDKEAWSLF  316 (426)
Q Consensus       252 ~~LlVlDdv~~~~---~~~~-l---~~~l~~~~~~s~iivTtr~~~va--------~~~~~~~~~~~l~~L~~~e~~~Lf  316 (426)
                      -=++++||++...   .|+. +   ...+..  .|-+||+|++..+-.        .......-++.+.+.+.+....++
T Consensus       176 ~dlllIDDiq~l~gk~~~qeefFh~FN~l~~--~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL  253 (408)
T COG0593         176 LDLLLIDDIQFLAGKERTQEEFFHTFNALLE--NGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAIL  253 (408)
T ss_pred             cCeeeechHhHhcCChhHHHHHHHHHHHHHh--cCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHH
Confidence            2389999997542   2222 2   222222  233899998665321        112234568999999999999999


Q ss_pred             HHhhCCC--CCCCchHHHHHHHHHHcCC----chHHHHHHHHHhh--c-C-CHHHHHHHHHHHhh
Q 044858          317 KKMTGDC--IENGELKSVVTEVVKECAG----LPIAIVPIAKALK--N-K-SPYEWRNALRQLKR  371 (426)
Q Consensus       317 ~~~~~~~--~~~~~~~~~~~~i~~~c~G----lPlai~~~~~~l~--~-~-~~~~w~~~l~~l~~  371 (426)
                      .+.+...  ..++   ++..-|++....    +.-|+..+..+-.  + . |...-+.++..+..
T Consensus       254 ~kka~~~~~~i~~---ev~~~la~~~~~nvReLegaL~~l~~~a~~~~~~iTi~~v~e~L~~~~~  315 (408)
T COG0593         254 RKKAEDRGIEIPD---EVLEFLAKRLDRNVRELEGALNRLDAFALFTKRAITIDLVKEILKDLLR  315 (408)
T ss_pred             HHHHHhcCCCCCH---HHHHHHHHHhhccHHHHHHHHHHHHHHHHhcCccCcHHHHHHHHHHhhc
Confidence            9877422  1222   233334433333    3334433322221  2 1 66666666666543

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.77  E-value=0.00026  Score=67.09  Aligned_cols=100  Identities=12%  Similarity=0.174  Sum_probs=65.9

Q ss_pred             HHHHHHhcc-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccce-EEEEEecC-CcCHHHHHHHHHHHhCCCccccCcH
Q 044858          161 KGILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEK-VISSRVSQ-TPQIKEIQREIAEKLGLKIDQESES  237 (426)
Q Consensus       161 ~~l~~~l~~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~-~~~~~~il~~i~~~l~~~~~~~~~~  237 (426)
                      ..+++.+.. ++-.-+.|+|++|+|||||++.+.+....+ +-+. ++|+.+.+ ..++.++++.+...+..+....+..
T Consensus       121 ~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~-~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~  199 (380)
T PRK12608        121 MRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAAN-HPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPD  199 (380)
T ss_pred             HhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHH
Confidence            346666552 233467999999999999999999877543 3344 46766664 4578889999888776544322221


Q ss_pred             H------HHHHHHHHH-hcCCeEEEEEeCCC
Q 044858          238 V------RAWRLLEQL-KKETKILIILDDIW  261 (426)
Q Consensus       238 ~------~~~~l~~~l-~~~k~~LlVlDdv~  261 (426)
                      .      .+....+++ .++++.+||+|++.
T Consensus       200 ~~~~v~~~~~~~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        200 EHIRVAELVLERAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEEEeCcH
Confidence            1      122333333 35899999999985

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

Probab=97.76  E-value=0.0029  Score=66.86  Aligned_cols=158  Identities=15%  Similarity=0.167  Sum_probs=87.8

Q ss_pred             ccccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          151 MHFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ...+|.++.++.|++++.      ..+..++.++|++|+||||+++.+.......  |   +-+..+...+..++...-.
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~--~---~~i~~~~~~d~~~i~g~~~  396 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRK--Y---VRMALGGVRDEAEIRGHRR  396 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCCC--E---EEEEcCCCCCHHHhccchh
Confidence            346788888888888776      1245689999999999999999999865432  3   2233343334333221111


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC------hhhhcCCCCC---------------CCCCeEEE
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD------LEAIGIPLAD---------------DNGGCKVL  283 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~------~~~l~~~l~~---------------~~~~s~ii  283 (426)
                      ...+.     ......+.+. ... ...-+++||+++....      ...+...+-.               .-.+.-+|
T Consensus       397 ~~~g~-----~~G~~~~~l~-~~~-~~~~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i  469 (784)
T PRK10787        397 TYIGS-----MPGKLIQKMA-KVG-VKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFV  469 (784)
T ss_pred             ccCCC-----CCcHHHHHHH-hcC-CCCCEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEE
Confidence            11110     1111111121 111 1234788999964421      1222221111               11344455


Q ss_pred             EeecchhhhhccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          284 LTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       284 vTtr~~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      .|+....+.....+....+.+.+++.++-.++.++++
T Consensus       470 ~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        470 ATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             EcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHHHhh
Confidence            5654444333334455789999999999999988776

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

Probab=97.74  E-value=0.0016  Score=65.56  Aligned_cols=156  Identities=18%  Similarity=0.206  Sum_probs=89.8

Q ss_pred             ccccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          151 MHFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .+.+|-++.++.+++++.      +.+-+++..+||+|+|||++++.++.....+  |   +-++++.-.+..+|-..=-
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRk--F---fRfSvGG~tDvAeIkGHRR  485 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRK--F---FRFSVGGMTDVAEIKGHRR  485 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCc--e---EEEeccccccHHhhcccce
Confidence            445788888888888875      3356799999999999999999999887643  3   2455666555555321100


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhc--CCeEEEEEeCCCCcc------ChhhhcCCCCC-CC------------CCeEEE
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKK--ETKILIILDDIWGSL------DLEAIGIPLAD-DN------------GGCKVL  283 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~--~k~~LlVlDdv~~~~------~~~~l~~~l~~-~~------------~~s~ii  283 (426)
                      ..+|     .-.    .++.+.|+.  -.+-|+.||+|+...      .-..+...+-+ .+            -=|+|+
T Consensus       486 TYVG-----AMP----GkiIq~LK~v~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVL  556 (906)
T KOG2004|consen  486 TYVG-----AMP----GKIIQCLKKVKTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVL  556 (906)
T ss_pred             eeec-----cCC----hHHHHHHHhhCCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhheE
Confidence            0111     000    123333321  245688899986431      11111111110 00            125665


Q ss_pred             Eeecchhhh---hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          284 LTARSQDVL---SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       284 vTtr~~~va---~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      +...-..+.   .........|++.+...+|-..+-.+++
T Consensus       557 FicTAN~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~yL  596 (906)
T KOG2004|consen  557 FICTANVIDTIPPPLLDRMEVIELSGYVAEEKVKIAERYL  596 (906)
T ss_pred             EEEeccccccCChhhhhhhheeeccCccHHHHHHHHHHhh
Confidence            533332221   2233455789999999999888887765

>PHA00729 NTP-binding motif containing protein

Probab=97.74  E-value=0.0003  Score=62.11  Aligned_cols=36  Identities=33%  Similarity=0.462  Sum_probs=28.5

Q ss_pred             HHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          162 GILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       162 ~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++..+...+...|.|+|.+|+||||||..+.+...
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            344555555666899999999999999999998753

>PRK08116 hypothetical protein; Validated

Probab=97.73  E-value=0.00013  Score=66.99  Aligned_cols=102  Identities=18%  Similarity=0.165  Sum_probs=60.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .-+.++|..|+|||.||..+++....+  ...+++++      ..+++..+.........     .....+.+.+.+ - 
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~--~~~v~~~~------~~~ll~~i~~~~~~~~~-----~~~~~~~~~l~~-~-  179 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEK--GVPVIFVN------FPQLLNRIKSTYKSSGK-----EDENEIIRSLVN-A-  179 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEE------HHHHHHHHHHHHhcccc-----ccHHHHHHHhcC-C-
Confidence            358899999999999999999987654  23455554      45566666555432111     112234455543 2 


Q ss_pred             EEEEEeCCCC--ccChhh--hcCCCCC-CCCCeEEEEeecch
Q 044858          253 ILIILDDIWG--SLDLEA--IGIPLAD-DNGGCKVLLTARSQ  289 (426)
Q Consensus       253 ~LlVlDdv~~--~~~~~~--l~~~l~~-~~~~s~iivTtr~~  289 (426)
                      =||||||+..  ..+|..  +...+.. ..++..+|+||...
T Consensus       180 dlLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        180 DLLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             CEEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            3899999943  344432  2221111 12455688888654

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

Probab=97.73  E-value=0.00051  Score=60.80  Aligned_cols=172  Identities=19%  Similarity=0.278  Sum_probs=99.3

Q ss_pred             cccccchHHHHH---HHHHHhccC------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHH
Q 044858          150 FMHFESRKSTLK---GILDALSNR------NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQ  220 (426)
Q Consensus       150 ~~~~~gR~~~~~---~l~~~l~~~------~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il  220 (426)
                      ..+++|.++...   -|++.|.++      .++.|..+|++|.|||.+|+.+.+..++.  |     +.+..    .++ 
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp--~-----l~vka----t~l-  187 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVP--L-----LLVKA----TEL-  187 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCc--e-----EEech----HHH-
Confidence            455677766544   366777654      47889999999999999999999988764  2     22211    111 


Q ss_pred             HHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc----------cC----hhhhcCCCC--CCCCCeEEEE
Q 044858          221 REIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS----------LD----LEAIGIPLA--DDNGGCKVLL  284 (426)
Q Consensus       221 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~----------~~----~~~l~~~l~--~~~~~s~iiv  284 (426)
                        |-+..|      +....+.++++...+.-+|++.||.++-.          .+    .+.+...+.  ..+.|...|-
T Consensus       188 --iGehVG------dgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIa  259 (368)
T COG1223         188 --IGEHVG------DGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIA  259 (368)
T ss_pred             --HHHHhh------hHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEe
Confidence              111221      22345667777777778999999998532          11    222222221  2234655555


Q ss_pred             eecchhhhhcc--CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          285 TARSQDVLSCE--MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       285 Ttr~~~va~~~--~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                      .|.+.......  ..-...|+...=+++|-.+++...+..-..+-+  .-.+.++++.+|+
T Consensus       260 aTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~--~~~~~~~~~t~g~  318 (368)
T COG1223         260 ATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVD--ADLRYLAAKTKGM  318 (368)
T ss_pred             ecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCccc--cCHHHHHHHhCCC
Confidence            55555443111  122345666666788888888877742211111  1145566677664

>PRK08118 topology modulation protein; Reviewed

Probab=97.71  E-value=2.2e-05  Score=66.86  Aligned_cols=34  Identities=26%  Similarity=0.467  Sum_probs=28.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEE
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVIS  207 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~w  207 (426)
                      -|.|+|++|+||||||+.+++..... -+||..+|
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            58999999999999999999987653 45676665

>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=97.68  E-value=0.002  Score=61.79  Aligned_cols=192  Identities=17%  Similarity=0.200  Sum_probs=118.4

Q ss_pred             hHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHH-HHHHHHhhhcCccceEEEEEecC---CcCHHHHHHHHHHHhCCC-
Q 044858          156 RKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLV-KEVGRQAKENNLFEKVISSRVSQ---TPQIKEIQREIAEKLGLK-  230 (426)
Q Consensus       156 R~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~~~wv~v~~---~~~~~~il~~i~~~l~~~-  230 (426)
                      |.+..++|..||.+..-.+|.|.||.|+||+.|+ .++..+.+.      +..+.+.+   ..+-..+++.++.++|.. 
T Consensus         1 R~e~~~~L~~wL~e~~~TFIvV~GPrGSGK~elV~d~~L~~r~~------vL~IDC~~i~~ar~D~~~I~~lA~qvGY~P   74 (431)
T PF10443_consen    1 RKEAIEQLKSWLNENPNTFIVVQGPRGSGKRELVMDHVLKDRKN------VLVIDCDQIVKARGDAAFIKNLASQVGYFP   74 (431)
T ss_pred             CchHHHHHHHHHhcCCCeEEEEECCCCCCccHHHHHHHHhCCCC------EEEEEChHhhhccChHHHHHHHHHhcCCCc
Confidence            5667889999999888889999999999999999 777765432      44444432   123344555555555421 


Q ss_pred             ----------------------ccc--cCcHHHHHHHH-------HH--------------------H--hcCCeEEEEE
Q 044858          231 ----------------------IDQ--ESESVRAWRLL-------EQ--------------------L--KKETKILIIL  257 (426)
Q Consensus       231 ----------------------~~~--~~~~~~~~~l~-------~~--------------------l--~~~k~~LlVl  257 (426)
                                            ..+  ++....+.+++       +.                    +  ...++=+|||
T Consensus        75 vFsw~nSiss~IDLa~qGltGqKaGfSes~e~Ql~~IL~~t~~ALr~ial~~~~~~~~~~~l~e~~yl~~hPe~~PVVVI  154 (431)
T PF10443_consen   75 VFSWMNSISSFIDLAVQGLTGQKAGFSESLETQLKKILQTTATALRDIALSNRKKDDKDANLKEEDYLEAHPERRPVVVI  154 (431)
T ss_pred             chHHHHHHHHHHHHHHhhccccccCCCCChHHHHHHHHHHHHHHHHHHHHHhhhccccccccCchhhhhhCCccCCEEEE
Confidence                                  000  11111111111       11                    0  0123678999


Q ss_pred             eCCCCcc-----------ChhhhcCCCCCCCCCeEEEEeecchhhh-----hccCCceeeEEccCCCHHHHHHHHHHhhC
Q 044858          258 DDIWGSL-----------DLEAIGIPLADDNGGCKVLLTARSQDVL-----SCEMDCQQNFVVDVLNDKEAWSLFKKMTG  321 (426)
Q Consensus       258 Ddv~~~~-----------~~~~l~~~l~~~~~~s~iivTtr~~~va-----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  321 (426)
                      |+.-...           +|..   .+.. ++=-+||++|-+....     ..+....+.+.|.-.+++.|.++..+.+.
T Consensus       155 dnF~~k~~~~~~iy~~laeWAa---~Lv~-~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~~L~  230 (431)
T PF10443_consen  155 DNFLHKAEENDFIYDKLAEWAA---SLVQ-NNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLSQLD  230 (431)
T ss_pred             cchhccCcccchHHHHHHHHHH---HHHh-cCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHHHhc
Confidence            9985431           2332   1211 2334688888775443     12345668899999999999999999986


Q ss_pred             CCCCC-------------------CchHHHHHHHHHHcCCchHHHHHHHHHhhcC
Q 044858          322 DCIEN-------------------GELKSVVTEVVKECAGLPIAIVPIAKALKNK  357 (426)
Q Consensus       322 ~~~~~-------------------~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~  357 (426)
                      .....                   .....-....+..+||=-.-+..+++.++.-
T Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksG  285 (431)
T PF10443_consen  231 EDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSG  285 (431)
T ss_pred             ccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcC
Confidence            32110                   1233445677888999999999999988843

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 [].

>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=97.67  E-value=0.00042  Score=58.66  Aligned_cols=137  Identities=18%  Similarity=0.177  Sum_probs=73.4

Q ss_pred             chHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCc------------------cceEEEEEecCC--
Q 044858          155 SRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNL------------------FEKVISSRVSQT--  213 (426)
Q Consensus       155 gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~------------------f~~~~wv~v~~~--  213 (426)
                      |.++..+.|.+.+..++. ..+.++|+.|+||+++|..+.+..-....                  .....|+.-...  
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~   80 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKK   80 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSS
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccc
Confidence            345666777777766664 46899999999999999998876532211                  122233322221  


Q ss_pred             -cCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchh
Q 044858          214 -PQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQD  290 (426)
Q Consensus       214 -~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~  290 (426)
                       ...+++. ++...+.....                .+++=++||||++..  ...+.+...+-.-..++.+|++|.+..
T Consensus        81 ~i~i~~ir-~i~~~~~~~~~----------------~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   81 SIKIDQIR-EIIEFLSLSPS----------------EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SBSHHHHH-HHHHHCTSS-T----------------TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             hhhHHHHH-HHHHHHHHHHh----------------cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChH
Confidence             2232222 33332221111                235678999999754  345555444433445788888888764


Q ss_pred             -hhhccCCceeeEEccCCC
Q 044858          291 -VLSCEMDCQQNFVVDVLN  308 (426)
Q Consensus       291 -va~~~~~~~~~~~l~~L~  308 (426)
                       +.....+....+.+.+||
T Consensus       144 ~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  144 KILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             GS-HHHHTTSEEEEE----
T ss_pred             HChHHHHhhceEEecCCCC
Confidence             332233445677777764

...

>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=97.67  E-value=0.00058  Score=61.00  Aligned_cols=36  Identities=25%  Similarity=0.330  Sum_probs=29.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV  210 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v  210 (426)
                      -.++|.|..|+|||||+..+.....  ..|..+++++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~~~--~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYYLR--HKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhc--ccCCEEEEEec
Confidence            3578999999999999999988765  45877766654

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

>PRK04132 replication factor C small subunit; Provisional

Probab=97.66  E-value=0.0013  Score=69.20  Aligned_cols=159  Identities=12%  Similarity=0.077  Sum_probs=96.3

Q ss_pred             Ec--CCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEE
Q 044858          178 YG--MGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKIL  254 (426)
Q Consensus       178 ~G--~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~L  254 (426)
                      .|  |.++||||+|..++++.-.. .+. .++-++++...+...+- +++..+....+              +...+.-+
T Consensus       570 ~G~lPh~lGKTT~A~ala~~l~g~-~~~~~~lElNASd~rgid~IR-~iIk~~a~~~~--------------~~~~~~KV  633 (846)
T PRK04132        570 GGNLPTVLHNTTAALALARELFGE-NWRHNFLELNASDERGINVIR-EKVKEFARTKP--------------IGGASFKI  633 (846)
T ss_pred             cCCCCCcccHHHHHHHHHHhhhcc-cccCeEEEEeCCCcccHHHHH-HHHHHHHhcCC--------------cCCCCCEE
Confidence            47  88999999999999886332 232 45667777655555433 33332211000              00124579


Q ss_pred             EEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecch-hhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHH
Q 044858          255 IILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKS  331 (426)
Q Consensus       255 lVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~  331 (426)
                      +|||+++...  ..+.+...+-.-...+++|++|.+. .+.....+....+++.+++.++....+...+....-. -..+
T Consensus       634 vIIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~-i~~e  712 (846)
T PRK04132        634 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE-LTEE  712 (846)
T ss_pred             EEEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCC-CCHH
Confidence            9999998663  4444444333223456666666554 3322233456799999999999998888766422111 1145


Q ss_pred             HHHHHHHHcCCchHHHHHHHHH
Q 044858          332 VVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       332 ~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      ....|++.|+|.+.....+...
T Consensus       713 ~L~~Ia~~s~GDlR~AIn~Lq~  734 (846)
T PRK04132        713 GLQAILYIAEGDMRRAINILQA  734 (846)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHH
Confidence            7889999999988655444443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.66  E-value=0.00055  Score=72.98  Aligned_cols=46  Identities=15%  Similarity=0.268  Sum_probs=35.4

Q ss_pred             cccchHHHHHHHHHHhc-------cC--CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALS-------NR--NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~-------~~--~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|.+..++.+.+.+.       ++  ...++.++|+.|+|||.||+.+....-
T Consensus       567 ~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~  621 (852)
T TIGR03345       567 RVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLY  621 (852)
T ss_pred             eEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHh
Confidence            46788888888777764       11  234789999999999999999987753

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.

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=97.64  E-value=0.00078  Score=69.03  Aligned_cols=178  Identities=19%  Similarity=0.156  Sum_probs=108.4

Q ss_pred             cccccchH---HHHHHHHHHhccC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHH
Q 044858          150 FMHFESRK---STLKGILDALSNR---------NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIK  217 (426)
Q Consensus       150 ~~~~~gR~---~~~~~l~~~l~~~---------~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  217 (426)
                      +.++.|-+   +|+.++++.|.++         -++=+.++|++|+|||-||+.++-...+.       |++++..    
T Consensus       310 FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVP-------F~svSGS----  378 (774)
T KOG0731|consen  310 FKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVP-------FFSVSGS----  378 (774)
T ss_pred             cccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCc-------eeeechH----
Confidence            44555654   5667777777643         25568899999999999999999888765       4555432    


Q ss_pred             HHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-----------------hhhhcCCCCCC--CC
Q 044858          218 EIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-----------------LEAIGIPLADD--NG  278 (426)
Q Consensus       218 ~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-----------------~~~l~~~l~~~--~~  278 (426)
                      ++...    +..     .....+..++...+...++++.+|+++...-                 ++.+...+-..  ..
T Consensus       379 EFvE~----~~g-----~~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~  449 (774)
T KOG0731|consen  379 EFVEM----FVG-----VGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSK  449 (774)
T ss_pred             HHHHH----hcc-----cchHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCC
Confidence            11111    110     0124566677777778899999999864311                 22221111111  12


Q ss_pred             CeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHH
Q 044858          279 GCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       279 ~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                      +.-++-+|...++.+    +...-...+.++.=+.....++|.-++.......+..++.+ |+...-|.+=|..
T Consensus       450 ~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~-~a~~t~gf~gadl  522 (774)
T KOG0731|consen  450 GVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSK-LASLTPGFSGADL  522 (774)
T ss_pred             cEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHH-HHhcCCCCcHHHH
Confidence            233334555554431    12233457778877888889999988875554455566666 8888888876543

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

Probab=97.62  E-value=0.00074  Score=68.06  Aligned_cols=155  Identities=17%  Similarity=0.211  Sum_probs=89.8

Q ss_pred             cccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          152 HFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      +.+|-++..+.|+++|.      .-+-++++++||+|+|||+|++.+++....+  |   +-++++.-.|..+|-..=-.
T Consensus       324 dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~Rk--f---vR~sLGGvrDEAEIRGHRRT  398 (782)
T COG0466         324 DHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRK--F---VRISLGGVRDEAEIRGHRRT  398 (782)
T ss_pred             cccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCC--E---EEEecCccccHHHhcccccc
Confidence            45688888899998885      2244799999999999999999999987644  4   23444444444433111000


Q ss_pred             HhCCCccccCcHHHHHHHHHHHh--cCCeEEEEEeCCCCcc------ChhhhcCCCCC-CC------------CCeEE-E
Q 044858          226 KLGLKIDQESESVRAWRLLEQLK--KETKILIILDDIWGSL------DLEAIGIPLAD-DN------------GGCKV-L  283 (426)
Q Consensus       226 ~l~~~~~~~~~~~~~~~l~~~l~--~~k~~LlVlDdv~~~~------~~~~l~~~l~~-~~------------~~s~i-i  283 (426)
                      .+|     .-.    .++.+.+.  +.++-+++||.++...      .-..+...|-+ .+            -=|.| .
T Consensus       399 YIG-----amP----GrIiQ~mkka~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmF  469 (782)
T COG0466         399 YIG-----AMP----GKIIQGMKKAGVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMF  469 (782)
T ss_pred             ccc-----cCC----hHHHHHHHHhCCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEE
Confidence            111     000    12333332  2356789999986431      11111111110 00            11334 3


Q ss_pred             Eeecch-h-hhhccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          284 LTARSQ-D-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       284 vTtr~~-~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      |+|-+. . +.........+|++.+-+++|=.++-++++
T Consensus       470 iaTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         470 IATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             EeecCccccCChHHhcceeeeeecCCChHHHHHHHHHhc
Confidence            444442 2 222245567899999999999999988876

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

Probab=97.62  E-value=0.00064  Score=71.73  Aligned_cols=102  Identities=16%  Similarity=0.222  Sum_probs=56.5

Q ss_pred             cccchHHHHHHHHHHhc-------cC--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          152 HFESRKSTLKGILDALS-------NR--NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~-------~~--~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .++|.+..++.+...+.       ++  ...++.++|+.|+|||+||+.+.....     ...+.++.+...+...    
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~-----~~~~~~d~se~~~~~~----  525 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALG-----VHLERFDMSEYMEKHT----  525 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhc-----CCeEEEeCchhhhccc----
Confidence            35666777777666654       11  234688999999999999999988663     2234444443222111    


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      +...++.+..... .+....+.+.+......+|+||+++..
T Consensus       526 ~~~lig~~~gyvg-~~~~~~l~~~~~~~p~~VvllDEieka  565 (731)
T TIGR02639       526 VSRLIGAPPGYVG-FEQGGLLTEAVRKHPHCVLLLDEIEKA  565 (731)
T ss_pred             HHHHhcCCCCCcc-cchhhHHHHHHHhCCCeEEEEechhhc
Confidence            1112222211111 111223444454444569999999754

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.61  E-value=0.00032  Score=70.98  Aligned_cols=50  Identities=28%  Similarity=0.397  Sum_probs=40.5

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+..++|.+..+..+...+......-+.|+|++|+|||++|+.+++..+
T Consensus        62 ~~f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~  111 (531)
T TIGR02902        62 KSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEAK  111 (531)
T ss_pred             CCHHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhh
Confidence            34567889998888888777665566678999999999999999987543

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.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=97.58  E-value=0.00022  Score=69.14  Aligned_cols=94  Identities=21%  Similarity=0.237  Sum_probs=63.6

Q ss_pred             cccccch---HHHHHHHHHHhccC--------C-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHH
Q 044858          150 FMHFESR---KSTLKGILDALSNR--------N-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIK  217 (426)
Q Consensus       150 ~~~~~gR---~~~~~~l~~~l~~~--------~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  217 (426)
                      +.+..|-   .+|+++++++|.++        + ++=|.++|++|.|||-||+.+.-...+.  |    |...+..|+. 
T Consensus       303 F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VP--F----F~~sGSEFdE-  375 (752)
T KOG0734|consen  303 FEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVP--F----FYASGSEFDE-  375 (752)
T ss_pred             cccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCC--e----Eeccccchhh-
Confidence            3344444   56888999999853        2 4568899999999999999999887765  2    3333333331 


Q ss_pred             HHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          218 EIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       218 ~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                           ++-..        -..++..++...+..-+|+|++|+++..
T Consensus       376 -----m~VGv--------GArRVRdLF~aAk~~APcIIFIDEiDav  408 (752)
T KOG0734|consen  376 -----MFVGV--------GARRVRDLFAAAKARAPCIIFIDEIDAV  408 (752)
T ss_pred             -----hhhcc--------cHHHHHHHHHHHHhcCCeEEEEechhhh
Confidence                 11111        1245667777777778999999999754

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.55  E-value=0.0018  Score=58.62  Aligned_cols=171  Identities=20%  Similarity=0.259  Sum_probs=92.2

Q ss_pred             ccccchHHHHHHHHHHhc----------cC--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHH
Q 044858          151 MHFESRKSTLKGILDALS----------NR--NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKE  218 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~----------~~--~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  218 (426)
                      .++.|-+...+.|.+...          ..  .-+-|.++|++|.||+.||+.|.......       |.+||..    +
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAnST-------FFSvSSS----D  201 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANST-------FFSVSSS----D  201 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcCCc-------eEEeehH----H
Confidence            344555555566555432          12  24678999999999999999999776532       3445433    2


Q ss_pred             HHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc---------ChhhhcCCC-------CCCCCCeEE
Q 044858          219 IQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL---------DLEAIGIPL-------ADDNGGCKV  282 (426)
Q Consensus       219 il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~---------~~~~l~~~l-------~~~~~~s~i  282 (426)
                      +....+         .....++..+++..++.|+.+|++|++++..         .-+.+...|       .++..|.-|
T Consensus       202 LvSKWm---------GESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLV  272 (439)
T KOG0739|consen  202 LVSKWM---------GESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLV  272 (439)
T ss_pred             HHHHHh---------ccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEE
Confidence            222111         1223466777887788899999999997441         112222111       223345555


Q ss_pred             EEeecchhhhhccC--CceeeEEccCCCHHHHHH-HHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          283 LLTARSQDVLSCEM--DCQQNFVVDVLNDKEAWS-LFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       283 ivTtr~~~va~~~~--~~~~~~~l~~L~~~e~~~-Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                      +-.|...-+.....  .-...|.+ ||++..+.. +|+-.++... ..-.+.-.+.+.++..|.
T Consensus       273 LgATNiPw~LDsAIRRRFekRIYI-PLPe~~AR~~MF~lhlG~tp-~~LT~~d~~eL~~kTeGy  334 (439)
T KOG0739|consen  273 LGATNIPWVLDSAIRRRFEKRIYI-PLPEAHARARMFKLHLGDTP-HVLTEQDFKELARKTEGY  334 (439)
T ss_pred             EecCCCchhHHHHHHHHhhcceec-cCCcHHHhhhhheeccCCCc-cccchhhHHHHHhhcCCC
Confidence            55666554431111  11122222 455555543 4555555322 222233455667777765

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.51  E-value=0.00064  Score=60.20  Aligned_cols=86  Identities=16%  Similarity=0.204  Sum_probs=53.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh-C---CCc---cccC---cHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL-G---LKI---DQES---ESVRAW  241 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l-~---~~~---~~~~---~~~~~~  241 (426)
                      -.++.|+|++|+|||+++.++.......  ...++|++... ++...+.+. +... .   .+.   ...+   ....+.
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~--g~~v~yi~~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~~~~~~~~~~   87 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQ--GKKVVYIDTEG-LSPERFKQI-AEDRPERALSNFIVFEVFDFDEQGVAIQ   87 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC-CCHHHHHHH-HHhChHHHhcCEEEEECCCHHHHHHHHH
Confidence            4689999999999999999988776533  45788998875 665554443 2221 0   000   0011   112244


Q ss_pred             HHHHHHhcCCeEEEEEeCCC
Q 044858          242 RLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       242 ~l~~~l~~~k~~LlVlDdv~  261 (426)
                      .+.+.+.+.+.-+||+|.+.
T Consensus        88 ~l~~~~~~~~~~lvVIDSis  107 (209)
T TIGR02237        88 KTSKFIDRDSASLVVVDSFT  107 (209)
T ss_pred             HHHHHHhhcCccEEEEeCcH
Confidence            44444544456799999985

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.51  E-value=0.0065  Score=57.63  Aligned_cols=102  Identities=17%  Similarity=0.224  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhccCCceeeEEccCCCHH
Q 044858          238 VRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSCEMDCQQNFVVDVLNDK  310 (426)
Q Consensus       238 ~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~~~~~~~~~l~~L~~~  310 (426)
                      +.+..+.+.+.    .+++-++|+|+++..  ...+.+...+-.-.+++.+|++|.+ ..+.....+....+.+.+++.+
T Consensus       115 dqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~  194 (342)
T PRK06964        115 EQVRALLDFCGVGTHRGGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPE  194 (342)
T ss_pred             HHHHHHHHHhccCCccCCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHH
Confidence            34444444442    245568899999754  3455554444333345655555554 5444333444578999999999


Q ss_pred             HHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHH
Q 044858          311 EAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       311 e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                      +..+.+... +  .  ++    ...++..++|.|+...
T Consensus       195 ~~~~~L~~~-~--~--~~----~~~~l~~~~Gsp~~Al  223 (342)
T PRK06964        195 AAAAWLAAQ-G--V--AD----ADALLAEAGGAPLAAL  223 (342)
T ss_pred             HHHHHHHHc-C--C--Ch----HHHHHHHcCCCHHHHH
Confidence            999988764 1  1  11    2235778899997544

>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=97.49  E-value=0.00074  Score=58.96  Aligned_cols=88  Identities=24%  Similarity=0.246  Sum_probs=55.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCccc----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQ----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~----~~~~~~~~~l~~~  246 (426)
                      +++|.++|+.|+||||.+..++.....+  -..+..++... .....+-++..++.++.+...    .+......+..+.
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~   78 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEK   78 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHH
Confidence            4789999999999999999888877654  33455666542 234566778888888876422    1233344444444


Q ss_pred             HhcCCeEEEEEeCCC
Q 044858          247 LKKETKILIILDDIW  261 (426)
Q Consensus       247 l~~~k~~LlVlDdv~  261 (426)
                      +..++.=++++|=.-
T Consensus        79 ~~~~~~D~vlIDT~G   93 (196)
T PF00448_consen   79 FRKKGYDLVLIDTAG   93 (196)
T ss_dssp             HHHTTSSEEEEEE-S
T ss_pred             HhhcCCCEEEEecCC
Confidence            443333477788663

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 ....

>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=97.49  E-value=0.0095  Score=56.59  Aligned_cols=43  Identities=28%  Similarity=0.486  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHhcc---CCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          157 KSTLKGILDALSN---RNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       157 ~~~~~~l~~~l~~---~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      +...+.|.+.+.+   +.+.+|+|.|.=|+||||+.+.+.+.....
T Consensus         2 ~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen    2 KPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEELKED   47 (325)
T ss_pred             hHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            3344556666653   457799999999999999999999887764

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 [].

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

Probab=97.49  E-value=0.0032  Score=62.35  Aligned_cols=150  Identities=19%  Similarity=0.283  Sum_probs=90.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      +.=|.++|++|+|||-||+.|.|..+..       |+++-.+    +++....   |      .....+.++++..+..-
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEag~N-------FisVKGP----ELlNkYV---G------ESErAVR~vFqRAR~sa  604 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEAGAN-------FISVKGP----ELLNKYV---G------ESERAVRQVFQRARASA  604 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhccCc-------eEeecCH----HHHHHHh---h------hHHHHHHHHHHHhhcCC
Confidence            5568899999999999999999998865       4555432    2332221   1      12234567777777788


Q ss_pred             eEEEEEeCCCCc-------cCh------hhhcCCCC--CCCCCeEEEEeecchhhh-h---ccCCceeeEEccCCCHHHH
Q 044858          252 KILIILDDIWGS-------LDL------EAIGIPLA--DDNGGCKVLLTARSQDVL-S---CEMDCQQNFVVDVLNDKEA  312 (426)
Q Consensus       252 ~~LlVlDdv~~~-------~~~------~~l~~~l~--~~~~~s~iivTtr~~~va-~---~~~~~~~~~~l~~L~~~e~  312 (426)
                      +|+|+||+++..       ..|      +.+...+-  ....|..||-.|...++- +   +...-...+.++.=+.+|-
T Consensus       605 PCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR  684 (802)
T KOG0733|consen  605 PCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEER  684 (802)
T ss_pred             CeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHH
Confidence            999999999754       111      22222221  234566677766555442 1   1222345667777788888


Q ss_pred             HHHHHHhhCCCC----CCCchHHHHHHHHHHcCCc
Q 044858          313 WSLFKKMTGDCI----ENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       313 ~~Lf~~~~~~~~----~~~~~~~~~~~i~~~c~Gl  343 (426)
                      ..+++....+..    .+-++.+++..  .+|.|.
T Consensus       685 ~~ILK~~tkn~k~pl~~dVdl~eia~~--~~c~gf  717 (802)
T KOG0733|consen  685 VAILKTITKNTKPPLSSDVDLDEIARN--TKCEGF  717 (802)
T ss_pred             HHHHHHHhccCCCCCCcccCHHHHhhc--ccccCC
Confidence            889888876322    22344444432  355564

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.48  E-value=0.0055  Score=58.18  Aligned_cols=173  Identities=11%  Similarity=0.086  Sum_probs=94.3

Q ss_pred             HHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCcc---ce-----EEEEEecCCcCHHHHHHHHHHHhCCC
Q 044858          160 LKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLF---EK-----VISSRVSQTPQIKEIQREIAEKLGLK  230 (426)
Q Consensus       160 ~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f---~~-----~~wv~v~~~~~~~~il~~i~~~l~~~  230 (426)
                      -+.+...+..++ ...+.++|+.|+||+++|..+....--....   .|     +-++.....+|+..+.         +
T Consensus        11 ~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~---------p   81 (334)
T PRK07993         11 YEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLT---------P   81 (334)
T ss_pred             HHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEe---------c
Confidence            455666666554 4578899999999999999987665321100   00     0000000111100000         0


Q ss_pred             cc--ccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhccCCceee
Q 044858          231 ID--QESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSCEMDCQQN  301 (426)
Q Consensus       231 ~~--~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~~~~~~~  301 (426)
                      ..  ..-..+.+..+.+.+.    .+++-++|+|+++..  ..-+.+...+-.-..++.+|++|.+ ..+.....+....
T Consensus        82 ~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~  161 (334)
T PRK07993         82 EKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRL  161 (334)
T ss_pred             ccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcccc
Confidence            00  0011223334444432    356679999999754  3344444334332345666666655 4444323344568


Q ss_pred             EEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          302 FVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       302 ~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      +.+.+++.++..+.+....+  . +   .+.+..+++.++|.|...
T Consensus       162 ~~~~~~~~~~~~~~L~~~~~--~-~---~~~a~~~~~la~G~~~~A  201 (334)
T PRK07993        162 HYLAPPPEQYALTWLSREVT--M-S---QDALLAALRLSAGAPGAA  201 (334)
T ss_pred             ccCCCCCHHHHHHHHHHccC--C-C---HHHHHHHHHHcCCCHHHH
Confidence            89999999999988865422  1 1   233667899999999744

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.48  E-value=0.0013  Score=69.66  Aligned_cols=174  Identities=16%  Similarity=0.211  Sum_probs=93.5

Q ss_pred             CcccccchHHHHHHHHHHhcc-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          149 DFMHFESRKSTLKGILDALSN-------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~-------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      .+.++.|.+..++.+.+.+.-             ...+-+.++|++|+|||+||+.+++.....  |   +.++.+    
T Consensus       176 ~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~--~---i~i~~~----  246 (733)
T TIGR01243       176 TYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY--F---ISINGP----  246 (733)
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCe--E---EEEecH----
Confidence            445678888888877666531             234568899999999999999998876422  2   222211    


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------C-----hhhhcCCCCC-CCCCeE
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--------D-----LEAIGIPLAD-DNGGCK  281 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--------~-----~~~l~~~l~~-~~~~s~  281 (426)
                        ++...    .    . ......+..+++......+.+|+|||++...        .     ...+...+.. ...+..
T Consensus       247 --~i~~~----~----~-g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~v  315 (733)
T TIGR01243       247 --EIMSK----Y----Y-GESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRV  315 (733)
T ss_pred             --HHhcc----c----c-cHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCE
Confidence              11100    0    0 0111234445555555567899999986431        0     1112211111 112333


Q ss_pred             EEE-eecchh-hhh---ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          282 VLL-TARSQD-VLS---CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       282 iiv-Ttr~~~-va~---~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      +|| ||.... +..   ....-...+.+...+.++-.+++..........++  .....+++.+.|..
T Consensus       316 ivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d--~~l~~la~~t~G~~  381 (733)
T TIGR01243       316 IVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAED--VDLDKLAEVTHGFV  381 (733)
T ss_pred             EEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccc--cCHHHHHHhCCCCC
Confidence            444 444322 111   11112356788888888888888866543222111  12456777787764

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.

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.47  E-value=0.0016  Score=65.05  Aligned_cols=156  Identities=15%  Similarity=0.125  Sum_probs=86.1

Q ss_pred             CCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ....++-|-++.+.+|-+...             -+.++-|..+|++|+|||++|+.+.+.....       |+.++.+ 
T Consensus       431 v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~n-------Flsvkgp-  502 (693)
T KOG0730|consen  431 VSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMN-------FLSVKGP-  502 (693)
T ss_pred             CChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCC-------eeeccCH-
Confidence            344555566665555544332             1456788999999999999999999987754       3333321 


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-------------hhhhcCCCCCCCCCeE
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-------------LEAIGIPLADDNGGCK  281 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-------------~~~l~~~l~~~~~~s~  281 (426)
                         +++...        -. .....+..+++.-.+--++++.||+++....             +..+...+........
T Consensus       503 ---EL~sk~--------vG-eSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~  570 (693)
T KOG0730|consen  503 ---ELFSKY--------VG-ESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKN  570 (693)
T ss_pred             ---HHHHHh--------cC-chHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCc
Confidence               111111        11 1123455566666666789999999864411             1111111111111112


Q ss_pred             EEE---eecchhhhh---ccCCceeeEEccCCCHHHHHHHHHHhhCCC
Q 044858          282 VLL---TARSQDVLS---CEMDCQQNFVVDVLNDKEAWSLFKKMTGDC  323 (426)
Q Consensus       282 iiv---Ttr~~~va~---~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~  323 (426)
                      |+|   |-|...+-.   ....-...+.+++=+.+.-.++|+.++...
T Consensus       571 V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkm  618 (693)
T KOG0730|consen  571 VLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKM  618 (693)
T ss_pred             EEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcC
Confidence            333   233333221   122345677777777777888999888643

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

Probab=97.47  E-value=0.001  Score=68.65  Aligned_cols=160  Identities=16%  Similarity=0.194  Sum_probs=95.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc----eEEEEEecCCcCHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE----KVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~----~~~wv~v~~~~~~~~il~~i  223 (426)
                      ....+.+||++|++.+++.|....-..-.++|.+|+|||+++.-++.+....+-..    ..++.     .++..+    
T Consensus       167 gklDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~s-----LD~g~L----  237 (786)
T COG0542         167 GKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYS-----LDLGSL----  237 (786)
T ss_pred             CCCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEE-----ecHHHH----
Confidence            34677899999999999999843323345889999999999999888765432111    11110     011111    


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------Chh--h-hcCCCCCCCCCeEEEEeecchhh-
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--------DLE--A-IGIPLADDNGGCKVLLTARSQDV-  291 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--------~~~--~-l~~~l~~~~~~s~iivTtr~~~v-  291 (426)
                         .....-...-.+++..+.+.+.+..+.+|++|.++..-        ..+  . ++..|. .+.--.|--||-++.- 
T Consensus       238 ---vAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLA-RGeL~~IGATT~~EYRk  313 (786)
T COG0542         238 ---VAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALA-RGELRCIGATTLDEYRK  313 (786)
T ss_pred             ---hccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHh-cCCeEEEEeccHHHHHH
Confidence               11111112334566777777776669999999997541        111  1 222222 2222235566665532 


Q ss_pred             --h--hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          292 --L--SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       292 --a--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                        .  .......+.+.+..-+.+++..+++-..
T Consensus       314 ~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGlk  346 (786)
T COG0542         314 YIEKDAALERRFQKVLVDEPSVEDTIAILRGLK  346 (786)
T ss_pred             HhhhchHHHhcCceeeCCCCCHHHHHHHHHHHH
Confidence              0  1123456789999999999999987543

>PRK08181 transposase; Validated

Probab=97.45  E-value=0.00027  Score=64.75  Aligned_cols=99  Identities=19%  Similarity=0.186  Sum_probs=56.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.++|++|+|||.||..+.+....+  ...+.|++      ..+++..+.....    ..    .....++.+.  +.
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~~~--g~~v~f~~------~~~L~~~l~~a~~----~~----~~~~~l~~l~--~~  168 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALIEN--GWRVLFTR------TTDLVQKLQVARR----EL----QLESAIAKLD--KF  168 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHc--CCceeeee------HHHHHHHHHHHHh----CC----cHHHHHHHHh--cC
Confidence            458999999999999999999876543  22345554      3556666643321    11    1223444443  34


Q ss_pred             EEEEEeCCCCc--cCh-h-hhcCCCCCCCCCeEEEEeecch
Q 044858          253 ILIILDDIWGS--LDL-E-AIGIPLADDNGGCKVLLTARSQ  289 (426)
Q Consensus       253 ~LlVlDdv~~~--~~~-~-~l~~~l~~~~~~s~iivTtr~~  289 (426)
                      =||||||+...  ..+ . .+...+.....+..+||||...
T Consensus       169 dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        169 DLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             CEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            59999999643  222 1 1222221111123588888765

>PRK07261 topology modulation protein; Provisional

Probab=97.42  E-value=0.00055  Score=58.51  Aligned_cols=34  Identities=21%  Similarity=0.346  Sum_probs=25.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEE
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVIS  207 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~w  207 (426)
                      .|.|+|++|+||||||+.+....... -+.|...|
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~   36 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHF   36 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEe
Confidence            48899999999999999998765432 23444555

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

Probab=97.42  E-value=0.0018  Score=58.06  Aligned_cols=211  Identities=14%  Similarity=0.166  Sum_probs=118.2

Q ss_pred             cccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhh----cCccceEEEEEecCC----------c---
Q 044858          152 HFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE----NNLFEKVISSRVSQT----------P---  214 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~----~~~f~~~~wv~v~~~----------~---  214 (426)
                      .+.++++....+......+..+-..++|+.|.||-|.+..+.+..-.    +-.-+...|.+-|..          .   
T Consensus        14 ~l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlE   93 (351)
T KOG2035|consen   14 ELIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLE   93 (351)
T ss_pred             hcccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEE
Confidence            35566666666666655667888999999999999988777766432    111233445444432          1   


Q ss_pred             --------CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeE-EEEEeCCCCc--cChhhhcCCCCCCCCCeEEE
Q 044858          215 --------QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKI-LIILDDIWGS--LDLEAIGIPLADDNGGCKVL  283 (426)
Q Consensus       215 --------~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~-LlVlDdv~~~--~~~~~l~~~l~~~~~~s~ii  283 (426)
                              .-.-+.+++++.++...+-+          .  ...++| ++|+-.+++.  +.-..+......-.+.+|+|
T Consensus        94 itPSDaG~~DRvViQellKevAQt~qie----------~--~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlI  161 (351)
T KOG2035|consen   94 ITPSDAGNYDRVVIQELLKEVAQTQQIE----------T--QGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLI  161 (351)
T ss_pred             eChhhcCcccHHHHHHHHHHHHhhcchh----------h--ccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEE
Confidence                    11224444444433211110          0  012445 5556555443  11122222222224567777


Q ss_pred             Eeecchh-hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCC-CCCchHHHHHHHHHHcCCchHHHHHHHHHhh--cC--
Q 044858          284 LTARSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCI-ENGELKSVVTEVVKECAGLPIAIVPIAKALK--NK--  357 (426)
Q Consensus       284 vTtr~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~--~~--  357 (426)
                      +...+-+ +-....+..-.+++...+++|....+.+.+.... .-|  .+++.+|+++++|+---...+...++  +.  
T Consensus       162 l~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp--~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~  239 (351)
T KOG2035|consen  162 LVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLP--KELLKRIAEKSNRNLRRALLMLEAVRVNNEPF  239 (351)
T ss_pred             EEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCc--HHHHHHHHHHhcccHHHHHHHHHHHHhccccc
Confidence            6433211 1111223345788999999999999998875322 222  67899999999997554444443333  11  


Q ss_pred             -------CHHHHHHHHHHHhhccccC
Q 044858          358 -------SPYEWRNALRQLKRNFLRS  376 (426)
Q Consensus       358 -------~~~~w~~~l~~l~~~~~~~  376 (426)
                             +.-+|+-+..+.......+
T Consensus       240 ~a~~~~i~~~dWe~~i~e~a~~i~~e  265 (351)
T KOG2035|consen  240 TANSQVIPKPDWEIYIQEIARVILKE  265 (351)
T ss_pred             cccCCCCCCccHHHHHHHHHHHHHhc
Confidence                   4568999988877654443

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.40  E-value=0.0008  Score=60.77  Aligned_cols=90  Identities=20%  Similarity=0.212  Sum_probs=56.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEEEEecCCcCHHHHHHHHHHHhCCCccc-------------c
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-------------E  234 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-------------~  234 (426)
                      -.++.|+|++|+|||+|+.+++........    ...++|++....++..++. ++++..+.....             .
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~~   97 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLV-QIAERFGLDPEEVLDNIYVARAYNSD   97 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHH-HHHHHhccChHhHhcCEEEEecCCHH
Confidence            468999999999999999999755322211    2578899988877755443 344443322110             0


Q ss_pred             CcHHHHHHHHHHHhcC-CeEEEEEeCCCC
Q 044858          235 SESVRAWRLLEQLKKE-TKILIILDDIWG  262 (426)
Q Consensus       235 ~~~~~~~~l~~~l~~~-k~~LlVlDdv~~  262 (426)
                      .....+..+.+.+.+. +.-+||+|.+..
T Consensus        98 ~l~~~l~~l~~~l~~~~~~~liVIDSis~  126 (235)
T cd01123          98 HQLQLLEELEAILIESSRIKLVIVDSVTA  126 (235)
T ss_pred             HHHHHHHHHHHHHhhcCCeeEEEEeCcHH
Confidence            1112334455555555 788999999853

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 .

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

Probab=97.38  E-value=0.008  Score=62.29  Aligned_cols=114  Identities=17%  Similarity=0.221  Sum_probs=63.5

Q ss_pred             cccchHHHHHHHHHHhc-------cC--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          152 HFESRKSTLKGILDALS-------NR--NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~-------~~--~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .++|.++.+..+.+.+.       ++  ...++...||.|+|||.||+.+....-..+  +..+-++.|....-    ..
T Consensus       492 rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e--~aliR~DMSEy~Ek----Hs  565 (786)
T COG0542         492 RVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDE--QALIRIDMSEYMEK----HS  565 (786)
T ss_pred             ceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCC--ccceeechHHHHHH----HH
Confidence            35777888877777764       22  345778899999999999999988763211  23333333322111    11


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhcCCeE-EEEEeCCCCc--cChhhhcCCC
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKKETKI-LIILDDIWGS--LDLEAIGIPL  273 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~-LlVlDdv~~~--~~~~~l~~~l  273 (426)
                      +.+-+|.+..--.. +....+-+.+++ +|| +|+||++...  +..+-+...|
T Consensus       566 VSrLIGaPPGYVGy-eeGG~LTEaVRr-~PySViLlDEIEKAHpdV~nilLQVl  617 (786)
T COG0542         566 VSRLIGAPPGYVGY-EEGGQLTEAVRR-KPYSVILLDEIEKAHPDVFNLLLQVL  617 (786)
T ss_pred             HHHHhCCCCCCcee-ccccchhHhhhc-CCCeEEEechhhhcCHHHHHHHHHHh
Confidence            22223333322111 113345566654 566 8889999744  3344443333

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.36  E-value=0.012  Score=54.48  Aligned_cols=168  Identities=20%  Similarity=0.220  Sum_probs=99.9

Q ss_pred             ccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCH-HHHHHHHH
Q 044858          151 MHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQI-KEIQREIA  224 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~-~~il~~i~  224 (426)
                      ..++|-.++-.++-.++.    .+...-+.|+||.|+|||+|......+..   .+. ..+-|...+..-. +-.++.|.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q---~~~E~~l~v~Lng~~~~dk~al~~I~  100 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQ---ENGENFLLVRLNGELQTDKIALKGIT  100 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHH---hcCCeEEEEEECccchhhHHHHHHHH
Confidence            346666666666665554    34455688999999999999998887722   233 3344455443322 33666676


Q ss_pred             HHhCCCcc-----ccCcHHHHHHHHHHHhc-----CCeEEEEEeCCCCccC-------hhhhcCCCCCCCCCeEEEEeec
Q 044858          225 EKLGLKID-----QESESVRAWRLLEQLKK-----ETKILIILDDIWGSLD-------LEAIGIPLADDNGGCKVLLTAR  287 (426)
Q Consensus       225 ~~l~~~~~-----~~~~~~~~~~l~~~l~~-----~k~~LlVlDdv~~~~~-------~~~l~~~l~~~~~~s~iivTtr  287 (426)
                      +|+.....     ..+-.+....++..+..     +-++++|+|+++-...       .+-+...-....+=|-|-+|||
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            66643221     12334456667777653     3458888888754321       1111112123345677888998


Q ss_pred             chhhh------hccCCceeeEEccCCCHHHHHHHHHHhhC
Q 044858          288 SQDVL------SCEMDCQQNFVVDVLNDKEAWSLFKKMTG  321 (426)
Q Consensus       288 ~~~va------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  321 (426)
                      -....      ........++-+++++-++...++++.+.
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            76442      11223334667778899999999998874

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.36  E-value=0.00091  Score=62.65  Aligned_cols=116  Identities=17%  Similarity=0.197  Sum_probs=66.9

Q ss_pred             chHHHHHHHHHHhcc----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCC
Q 044858          155 SRKSTLKGILDALSN----RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLK  230 (426)
Q Consensus       155 gR~~~~~~l~~~l~~----~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~  230 (426)
                      +|........+++.+    ...+-+.++|+.|+|||.||..+++....+ .+ .+.++++      .+++.++.......
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~-g~-~v~~~~~------~~l~~~lk~~~~~~  206 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKK-GV-SSTLLHF------PEFIRELKNSISDG  206 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-CC-CEEEEEH------HHHHHHHHHHHhcC
Confidence            344444444455441    234578999999999999999999998643 23 3445544      35666665554211


Q ss_pred             ccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhh--hcCCCCCC--CCCeEEEEeecc
Q 044858          231 IDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEA--IGIPLADD--NGGCKVLLTARS  288 (426)
Q Consensus       231 ~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~--l~~~l~~~--~~~s~iivTtr~  288 (426)
                              .....++.+.  +-=||||||+...  ..|..  +...+...  ..+-.+|+||--
T Consensus       207 --------~~~~~l~~l~--~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        207 --------SVKEKIDAVK--EAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             --------cHHHHHHHhc--CCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence                    1223444453  4569999999643  45643  32222111  134457777754

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

Probab=97.35  E-value=0.0026  Score=60.44  Aligned_cols=141  Identities=18%  Similarity=0.158  Sum_probs=78.9

Q ss_pred             ccchHHHHHHHHHHhc-cCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------ccceEEEEEec
Q 044858          153 FESRKSTLKGILDALS-NRNFN-MIGVYGMGGIGKTTLVKEVGRQAKENN-------------------LFEKVISSRVS  211 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~-~~~~~-vi~I~G~~GiGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~v~  211 (426)
                      +++-+.....+..+.. .++.+ .+.++|+.|+||||+|..+.+......                   ..+.+..++.+
T Consensus         3 ~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s   82 (325)
T COG0470           3 LVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPS   82 (325)
T ss_pred             cccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEeccc
Confidence            3455556666666666 33344 499999999999999999998765321                   11233344444


Q ss_pred             CCcC---HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEee
Q 044858          212 QTPQ---IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTA  286 (426)
Q Consensus       212 ~~~~---~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTt  286 (426)
                      ....   ..+..+++.+.......                .++.-++++|+++...  .-..+...+......+++|++|
T Consensus        83 ~~~~~~i~~~~vr~~~~~~~~~~~----------------~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~  146 (325)
T COG0470          83 DLRKIDIIVEQVRELAEFLSESPL----------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILIT  146 (325)
T ss_pred             ccCCCcchHHHHHHHHHHhccCCC----------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEc
Confidence            3333   23333333333221111                2467799999997652  2333333333344567788877


Q ss_pred             cch-hhhhccCCceeeEEccCCCH
Q 044858          287 RSQ-DVLSCEMDCQQNFVVDVLND  309 (426)
Q Consensus       287 r~~-~va~~~~~~~~~~~l~~L~~  309 (426)
                      ... .+.....+....+++.+.+.
T Consensus       147 n~~~~il~tI~SRc~~i~f~~~~~  170 (325)
T COG0470         147 NDPSKILPTIRSRCQRIRFKPPSR  170 (325)
T ss_pred             CChhhccchhhhcceeeecCCchH
Confidence            743 33332334456777777333

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.35  E-value=0.0018  Score=69.23  Aligned_cols=46  Identities=17%  Similarity=0.289  Sum_probs=34.9

Q ss_pred             cccchHHHHHHHHHHhc-------cC-C-ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALS-------NR-N-FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~-------~~-~-~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|.+..++.+...+.       ++ + ..++.++|+.|+|||+||+.+.+...
T Consensus       569 ~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~  623 (857)
T PRK10865        569 RVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMF  623 (857)
T ss_pred             eEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhh
Confidence            46788887777777664       11 1 24788999999999999999997653

>PRK06526 transposase; Provisional

Probab=97.34  E-value=0.00026  Score=64.48  Aligned_cols=74  Identities=22%  Similarity=0.185  Sum_probs=44.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      ...+.++|++|+|||+||..+.+.....+ +. +.|+      +..+++.++.....    ..    .....+..+.  +
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~~~g-~~-v~f~------t~~~l~~~l~~~~~----~~----~~~~~l~~l~--~  159 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRACQAG-HR-VLFA------TAAQWVARLAAAHH----AG----RLQAELVKLG--R  159 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHHCC-Cc-hhhh------hHHHHHHHHHHHHh----cC----cHHHHHHHhc--c
Confidence            35689999999999999999988765432 22 2332      34455555543321    01    1112233332  3


Q ss_pred             eEEEEEeCCCCc
Q 044858          252 KILIILDDIWGS  263 (426)
Q Consensus       252 ~~LlVlDdv~~~  263 (426)
                      .-||||||+...
T Consensus       160 ~dlLIIDD~g~~  171 (254)
T PRK06526        160 YPLLIVDEVGYI  171 (254)
T ss_pred             CCEEEEcccccC
Confidence            469999999643

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.30  E-value=0.0031  Score=63.57  Aligned_cols=153  Identities=15%  Similarity=0.100  Sum_probs=83.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC--CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ--TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~--~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      .+.|.|.|+.|+|||+||+.+++.... .+.-.+.+++.+.  ..+.+.+++.+..                 ++..-..
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~k-~~~~hv~~v~Cs~l~~~~~e~iQk~l~~-----------------vfse~~~  492 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYSK-DLIAHVEIVSCSTLDGSSLEKIQKFLNN-----------------VFSEALW  492 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhcc-ccceEEEEEechhccchhHHHHHHHHHH-----------------HHHHHHh
Confidence            457899999999999999999998773 3344455555543  2233333333322                 1211222


Q ss_pred             CCeEEEEEeCCCCc--------cChhhh---cCCCC------CCCCCe--EEEEeecchhhhh----ccCCceeeEEccC
Q 044858          250 ETKILIILDDIWGS--------LDLEAI---GIPLA------DDNGGC--KVLLTARSQDVLS----CEMDCQQNFVVDV  306 (426)
Q Consensus       250 ~k~~LlVlDdv~~~--------~~~~~l---~~~l~------~~~~~s--~iivTtr~~~va~----~~~~~~~~~~l~~  306 (426)
                      -.+-+|||||++..        .+|...   ...+.      -...+.  .+|.|.....-..    ...--.....|.+
T Consensus       493 ~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~a  572 (952)
T KOG0735|consen  493 YAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPA  572 (952)
T ss_pred             hCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCC
Confidence            35899999998632        122211   00000      012233  3444444332211    1112235788999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          307 LNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       307 L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                      +...+-.++++........ ........-+..+|+|.
T Consensus       573 p~~~~R~~IL~~~~s~~~~-~~~~~dLd~ls~~TEGy  608 (952)
T KOG0735|consen  573 PAVTRRKEILTTIFSKNLS-DITMDDLDFLSVKTEGY  608 (952)
T ss_pred             cchhHHHHHHHHHHHhhhh-hhhhHHHHHHHHhcCCc
Confidence            9988888888876643221 11223334488889885

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.28  E-value=0.0019  Score=59.95  Aligned_cols=87  Identities=22%  Similarity=0.257  Sum_probs=50.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEEEEecCC-cCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQT-PQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK  248 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~  248 (426)
                      +..++.|+|+.|+||||++..+....... +.+ .+..++.... ....+-+....+.++.+.........+...++.+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~-~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~~  271 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNK-KVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRLR  271 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCC-eEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHcc
Confidence            35689999999999999999998876543 222 3445554321 12233444445555555433333333444444443


Q ss_pred             cCCeEEEEEeCC
Q 044858          249 KETKILIILDDI  260 (426)
Q Consensus       249 ~~k~~LlVlDdv  260 (426)
                        ..=+|++|..
T Consensus       272 --~~d~vliDt~  281 (282)
T TIGR03499       272 --DKDLILIDTA  281 (282)
T ss_pred             --CCCEEEEeCC
Confidence              2347777753

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.28  E-value=0.018  Score=57.34  Aligned_cols=88  Identities=19%  Similarity=0.268  Sum_probs=50.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ..+|+|+|++|+||||++..+......+.....+..++... .....+-++...+.++...........+...++.+.  
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~--  427 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLR--  427 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhc--
Confidence            47899999999999999999887654432223344554422 112233344444445544333333333444455443  


Q ss_pred             CeEEEEEeCCC
Q 044858          251 TKILIILDDIW  261 (426)
Q Consensus       251 k~~LlVlDdv~  261 (426)
                      ..=+|++|..-
T Consensus       428 ~~DLVLIDTaG  438 (559)
T PRK12727        428 DYKLVLIDTAG  438 (559)
T ss_pred             cCCEEEecCCC
Confidence            34588888874

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

Probab=97.27  E-value=0.0004  Score=59.71  Aligned_cols=74  Identities=27%  Similarity=0.353  Sum_probs=44.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      ..-+.++|+.|+|||.||..+.+.....+ + .+.|++      ..+++..+-..-    ....    ...+.+.+.+  
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g-~-~v~f~~------~~~L~~~l~~~~----~~~~----~~~~~~~l~~--  108 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKG-Y-SVLFIT------ASDLLDELKQSR----SDGS----YEELLKRLKR--  108 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT----EEEEE------HHHHHHHHHCCH----CCTT----HCHHHHHHHT--
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCC-c-ceeEee------cCceeccccccc----cccc----hhhhcCcccc--
Confidence            45699999999999999999998766532 2 345554      345555553221    1111    1234455542  


Q ss_pred             eEEEEEeCCCCc
Q 044858          252 KILIILDDIWGS  263 (426)
Q Consensus       252 ~~LlVlDdv~~~  263 (426)
                      -=||||||+-..
T Consensus       109 ~dlLilDDlG~~  120 (178)
T PF01695_consen  109 VDLLILDDLGYE  120 (178)
T ss_dssp             SSCEEEETCTSS
T ss_pred             ccEeccccccee
Confidence            458889999644

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=97.27  E-value=0.0026  Score=66.04  Aligned_cols=148  Identities=20%  Similarity=0.262  Sum_probs=79.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      +-|.++|++|+|||++|+.+.......  |   +.++.+      ++.. +.  .+      .....+..++.......+
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~~~~--f---~~is~~------~~~~-~~--~g------~~~~~~~~~f~~a~~~~P  245 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEAKVP--F---FTISGS------DFVE-MF--VG------VGASRVRDMFEQAKKAAP  245 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHcCCC--E---EEEehH------HhHH-hh--hc------ccHHHHHHHHHHHHhcCC
Confidence            458999999999999999998876542  2   222221      1111 00  00      011223344444445578


Q ss_pred             EEEEEeCCCCcc------------Ch----hhhcCCCC--CCCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHH
Q 044858          253 ILIILDDIWGSL------------DL----EAIGIPLA--DDNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDK  310 (426)
Q Consensus       253 ~LlVlDdv~~~~------------~~----~~l~~~l~--~~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~  310 (426)
                      ++|+||+++...            ..    ..+...+.  ....+.-+|.||.......    ....-...+.+..-+.+
T Consensus       246 ~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~  325 (644)
T PRK10733        246 CIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVR  325 (644)
T ss_pred             cEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHH
Confidence            999999986531            01    11111111  1123444555666554321    11223467888888888


Q ss_pred             HHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC
Q 044858          311 EAWSLFKKMTGDCIENGELKSVVTEVVKECAG  342 (426)
Q Consensus       311 e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G  342 (426)
                      +-.+++..++......++.  ....+++.+.|
T Consensus       326 ~R~~Il~~~~~~~~l~~~~--d~~~la~~t~G  355 (644)
T PRK10733        326 GREQILKVHMRRVPLAPDI--DAAIIARGTPG  355 (644)
T ss_pred             HHHHHHHHHhhcCCCCCcC--CHHHHHhhCCC
Confidence            8888888777533222211  12346666666

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

Probab=97.27  E-value=0.0021  Score=67.42  Aligned_cols=101  Identities=13%  Similarity=0.197  Sum_probs=55.7

Q ss_pred             ccchHHHHHHHHHHhc-------c-C-CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          153 FESRKSTLKGILDALS-------N-R-NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~-------~-~-~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ++|.++.++.+...+.       + + ....+.++|++|+|||+||+.+......     ..+.++.+.......    +
T Consensus       460 ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~-----~~i~id~se~~~~~~----~  530 (758)
T PRK11034        460 VFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGI-----ELLRFDMSEYMERHT----V  530 (758)
T ss_pred             EeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhCC-----CcEEeechhhccccc----H
Confidence            5677777777777665       1 1 2346889999999999999999887632     123334333221111    1


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      .+-+|.+..... ......+.+.+......+|+||++...
T Consensus       531 ~~LiG~~~gyvg-~~~~g~L~~~v~~~p~sVlllDEieka  569 (758)
T PRK11034        531 SRLIGAPPGYVG-FDQGGLLTDAVIKHPHAVLLLDEIEKA  569 (758)
T ss_pred             HHHcCCCCCccc-ccccchHHHHHHhCCCcEEEeccHhhh
Confidence            112232211111 011112334444444579999999754

>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=97.26  E-value=0.00026  Score=56.65  Aligned_cols=24  Identities=38%  Similarity=0.505  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.|.|++|+||||+|+.+.+...
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~~   24 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERLG   24 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHC
Confidence            689999999999999999998753

...

>PRK12377 putative replication protein; Provisional

Probab=97.25  E-value=0.0017  Score=58.67  Aligned_cols=73  Identities=22%  Similarity=0.287  Sum_probs=47.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      ...+.++|++|+|||+||..+.+....+  ...++++++      .+++..+.......   .    ....+++.+.  +
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~--g~~v~~i~~------~~l~~~l~~~~~~~---~----~~~~~l~~l~--~  163 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAK--GRSVIVVTV------PDVMSRLHESYDNG---Q----SGEKFLQELC--K  163 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEH------HHHHHHHHHHHhcc---c----hHHHHHHHhc--C
Confidence            4678999999999999999999988754  233455544      35555554443211   0    1123445553  4


Q ss_pred             eEEEEEeCCC
Q 044858          252 KILIILDDIW  261 (426)
Q Consensus       252 ~~LlVlDdv~  261 (426)
                      --||||||+.
T Consensus       164 ~dLLiIDDlg  173 (248)
T PRK12377        164 VDLLVLDEIG  173 (248)
T ss_pred             CCEEEEcCCC
Confidence            5699999994

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.24  E-value=0.0011  Score=71.25  Aligned_cols=105  Identities=14%  Similarity=0.221  Sum_probs=58.3

Q ss_pred             cccchHHHHHHHHHHhcc-------C--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          152 HFESRKSTLKGILDALSN-------R--NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~-------~--~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .++|.+..++.+...+..       +  ...++.++|+.|+|||++|+.+.......  -...+.++.+...+... .  
T Consensus       566 ~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~--~~~~i~~d~s~~~~~~~-~--  640 (852)
T TIGR03346       566 RVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDD--EDAMVRIDMSEYMEKHS-V--  640 (852)
T ss_pred             ccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCC--CCcEEEEechhhcccch-H--
Confidence            467888888888777752       1  13468899999999999999999875422  12233444443222111 1  


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                       ..-++.+..... ......+...+......+|+||++...
T Consensus       641 -~~l~g~~~g~~g-~~~~g~l~~~v~~~p~~vlllDeieka  679 (852)
T TIGR03346       641 -ARLIGAPPGYVG-YEEGGQLTEAVRRKPYSVVLFDEVEKA  679 (852)
T ss_pred             -HHhcCCCCCccC-cccccHHHHHHHcCCCcEEEEeccccC
Confidence             111222211111 011123344444334469999999754

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.

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=97.21  E-value=0.019  Score=58.65  Aligned_cols=171  Identities=19%  Similarity=0.197  Sum_probs=97.1

Q ss_pred             CCcccccchHHHHHHHHHHhc---------cC---CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDALS---------NR---NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~---------~~---~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ....++-|-++.+.+|.+.+.         ..   +..=|.++|++|.|||-||+.|+-...-.       |++|-.+  
T Consensus       669 V~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL~-------FlSVKGP--  739 (953)
T KOG0736|consen  669 VSWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSLN-------FLSVKGP--  739 (953)
T ss_pred             cchhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhceee-------EEeecCH--
Confidence            345667788888888887664         11   24468899999999999999999775532       4555432  


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-----------Chh----hhcC---CCCC-C
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-----------DLE----AIGI---PLAD-D  276 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-----------~~~----~l~~---~l~~-~  276 (426)
                        +++..-.   |      ..+.-+.++++..++.++|+|.||++++..           ..+    .+..   -+.+ .
T Consensus       740 --ELLNMYV---G------qSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~  808 (953)
T KOG0736|consen  740 --ELLNMYV---G------QSEENVREVFERARSAAPCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSS  808 (953)
T ss_pred             --HHHHHHh---c------chHHHHHHHHHHhhccCCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCC
Confidence              3333222   1      112345677787878899999999998651           111    1111   1112 2


Q ss_pred             CCCeEEEEeecchhhh----hccCCceeeEEccCCCHHHHHHHHHHhh---CCCCCCCchHHHHHHHHHHcCC
Q 044858          277 NGGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDKEAWSLFKKMT---GDCIENGELKSVVTEVVKECAG  342 (426)
Q Consensus       277 ~~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~---~~~~~~~~~~~~~~~i~~~c~G  342 (426)
                      ..+.-||=.|...+..    -+...-.+.+.+++=+++++..=..+..   +.-..+-+    ..+|+++|.-
T Consensus       809 s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVd----L~eiAk~cp~  877 (953)
T KOG0736|consen  809 SQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVD----LVEIAKKCPP  877 (953)
T ss_pred             CCceEEEecCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcC----HHHHHhhCCc
Confidence            2333444445444332    1223334677788777666655443332   22222333    3456667753

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

Probab=97.20  E-value=0.0011  Score=66.95  Aligned_cols=75  Identities=20%  Similarity=0.344  Sum_probs=54.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .-++..++|++|.||||||+.+++...    | .++=+++|...+...+-..|...+....-..             ..+
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqaG----Y-sVvEINASDeRt~~~v~~kI~~avq~~s~l~-------------ads  386 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQAG----Y-SVVEINASDERTAPMVKEKIENAVQNHSVLD-------------ADS  386 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhcC----c-eEEEecccccccHHHHHHHHHHHHhhccccc-------------cCC
Confidence            347899999999999999999998754    2 3667888888888877777765543221100             125


Q ss_pred             CeEEEEEeCCCCc
Q 044858          251 TKILIILDDIWGS  263 (426)
Q Consensus       251 k~~LlVlDdv~~~  263 (426)
                      ++..||+|+++-.
T Consensus       387 rP~CLViDEIDGa  399 (877)
T KOG1969|consen  387 RPVCLVIDEIDGA  399 (877)
T ss_pred             CcceEEEecccCC
Confidence            7889999999754

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.20  E-value=0.012  Score=57.60  Aligned_cols=158  Identities=19%  Similarity=0.290  Sum_probs=86.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHH---HHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVR---AWRLLEQL  247 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~---~~~l~~~l  247 (426)
                      ....+.+.|++|+|||+||..+.....    |+-+--++      ++++       .|     .++...   +...++-.
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~S~----FPFvKiiS------pe~m-------iG-----~sEsaKc~~i~k~F~DA  594 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALSSD----FPFVKIIS------PEDM-------IG-----LSESAKCAHIKKIFEDA  594 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhhcC----CCeEEEeC------hHHc-------cC-----ccHHHHHHHHHHHHHHh
Confidence            455678999999999999999987644    55332221      1111       01     111112   22223222


Q ss_pred             hcCCeEEEEEeCCCCccChhhhcCCC---------------CCCCCCeEEEEeecchhhhhc--cCC-ceeeEEccCCCH
Q 044858          248 KKETKILIILDDIWGSLDLEAIGIPL---------------ADDNGGCKVLLTARSQDVLSC--EMD-CQQNFVVDVLND  309 (426)
Q Consensus       248 ~~~k~~LlVlDdv~~~~~~~~l~~~l---------------~~~~~~s~iivTtr~~~va~~--~~~-~~~~~~l~~L~~  309 (426)
                      -+..--+||+||+...-+|-.++..|               |+.++.--|+-||....+...  ... -...|.++.++.
T Consensus       595 YkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~  674 (744)
T KOG0741|consen  595 YKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTT  674 (744)
T ss_pred             hcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCc
Confidence            23345799999998777766554432               233333335556666665421  111 235788888876


Q ss_pred             -HHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          310 -KEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       310 -~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                       ++..+.++..-  ...+.+.+.++++...+|  +-..|+.+..++
T Consensus       675 ~~~~~~vl~~~n--~fsd~~~~~~~~~~~~~~--~~vgIKklL~li  716 (744)
T KOG0741|consen  675 GEQLLEVLEELN--IFSDDEVRAIAEQLLSKK--VNVGIKKLLMLI  716 (744)
T ss_pred             hHHHHHHHHHcc--CCCcchhHHHHHHHhccc--cchhHHHHHHHH
Confidence             77777776542  122344556666777666  223344444444

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=97.19  E-value=0.0017  Score=61.22  Aligned_cols=30  Identities=20%  Similarity=0.270  Sum_probs=26.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ..+..+.|+|++|+|||.+|+.+++.....
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~~  175 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGIE  175 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCCC
Confidence            346789999999999999999999987653

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.18  E-value=0.02  Score=57.88  Aligned_cols=201  Identities=14%  Similarity=0.090  Sum_probs=119.5

Q ss_pred             ccccchHHHHHHHHHHhc----c-CCccEEEEEcCCCCcHHHHHHHHHHHhh---hcCccce--EEEEEecCCcCHHHHH
Q 044858          151 MHFESRKSTLKGILDALS----N-RNFNMIGVYGMGGIGKTTLVKEVGRQAK---ENNLFEK--VISSRVSQTPQIKEIQ  220 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~----~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~---~~~~f~~--~~wv~v~~~~~~~~il  220 (426)
                      ..+-+|+.+..+|-..+.    + +.-..+-|.|.+|+|||..+..|.+...   .++.-..  .+.++.-.-.++.++.
T Consensus       396 ~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y  475 (767)
T KOG1514|consen  396 ESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIY  475 (767)
T ss_pred             ccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHH
Confidence            446689999998888775    3 3344889999999999999999998654   1121222  3344444555789999


Q ss_pred             HHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCccC--hhhhcCCC-CCCCCCeEEEEeecchh--h
Q 044858          221 REIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGSLD--LEAIGIPL-ADDNGGCKVLLTARSQD--V  291 (426)
Q Consensus       221 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~~--~~~l~~~l-~~~~~~s~iivTtr~~~--v  291 (426)
                      ..|..++.......  ...+..+..++.    ..+.++|++|+++..-.  -+-+...| +...++|+++|.+=...  .
T Consensus       476 ~~I~~~lsg~~~~~--~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaNTmdl  553 (767)
T KOG1514|consen  476 EKIWEALSGERVTW--DAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIANTMDL  553 (767)
T ss_pred             HHHHHhcccCcccH--HHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEecccccC
Confidence            99999886543221  122233333332    24678999999865422  11122222 13445777766543221  1


Q ss_pred             hhc-------cCCceeeEEccCCCHHHHHHHHHHhhCCC--CCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          292 LSC-------EMDCQQNFVVDVLNDKEAWSLFKKMTGDC--IENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       292 a~~-------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~--~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      ...       ..-....+...|-+.++-.++...++.+.  ..+...+-+++.++...|..-.|+...-+.
T Consensus       554 PEr~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGDaRraldic~RA  624 (767)
T KOG1514|consen  554 PERLLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGDARRALDICRRA  624 (767)
T ss_pred             HHHHhccchhhhccceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccccHHHHHHHHHHH
Confidence            100       01123567888889988888888777532  233344556666666666666665555433

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.18  E-value=0.013  Score=56.40  Aligned_cols=166  Identities=15%  Similarity=0.186  Sum_probs=89.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      +=-.++||+|.||||+...+++...    |+..- ...+...+-.+ ++.++                    ..-  ..+
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L~----ydIyd-LeLt~v~~n~d-Lr~LL--------------------~~t--~~k  287 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYLN----YDIYD-LELTEVKLDSD-LRHLL--------------------LAT--PNK  287 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhcC----CceEE-eeeccccCcHH-HHHHH--------------------HhC--CCC
Confidence            3457999999999999999999875    44321 12222111111 22222                    222  346


Q ss_pred             EEEEEeCCCCccC--------------------hhhhcCCC---CCCCCCeEEE-Eeecchhhh----hccCCceeeEEc
Q 044858          253 ILIILDDIWGSLD--------------------LEAIGIPL---ADDNGGCKVL-LTARSQDVL----SCEMDCQQNFVV  304 (426)
Q Consensus       253 ~LlVlDdv~~~~~--------------------~~~l~~~l---~~~~~~s~ii-vTtr~~~va----~~~~~~~~~~~l  304 (426)
                      -+|||.|++...+                    +.-|...+   ...+.+=||| .||....-.    -++..-...+.+
T Consensus       288 SIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~m  367 (457)
T KOG0743|consen  288 SILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYM  367 (457)
T ss_pred             cEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEc
Confidence            7888888764311                    01111111   1112233555 466554322    122233467889


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh-hcC-C-HHHHHHHHHHHh
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL-KNK-S-PYEWRNALRQLK  370 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l-~~~-~-~~~w~~~l~~l~  370 (426)
                      .-=+.+....||.+.++...+.+    +..+|.+...|.-+.=..++..| .++ + ....+.+.+.+.
T Consensus       368 gyCtf~~fK~La~nYL~~~~~h~----L~~eie~l~~~~~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~  432 (457)
T KOG0743|consen  368 GYCTFEAFKTLASNYLGIEEDHR----LFDEIERLIEETEVTPAQVAEELMKNKNDADVALKGLVEALE  432 (457)
T ss_pred             CCCCHHHHHHHHHHhcCCCCCcc----hhHHHHHHhhcCccCHHHHHHHHhhccccHHHHHHHHHHHHH
Confidence            99999999999999987543222    45556666666655555565555 454 2 223344444443

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.16  E-value=0.00068  Score=64.04  Aligned_cols=47  Identities=19%  Similarity=0.311  Sum_probs=40.2

Q ss_pred             cccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          152 HFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .++|-++.++++++++.      +.+.+++.++|++|+||||||+.+.+....
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            68899999999999886      234578999999999999999999988754

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

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

Probab=97.16  E-value=0.0028  Score=57.72  Aligned_cols=76  Identities=22%  Similarity=0.253  Sum_probs=49.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      +..-+.++|++|+|||.||..+.+... +..+ .+.+++      ..++..++.......       ....++.+.+.  
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~-sv~f~~------~~el~~~Lk~~~~~~-------~~~~~l~~~l~--  166 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-KAGI-SVLFIT------APDLLSKLKAAFDEG-------RLEEKLLRELK--  166 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-HcCC-eEEEEE------HHHHHHHHHHHHhcC-------chHHHHHHHhh--
Confidence            556799999999999999999999987 3323 344443      456777776654320       11223344343  


Q ss_pred             CeEEEEEeCCCCc
Q 044858          251 TKILIILDDIWGS  263 (426)
Q Consensus       251 k~~LlVlDdv~~~  263 (426)
                      +-=||||||+-..
T Consensus       167 ~~dlLIiDDlG~~  179 (254)
T COG1484         167 KVDLLIIDDIGYE  179 (254)
T ss_pred             cCCEEEEecccCc
Confidence            3459999999643

>PRK09183 transposase/IS protein; Provisional

Probab=97.16  E-value=0.0012  Score=60.44  Aligned_cols=26  Identities=35%  Similarity=0.500  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..+.|+|++|+|||+||..+......
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~~  128 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAVR  128 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            46789999999999999999876543

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.15  E-value=0.0027  Score=60.77  Aligned_cols=89  Identities=19%  Similarity=0.178  Sum_probs=54.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ..++.++|+.|+||||++..+............+..++... .....+-++...+.++.+.............+..+.  
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~--  214 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELR--  214 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhc--
Confidence            46899999999999999999988764321123455555332 224455666667777766543332222334444443  


Q ss_pred             CeEEEEEeCCCC
Q 044858          251 TKILIILDDIWG  262 (426)
Q Consensus       251 k~~LlVlDdv~~  262 (426)
                      ++-++++|..-.
T Consensus       215 ~~DlVLIDTaG~  226 (374)
T PRK14722        215 NKHMVLIDTIGM  226 (374)
T ss_pred             CCCEEEEcCCCC
Confidence            245677998853

>PRK06696 uridine kinase; Validated

Probab=97.14  E-value=0.00078  Score=60.34  Aligned_cols=44  Identities=25%  Similarity=0.354  Sum_probs=35.3

Q ss_pred             chHHHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          155 SRKSTLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       155 gR~~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|.+.+++|.+.+.   .+++.+|+|.|.+|+||||||+.+.+....
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~   48 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKK   48 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            35666677777664   456789999999999999999999988754

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

Probab=97.14  E-value=0.0035  Score=55.07  Aligned_cols=115  Identities=15%  Similarity=0.218  Sum_probs=68.6

Q ss_pred             CcccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      +...++|-+...+.+++.-.    .....-|.+||-.|+|||+|++.+.+....+  .-..+-|  ...           
T Consensus        58 ~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~--glrLVEV--~k~-----------  122 (287)
T COG2607          58 DLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADE--GLRLVEV--DKE-----------  122 (287)
T ss_pred             CHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhc--CCeEEEE--cHH-----------
Confidence            44567787777777665432    3334468899999999999999999988754  2222222  211           


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHh-cCCeEEEEEeCCCCc---cChhhhcCCCCCC---CCCeEEEEeecch
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLK-KETKILIILDDIWGS---LDLEAIGIPLADD---NGGCKVLLTARSQ  289 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~---~~~~~l~~~l~~~---~~~s~iivTtr~~  289 (426)
                                 +...+-.+.+.|+ ...||+|..||+.-.   +....++..+-.+   .+..-++..|.+.
T Consensus       123 -----------dl~~Lp~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNR  183 (287)
T COG2607         123 -----------DLATLPDLVELLRARPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNR  183 (287)
T ss_pred             -----------HHhhHHHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCC
Confidence                       1112223344443 257899999999533   3456666555322   3444455555554

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.12  E-value=0.0026  Score=57.01  Aligned_cols=49  Identities=20%  Similarity=0.205  Sum_probs=35.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEEEecCCcCHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISSRVSQTPQIKEIQ  220 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~il  220 (426)
                      -.++.|+|++|+|||+|+.++.......+    .=..++|++....++...+.
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~   71 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLV   71 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHH
Confidence            46899999999999999999976653221    01457888887777665543

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=97.12  E-value=0.0026  Score=59.55  Aligned_cols=83  Identities=20%  Similarity=0.192  Sum_probs=52.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcc------ccCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID------QESESVRAWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~------~~~~~~~~~~l~~  245 (426)
                      -+++-|+|++|+||||||.++.......  -..++|++....++..     .+++++.+.+      ..........+..
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~--g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~~  127 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAET  127 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            4689999999999999999987766533  3456788777666543     3455554322      1122222333333


Q ss_pred             HHhcCCeEEEEEeCCC
Q 044858          246 QLKKETKILIILDDIW  261 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~  261 (426)
                      .+.++..-+||+|.+-
T Consensus       128 li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       128 LVRSGAVDIIVVDSVA  143 (321)
T ss_pred             HhhccCCcEEEEcchh
Confidence            3344567799999985

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.11  E-value=0.0023  Score=68.49  Aligned_cols=106  Identities=16%  Similarity=0.199  Sum_probs=57.3

Q ss_pred             ccccchHHHHHHHHHHhc-------cC-C-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHH
Q 044858          151 MHFESRKSTLKGILDALS-------NR-N-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~-------~~-~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~  221 (426)
                      ..++|.+..+..+...+.       ++ + ...+.++|+.|+|||+||+.+.+..-..  -...+-++.+.-.+...+  
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~--~~~~~~~d~s~~~~~~~~--  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGS--EDAMIRLDMSEYMEKHTV--  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCC--ccceEEEEchhccccccH--
Confidence            346788888888777664       12 1 2356789999999999999998765321  122334444432221111  


Q ss_pred             HHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          222 EIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       222 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                        ..-++.+..... ......+.+.+......+++||+++..
T Consensus       585 --~~l~g~~~gyvg-~~~~~~l~~~~~~~p~~VvllDeieka  623 (821)
T CHL00095        585 --SKLIGSPPGYVG-YNEGGQLTEAVRKKPYTVVLFDEIEKA  623 (821)
T ss_pred             --HHhcCCCCcccC-cCccchHHHHHHhCCCeEEEECChhhC
Confidence              111222211100 011123445555433469999999754

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.10  E-value=0.0019  Score=55.48  Aligned_cols=36  Identities=33%  Similarity=0.416  Sum_probs=28.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEE
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISS  208 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv  208 (426)
                      +..+|.+.|+.|+||||+|+.+++.....  +...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~~--~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKLK--YSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEE
Confidence            45689999999999999999999887643  4444444

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.10  E-value=0.0028  Score=59.52  Aligned_cols=89  Identities=25%  Similarity=0.220  Sum_probs=56.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc----CccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc----------Cc-
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN----NLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE----------SE-  236 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~----------~~-  236 (426)
                      -.++-|+|++|+|||+|+.+++-.....    ..-..++|++....+++.++. ++++.++.+.+..          +. 
T Consensus        96 G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d~~~~l~~i~~~~~~~~e  174 (313)
T TIGR02238        96 MSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVDPDAVLDNILYARAYTSE  174 (313)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCChHHhcCcEEEecCCCHH
Confidence            3678899999999999999876433211    112368899999988888865 4566666542210          11 


Q ss_pred             --HHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          237 --SVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       237 --~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                        ...+..+...+.+.+.-|||+|.+.
T Consensus       175 ~~~~~l~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       175 HQMELLDYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             HHHHHHHHHHHHhhccCCCEEEEEcch
Confidence              1222333344444456689999985

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.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=97.09  E-value=0.0045  Score=55.63  Aligned_cols=30  Identities=23%  Similarity=0.432  Sum_probs=26.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      +++.+++|.|+.|+|||||++.+.......
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~~~   60 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQQD   60 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            557799999999999999999999887653

>PRK04296 thymidine kinase; Provisional

Probab=97.09  E-value=0.00071  Score=58.93  Aligned_cols=110  Identities=17%  Similarity=0.140  Sum_probs=60.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc---cCcHHHHHHHHHHHhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ---ESESVRAWRLLEQLKK  249 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~---~~~~~~~~~l~~~l~~  249 (426)
                      .++.|+|+.|.||||++..+..+....  ...++.+.  ..++.......++.+++.....   ....+....+.+  ..
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~--g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~--~~   76 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEER--GMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE--EG   76 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHc--CCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh--hC
Confidence            467899999999999999998877543  22233331  2212222234455666543332   111222222222  33


Q ss_pred             CCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchh
Q 044858          250 ETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQD  290 (426)
Q Consensus       250 ~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~  290 (426)
                      ++.-+||+|.+.-.  ++...+...+  ...|..||+|.++..
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            34458999999643  2122222221  235778999998854

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.07  E-value=0.0051  Score=51.63  Aligned_cols=39  Identities=28%  Similarity=0.347  Sum_probs=29.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ++.|+|++|+||||++..+.......  -..++|+......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~e~~~   39 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATK--GGKVVYVDIEEEI   39 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhc--CCEEEEEECCcch
Confidence            36899999999999999998877542  3456777766544

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.05  E-value=0.0053  Score=55.16  Aligned_cols=86  Identities=19%  Similarity=0.188  Sum_probs=49.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc---------------c--
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ---------------E--  234 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~---------------~--  234 (426)
                      ..++.|.|+.|+|||||+.++......++  ..+++++  ...+..++++.+ .+++...+.               .  
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~~~~g--~~~~yi~--~e~~~~~~~~~~-~~~g~~~~~~~~~~~l~~~~~~~~~~~   98 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGFLQNG--YSVSYVS--TQLTTTEFIKQM-MSLGYDINKKLISGKLLYIPVYPLLSG   98 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhCC--CcEEEEe--CCCCHHHHHHHH-HHhCCchHHHhhcCcEEEEEecccccC
Confidence            35899999999999999877766543222  3455665  333556666666 344432210               0  


Q ss_pred             --CcHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 044858          235 --SESVRAWRLLEQLKKETKILIILDDIWG  262 (426)
Q Consensus       235 --~~~~~~~~l~~~l~~~k~~LlVlDdv~~  262 (426)
                        .....+..+.+.....++-++|+|.+-.
T Consensus        99 ~~~~~~~l~~il~~~~~~~~~~lVIDe~t~  128 (230)
T PRK08533         99 NSEKRKFLKKLMNTRRFYEKDVIIIDSLSS  128 (230)
T ss_pred             hHHHHHHHHHHHHHHHhcCCCEEEEECccH
Confidence              0122233344443333567899999853

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=97.05  E-value=0.008  Score=60.70  Aligned_cols=152  Identities=20%  Similarity=0.191  Sum_probs=83.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .++.+.++|++|.|||.||+.+.+.....  |     +.+...    +++..-        - ......+..++....+.
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~~~~--f-----i~v~~~----~l~sk~--------v-Gesek~ir~~F~~A~~~  334 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALESRSR--F-----ISVKGS----ELLSKW--------V-GESEKNIRELFEKARKL  334 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHhhCCCe--E-----EEeeCH----HHhccc--------c-chHHHHHHHHHHHHHcC
Confidence            45678999999999999999999965533  3     222211    111100        0 11122344555555556


Q ss_pred             CeEEEEEeCCCCccChh-------------hhcCCCC--CCCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHH
Q 044858          251 TKILIILDDIWGSLDLE-------------AIGIPLA--DDNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKE  311 (426)
Q Consensus       251 k~~LlVlDdv~~~~~~~-------------~l~~~l~--~~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e  311 (426)
                      .+++|++|+++....+.             .+...+.  ....+..||-||-......    ....-...+.+.+=+.++
T Consensus       335 ~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~  414 (494)
T COG0464         335 APSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEE  414 (494)
T ss_pred             CCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHH
Confidence            89999999997542211             1211221  1223334444554443221    111334688888889999


Q ss_pred             HHHHHHHhhCCCCCCCchHHHHHHHHHHcCC
Q 044858          312 AWSLFKKMTGDCIENGELKSVVTEVVKECAG  342 (426)
Q Consensus       312 ~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G  342 (426)
                      ..+.|+.........-...-..+.+++.+.|
T Consensus       415 r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~  445 (494)
T COG0464         415 RLEIFKIHLRDKKPPLAEDVDLEELAEITEG  445 (494)
T ss_pred             HHHHHHHHhcccCCcchhhhhHHHHHHHhcC
Confidence            9999999886333221112223445555555

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.04  E-value=0.006  Score=55.07  Aligned_cols=76  Identities=17%  Similarity=0.248  Sum_probs=47.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      ...+.++|.+|+|||+|+..+.+.....+  ..+++++      ..+++..+......  ...    ....+++.+.  +
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~~g--~~v~~it------~~~l~~~l~~~~~~--~~~----~~~~~l~~l~--~  162 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLLRG--KSVLIIT------VADIMSAMKDTFSN--SET----SEEQLLNDLS--N  162 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhcC--CeEEEEE------HHHHHHHHHHHHhh--ccc----cHHHHHHHhc--c
Confidence            35788999999999999999999876532  3445553      45566555544321  111    1223444554  3


Q ss_pred             eEEEEEeCCCCc
Q 044858          252 KILIILDDIWGS  263 (426)
Q Consensus       252 ~~LlVlDdv~~~  263 (426)
                      .=+|||||+...
T Consensus       163 ~dlLvIDDig~~  174 (244)
T PRK07952        163 VDLLVIDEIGVQ  174 (244)
T ss_pred             CCEEEEeCCCCC
Confidence            458899999643

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=97.03  E-value=0.009  Score=56.51  Aligned_cols=89  Identities=16%  Similarity=0.163  Sum_probs=48.1

Q ss_pred             CCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecchh-hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCC
Q 044858          250 ETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIEN  326 (426)
Q Consensus       250 ~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~  326 (426)
                      +++-++++|++...+  .-+.+...+..-..++.+|++|.+.. +.....+....+.+.+++.++..+.+.+. +  . +
T Consensus       112 ~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~-~--~-~  187 (325)
T PRK08699        112 GGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRER-G--V-A  187 (325)
T ss_pred             CCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhc-C--C-C
Confidence            344455667776542  22222222211123455777776643 43323344578999999999998888653 1  1 1


Q ss_pred             CchHHHHHHHHHHcCCchHHH
Q 044858          327 GELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       327 ~~~~~~~~~i~~~c~GlPlai  347 (426)
                      .. .    ..+..++|-|+..
T Consensus       188 ~~-~----~~l~~~~g~p~~~  203 (325)
T PRK08699        188 EP-E----ERLAFHSGAPLFD  203 (325)
T ss_pred             cH-H----HHHHHhCCChhhh
Confidence            11 1    1235678888643

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.03  E-value=0.0035  Score=58.82  Aligned_cols=83  Identities=22%  Similarity=0.197  Sum_probs=52.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc------cCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ------ESESVRAWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~------~~~~~~~~~l~~  245 (426)
                      -+++-|+|++|+||||||.+++......  -..++|++....+++.     .+++++.+.+.      .+.......+..
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~--g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~~  127 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKL--GGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIADS  127 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc--CCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHHH
Confidence            4688899999999999999988765433  3457788887766653     34445443211      111222223333


Q ss_pred             HHhcCCeEEEEEeCCC
Q 044858          246 QLKKETKILIILDDIW  261 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~  261 (426)
                      .+.++..-+||+|.+-
T Consensus       128 li~s~~~~lIVIDSva  143 (325)
T cd00983         128 LVRSGAVDLIVVDSVA  143 (325)
T ss_pred             HHhccCCCEEEEcchH
Confidence            3344567799999975

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK09354 recA recombinase A; Provisional

Probab=97.02  E-value=0.0039  Score=58.95  Aligned_cols=83  Identities=20%  Similarity=0.195  Sum_probs=54.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc------cCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ------ESESVRAWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~------~~~~~~~~~l~~  245 (426)
                      -+++-|+|++|+|||||+.++.......  -..++|++....++..     .+++++...+.      .+.......+..
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~--G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~~~  132 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIADT  132 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            4688999999999999999988765533  3567899888777753     45555543221      122222223333


Q ss_pred             HHhcCCeEEEEEeCCC
Q 044858          246 QLKKETKILIILDDIW  261 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~  261 (426)
                      .+.++..-+||+|.+-
T Consensus       133 li~s~~~~lIVIDSva  148 (349)
T PRK09354        133 LVRSGAVDLIVVDSVA  148 (349)
T ss_pred             HhhcCCCCEEEEeChh
Confidence            3345567799999985

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.02  E-value=0.0035  Score=56.22  Aligned_cols=45  Identities=24%  Similarity=0.285  Sum_probs=34.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEI  219 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i  219 (426)
                      -.++.|+|++|+|||+++.++.......  -..++|++.. .++...+
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~~--~~~v~yi~~e-~~~~~r~   67 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAKN--GKKVIYIDTE-GLSPERF   67 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEECC-CCCHHHH
Confidence            4689999999999999999998776543  3567888887 5555443

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=97.02  E-value=0.0046  Score=62.04  Aligned_cols=55  Identities=22%  Similarity=0.232  Sum_probs=40.0

Q ss_pred             cccchHHHHHHHHHHhcc-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe
Q 044858          152 HFESRKSTLKGILDALSN-----RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV  210 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~-----~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v  210 (426)
                      ++.-..+-++++..||.+     ...+++.++||+|+||||.++.+++...    |+.+-|.+-
T Consensus        20 eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg----~~v~Ew~np   79 (519)
T PF03215_consen   20 ELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG----FEVQEWINP   79 (519)
T ss_pred             HhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC----CeeEEecCC
Confidence            344445566777777762     2356899999999999999999998864    666667643

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=97.00  E-value=0.0067  Score=55.39  Aligned_cols=88  Identities=26%  Similarity=0.296  Sum_probs=55.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc----CccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-------------cC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN----NLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-------------ES  235 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-------------~~  235 (426)
                      .+.=|+|++|+|||.|+.+++-.....    +.-..++|++-...++...+. +|++..+...+.             ..
T Consensus        39 ~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~~~  117 (256)
T PF08423_consen   39 SITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDLEE  117 (256)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSHHH
T ss_pred             cEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCHHH
Confidence            578899999999999999887553321    122368999999999887765 566665432211             01


Q ss_pred             cHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          236 ESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       236 ~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                      ....+..+...+.+.+--|||+|.+-
T Consensus       118 l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  118 LLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHhhccccceEEEEecchH
Confidence            11223333344444566799999984

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 ....

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.97  E-value=0.0047  Score=58.56  Aligned_cols=89  Identities=21%  Similarity=0.165  Sum_probs=56.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh---c-CccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc---------CcHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE---N-NLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE---------SESV  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~---~-~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~---------~~~~  238 (426)
                      -.++-|+|++|+|||+|+.+++-....   . +.-..++|++....|++.++.+ +++.++.+.+..         ...+
T Consensus       126 G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~~~~~~~e  204 (344)
T PLN03187        126 RCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIYARAYTYE  204 (344)
T ss_pred             CeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEEecCCCHH
Confidence            357889999999999999998643321   1 1124689999999999888654 566666542210         1111


Q ss_pred             ----HHHHHHHHHhcCCeEEEEEeCCC
Q 044858          239 ----RAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       239 ----~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                          .+..+...+.+.+--|||+|.+-
T Consensus       205 ~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        205 HQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence                22233333434455689999984

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

Probab=96.95  E-value=0.0032  Score=53.42  Aligned_cols=27  Identities=26%  Similarity=0.341  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      -..+.|+|++|.|||||.+.+|...+.
T Consensus        28 Gef~fl~GpSGAGKSTllkLi~~~e~p   54 (223)
T COG2884          28 GEFVFLTGPSGAGKSTLLKLIYGEERP   54 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhhcC
Confidence            357899999999999999999988764

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

Probab=96.94  E-value=0.0094  Score=54.43  Aligned_cols=89  Identities=20%  Similarity=0.331  Sum_probs=55.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHH------
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESV------  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~------  238 (426)
                      +-+.|.|.+|+|||||+.++++....+ +-+.++++-+.+.. .+.++..++...-...       ...++...      
T Consensus        70 Qr~~If~~~G~GKTtLa~~i~~~i~~~-~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~~  148 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELINNIAKA-HGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVAL  148 (274)
T ss_pred             CEEEEecCCCCChhHHHHHHHHHHHhc-CCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            568999999999999999999988754 12345666666554 5566666665432111       11111111      


Q ss_pred             HHHHHHHHHh-c-CCeEEEEEeCCCC
Q 044858          239 RAWRLLEQLK-K-ETKILIILDDIWG  262 (426)
Q Consensus       239 ~~~~l~~~l~-~-~k~~LlVlDdv~~  262 (426)
                      ....+-+++. + ++++|+++||+-.
T Consensus       149 ~a~~~AEyfr~~~g~~Vl~~~Dsltr  174 (274)
T cd01133         149 TGLTMAEYFRDEEGQDVLLFIDNIFR  174 (274)
T ss_pred             HHHHHHHHHHHhcCCeEEEEEeChhH
Confidence            1223444443 3 7999999999853

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.93  E-value=0.0079  Score=54.37  Aligned_cols=48  Identities=17%  Similarity=0.182  Sum_probs=34.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ..++.|.|++|+|||++|.++......+  -...+|++...  ++.++.+.+
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~~~--ge~~lyvs~ee--~~~~i~~~~   68 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGIYVALEE--HPVQVRRNM   68 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEEEeeC--CHHHHHHHH
Confidence            4689999999999999999977654322  44577877654  455555553

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.93  E-value=0.012  Score=56.40  Aligned_cols=89  Identities=18%  Similarity=0.220  Sum_probs=49.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      ++++|+++|++|+||||++..+......++ + .+..++..... ...+-++...+.++.+.....+...+...+..+..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~~~G-k-kVglI~aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~  317 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFHGKK-K-TVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKE  317 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHHHcC-C-cEEEEecCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHh
Confidence            457999999999999999999987765332 2 33344443221 12223344444555554322333333444444442


Q ss_pred             C-CeEEEEEeCCC
Q 044858          250 E-TKILIILDDIW  261 (426)
Q Consensus       250 ~-k~~LlVlDdv~  261 (426)
                      . +.=+|++|-.-
T Consensus       318 ~~~~DvVLIDTaG  330 (436)
T PRK11889        318 EARVDYILIDTAG  330 (436)
T ss_pred             ccCCCEEEEeCcc
Confidence            1 22477788764

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.92  E-value=0.0073  Score=57.00  Aligned_cols=57  Identities=25%  Similarity=0.293  Sum_probs=41.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEEEecCCcCHHHHHHHHHHHhCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISSRVSQTPQIKEIQREIAEKLGL  229 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~il~~i~~~l~~  229 (426)
                      ..++-|+|++|+|||+++.+++.......    .-..++|++....++..++. ++++.++.
T Consensus        95 g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl  155 (310)
T TIGR02236        95 QAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGL  155 (310)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCC
Confidence            46889999999999999999976643210    01268899998888877654 44555544

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.91  E-value=0.0077  Score=57.03  Aligned_cols=89  Identities=25%  Similarity=0.287  Sum_probs=55.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEEEEecCCcCHHHHHHHHHHHhCCCccc----------cCc-
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ----------ESE-  236 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~----------~~~-  236 (426)
                      ..++-|+|++|+|||+++.+++........    =..++|++....+++..+. ++++.++...+.          .+. 
T Consensus       102 g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~-~~~~~~g~~~~~~l~~i~~~~~~~~~  180 (317)
T PRK04301        102 QSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE-QMAEALGLDPDEVLDNIHVARAYNSD  180 (317)
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH-HHHHHcCCChHhhhccEEEEeCCCHH
Confidence            468889999999999999999866432111    1368899998888877765 444555432211          000 


Q ss_pred             --HHHHHHHHHHHhc-CCeEEEEEeCCC
Q 044858          237 --SVRAWRLLEQLKK-ETKILIILDDIW  261 (426)
Q Consensus       237 --~~~~~~l~~~l~~-~k~~LlVlDdv~  261 (426)
                        ...+..+...+.. .+--|||+|.+-
T Consensus       181 ~~~~~~~~l~~~i~~~~~~~lvVIDSis  208 (317)
T PRK04301        181 HQMLLAEKAEELIKEGENIKLVIVDSLT  208 (317)
T ss_pred             HHHHHHHHHHHHHhccCceeEEEEECch
Confidence              1122333333433 344589999874

>TIGR01069 mutS2 MutS2 family protein

Probab=96.86  E-value=0.0017  Score=68.51  Aligned_cols=184  Identities=17%  Similarity=0.170  Sum_probs=87.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh-hhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCc------cc-cCcHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA-KENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKI------DQ-ESESVRAWR  242 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~-~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~------~~-~~~~~~~~~  242 (426)
                      +..++.|+|+.|.||||+.+.+.-.. ..+..    ++|.+..... -.++.++...++...      .. .........
T Consensus       321 ~~~~liItGpNg~GKSTlLK~i~~~~l~aq~G----~~Vpa~~~~~-~~~~d~i~~~i~~~~si~~~LStfS~~m~~~~~  395 (771)
T TIGR01069       321 EKRVLAITGPNTGGKTVTLKTLGLLALMFQSG----IPIPANEHSE-IPYFEEIFADIGDEQSIEQNLSTFSGHMKNISA  395 (771)
T ss_pred             CceEEEEECCCCCCchHHHHHHHHHHHHHHhC----CCccCCcccc-ccchhheeeecChHhHHhhhhhHHHHHHHHHHH
Confidence            34689999999999999999987652 11110    0111111000 000111111111000      00 001111222


Q ss_pred             HHHHHhcCCeEEEEEeCCCCccChh---hh----cCCCCCCCCCeEEEEeecchhhhhccCC--ceeeEEccCCCHHHHH
Q 044858          243 LLEQLKKETKILIILDDIWGSLDLE---AI----GIPLADDNGGCKVLLTARSQDVLSCEMD--CQQNFVVDVLNDKEAW  313 (426)
Q Consensus       243 l~~~l~~~k~~LlVlDdv~~~~~~~---~l----~~~l~~~~~~s~iivTtr~~~va~~~~~--~~~~~~l~~L~~~e~~  313 (426)
                      +...+  ..+-|+++|++-...+..   .+    ...+  ...|+.+|+||...........  ......+. ++.+ ..
T Consensus       396 il~~~--~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l--~~~g~~viitTH~~eL~~~~~~~~~v~~~~~~-~d~~-~l  469 (771)
T TIGR01069       396 ILSKT--TENSLVLFDELGAGTDPDEGSALAISILEYL--LKQNAQVLITTHYKELKALMYNNEGVENASVL-FDEE-TL  469 (771)
T ss_pred             HHHhc--CCCcEEEecCCCCCCCHHHHHHHHHHHHHHH--HhcCCEEEEECChHHHHHHhcCCCCeEEeEEE-EcCC-CC
Confidence            33322  368999999997553321   12    1122  1347889999998766421111  11111111 1111 11


Q ss_pred             HHHHHhh-CCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHHHhh
Q 044858          314 SLFKKMT-GDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKR  371 (426)
Q Consensus       314 ~Lf~~~~-~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~l~~  371 (426)
                      . |...+ .+...    ...+-.|++++ |+|-.|..-|..+......+++.++..+..
T Consensus       470 ~-p~Ykl~~G~~g----~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~L~~  522 (771)
T TIGR01069       470 S-PTYKLLKGIPG----ESYAFEIAQRY-GIPHFIIEQAKTFYGEFKEEINVLIEKLSA  522 (771)
T ss_pred             c-eEEEECCCCCC----CcHHHHHHHHh-CcCHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            0 11111 11111    23566777777 899998888888875555566666666543

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.

>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots

Probab=96.86  E-value=0.02  Score=47.19  Aligned_cols=106  Identities=16%  Similarity=0.179  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHH
Q 044858            5 ISVTAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVET   84 (426)
Q Consensus         5 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~i~~~l~~a~~~~~~~~~~~~~Wl~~l~~~~yd~ed   84 (426)
                      +++++.+++.+...+.+...-...+...++.+...++.|......|..       .+...+..-+.-++++.+...++++
T Consensus         8 gaalG~~~~eLlk~v~~~~~k~~~fk~~l~~L~sTl~~i~P~i~eI~~-------~~~eld~~~~ee~e~L~~~L~~g~~   80 (147)
T PF05659_consen    8 GAALGAVFGELLKAVIDASKKSLSFKSILKRLESTLESIIPIIKEIDK-------LNVELDRPRQEEIERLKELLEKGKE   80 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhHHHHHHH-------HhhhcCCchhHHHHHHHHHHHHHHH
Confidence            344556666666666555555455555555566666555555555444       3333344446778999999999999


Q ss_pred             HHhhhhhhhcccccccCCChHHHhHHHHHHHHHHHHHHHh
Q 044858           85 LIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGL  124 (426)
Q Consensus        85 ~ld~~~~~~~~~~~~~~~~~~~r~~~~~~i~~l~~~l~~~  124 (426)
                      +++.+....       ++++...++.+++|+++.+.+...
T Consensus        81 LV~k~sk~~-------r~n~~kk~~y~~Ki~~le~~l~~f  113 (147)
T PF05659_consen   81 LVEKCSKVR-------RWNLYKKPRYARKIEELEESLRRF  113 (147)
T ss_pred             HHHHhcccc-------HHHHHhhHhHHHHHHHHHHHHHHH
Confidence            998765433       355667788899999988888776

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].

>PHA02244 ATPase-like protein

Probab=96.86  E-value=0.0062  Score=57.75  Aligned_cols=35  Identities=14%  Similarity=0.236  Sum_probs=26.0

Q ss_pred             HHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          161 KGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       161 ~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+..++..+.  -|.|+|++|+|||+||+.+++...
T Consensus       110 ~ri~r~l~~~~--PVLL~GppGtGKTtLA~aLA~~lg  144 (383)
T PHA02244        110 ADIAKIVNANI--PVFLKGGAGSGKNHIAEQIAEALD  144 (383)
T ss_pred             HHHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHhC
Confidence            34445544433  367899999999999999998754

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.86  E-value=0.0081  Score=55.11  Aligned_cols=117  Identities=22%  Similarity=0.278  Sum_probs=63.3

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEE---ecCCcCHHHHHHHHH--HHh--CCCccccCcHHHHH
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSR---VSQTPQIKEIQREIA--EKL--GLKIDQESESVRAW  241 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~---v~~~~~~~~il~~i~--~~l--~~~~~~~~~~~~~~  241 (426)
                      ++....+.|.|+.|+|||||.+.+.......   ...+++.   +.......++...+.  .|.  +...+..+......
T Consensus       108 ~~~~~~~~i~g~~g~GKttl~~~l~~~~~~~---~G~i~~~g~~v~~~d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k~~  184 (270)
T TIGR02858       108 NNRVLNTLIISPPQCGKTTLLRDLARILSTG---ISQLGLRGKKVGIVDERSEIAGCVNGVPQHDVGIRTDVLDGCPKAE  184 (270)
T ss_pred             CCCeeEEEEEcCCCCCHHHHHHHHhCccCCC---CceEEECCEEeecchhHHHHHHHhcccccccccccccccccchHHH
Confidence            3445689999999999999999999776532   2222321   111111122221110  010  00001111111122


Q ss_pred             HHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          242 RLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       242 ~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                      .+...+..-.+-++++|++...+.+..+...+   ..|..+|+||.+..+
T Consensus       185 ~~~~~i~~~~P~villDE~~~~e~~~~l~~~~---~~G~~vI~ttH~~~~  231 (270)
T TIGR02858       185 GMMMLIRSMSPDVIVVDEIGREEDVEALLEAL---HAGVSIIATAHGRDV  231 (270)
T ss_pred             HHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHH---hCCCEEEEEechhHH
Confidence            34444443468899999997766565554443   247789999987655

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.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=96.85  E-value=0.0063  Score=57.73  Aligned_cols=84  Identities=25%  Similarity=0.383  Sum_probs=57.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc--CcHHHHHHHHHHHhcC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE--SESVRAWRLLEQLKKE  250 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~--~~~~~~~~l~~~l~~~  250 (426)
                      .+|.|-|.+|+|||||.-++..+...+.   .++||+-.+  +..++ +--+..++.+.+..  -....++.+.+.+.+.
T Consensus        94 s~iLIgGdPGIGKSTLLLQva~~lA~~~---~vLYVsGEE--S~~Qi-klRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~  167 (456)
T COG1066          94 SVILIGGDPGIGKSTLLLQVAARLAKRG---KVLYVSGEE--SLQQI-KLRADRLGLPTNNLYLLAETNLEDIIAELEQE  167 (456)
T ss_pred             cEEEEccCCCCCHHHHHHHHHHHHHhcC---cEEEEeCCc--CHHHH-HHHHHHhCCCccceEEehhcCHHHHHHHHHhc
Confidence            6899999999999999999999987653   566665443  33332 22244566444321  1223455677777778


Q ss_pred             CeEEEEEeCCCC
Q 044858          251 TKILIILDDIWG  262 (426)
Q Consensus       251 k~~LlVlDdv~~  262 (426)
                      ++-++|+|-+..
T Consensus       168 ~p~lvVIDSIQT  179 (456)
T COG1066         168 KPDLVVIDSIQT  179 (456)
T ss_pred             CCCEEEEeccce
Confidence            899999999854

>PTZ00494 tuzin-like protein; Provisional

Probab=96.85  E-value=0.11  Score=50.25  Aligned_cols=165  Identities=11%  Similarity=0.162  Sum_probs=98.3

Q ss_pred             cCCcccccchHHHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          147 TQDFMHFESRKSTLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       147 ~~~~~~~~gR~~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      +.....++.|+.+-..+.+.|.   ...++++++.|..|.||++|.+.........     .++|.+...   ++-++.|
T Consensus       367 ~a~~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE~~p-----aV~VDVRg~---EDtLrsV  438 (664)
T PTZ00494        367 AAAEAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVEGVA-----LVHVDVGGT---EDTLRSV  438 (664)
T ss_pred             ccccccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHcCCC-----eEEEEecCC---cchHHHH
Confidence            3445668888777555555443   5678999999999999999999988765542     567777755   4567888


Q ss_pred             HHHhCCCccc-cCc-HHHHHHHHHHH---hcCCeEEEEEeCCCCccChhhh---cCCCCCCCCCeEEEEeecchhhh--h
Q 044858          224 AEKLGLKIDQ-ESE-SVRAWRLLEQL---KKETKILIILDDIWGSLDLEAI---GIPLADDNGGCKVLLTARSQDVL--S  293 (426)
Q Consensus       224 ~~~l~~~~~~-~~~-~~~~~~l~~~l---~~~k~~LlVlDdv~~~~~~~~l---~~~l~~~~~~s~iivTtr~~~va--~  293 (426)
                      .+.++.+.-+ ..+ .+.+..-...-   .+++.-+||+- +.+...+..+   ...|.....-|.|++---.+..-  .
T Consensus       439 VKALgV~nve~CGDlLdFI~ea~~~A~~~~~g~~P~lVlk-LREGssL~RVYnE~vaLacDrRlCHvv~EVplESLT~~n  517 (664)
T PTZ00494        439 VRALGVSNVEVCGDLLGFVEEAMRGATVKASDGVPFLVMR-LREGSDLGRVYGEVVSLVSDCQACHIVLAVPMKALTPLN  517 (664)
T ss_pred             HHHhCCCChhhhccHHHHHHHHHHHHHHhcCCCCCEEEEE-eccCCcHHHHHHHHHHHHccchhheeeeechHhhhchhh
Confidence            8899876432 222 22222222111   23444455542 1222222111   01233344567777755444331  1


Q ss_pred             ccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          294 CEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       294 ~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      ........|.+++|+..++.++-.+.+
T Consensus       518 ~~LPRLDFy~VPnFSr~QAf~YtqH~l  544 (664)
T PTZ00494        518 VSSRRLDFYCIPPFSRRQAFAYAEHTL  544 (664)
T ss_pred             ccCccceeEecCCcCHHHHHHHHhccc
Confidence            123344678999999999999887765

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.85  E-value=0.0078  Score=55.71  Aligned_cols=28  Identities=18%  Similarity=0.217  Sum_probs=23.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.+.+|+|.|+.|+||||+|+.+.....
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll~   87 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALLS   87 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4567999999999999999988766554

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.

>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=96.84  E-value=0.0063  Score=52.06  Aligned_cols=54  Identities=28%  Similarity=0.409  Sum_probs=33.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCC
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGL  229 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~  229 (426)
                      ++.++|++|+||||++..+.......+ + .++.++... .....+.+.......+.
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~g-~-~v~~i~~D~~~~~~~~~l~~~~~~~~~   56 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKG-K-KVLLVAADTYRPAAIEQLRVLGEQVGV   56 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC-C-cEEEEEcCCCChHHHHHHHHhcccCCe
Confidence            678999999999999999988766431 2 233344322 22333444444555443

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.83  E-value=0.0065  Score=58.73  Aligned_cols=85  Identities=18%  Similarity=0.150  Sum_probs=45.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ..++.++|++|+||||++..+.........+ .+..++... .....+.++..++.++.+....   .....+.+.+...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~-~V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~~~---~~~~~l~~~l~~~  298 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGK-SVSLYTTDNYRIAAIEQLKRYADTMGMPFYPV---KDIKKFKETLARD  298 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCC-eEEEecccchhhhHHHHHHHHHHhcCCCeeeh---HHHHHHHHHHHhC
Confidence            4689999999999999999998765322222 222333221 1122334444455555543221   1223444444332


Q ss_pred             CeEEEEEeCC
Q 044858          251 TKILIILDDI  260 (426)
Q Consensus       251 k~~LlVlDdv  260 (426)
                      ..=+|++|-.
T Consensus       299 ~~D~VLIDTa  308 (432)
T PRK12724        299 GSELILIDTA  308 (432)
T ss_pred             CCCEEEEeCC
Confidence            3346888843

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.82  E-value=0.0017  Score=53.37  Aligned_cols=46  Identities=28%  Similarity=0.472  Sum_probs=36.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcc
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID  232 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~  232 (426)
                      +|.|.|++|+||||+|+.+.+...-.       .+      +...+++++++..+.+..
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~-------~v------saG~iFR~~A~e~gmsl~   47 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLK-------LV------SAGTIFREMARERGMSLE   47 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCc-------ee------eccHHHHHHHHHcCCCHH
Confidence            68999999999999999999887643       11      345788999998887643

>PRK06921 hypothetical protein; Provisional

Probab=96.82  E-value=0.0074  Score=55.45  Aligned_cols=72  Identities=19%  Similarity=0.236  Sum_probs=44.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ....+.++|..|+|||.|+..+++....+. ...++|++.      .+++..+...+          .......+.+.  
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~-g~~v~y~~~------~~l~~~l~~~~----------~~~~~~~~~~~--  176 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKK-GVPVLYFPF------VEGFGDLKDDF----------DLLEAKLNRMK--  176 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhc-CceEEEEEH------HHHHHHHHHHH----------HHHHHHHHHhc--
Confidence            356789999999999999999999876431 233556553      33344433221          11122334443  


Q ss_pred             CeEEEEEeCCC
Q 044858          251 TKILIILDDIW  261 (426)
Q Consensus       251 k~~LlVlDdv~  261 (426)
                      +-=||||||+.
T Consensus       177 ~~dlLiIDDl~  187 (266)
T PRK06921        177 KVEVLFIDDLF  187 (266)
T ss_pred             CCCEEEEeccc
Confidence            34599999993

>PTZ00035 Rad51 protein; Provisional

Probab=96.81  E-value=0.0091  Score=56.78  Aligned_cols=90  Identities=19%  Similarity=0.158  Sum_probs=54.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh---c-CccceEEEEEecCCcCHHHHHHHHHHHhCCCccc----------cCc-
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE---N-NLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ----------ESE-  236 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~---~-~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~----------~~~-  236 (426)
                      -.++.|+|++|+|||+|+.+++-....   . ..-..++|++....+++.+ +.++++.++.....          .+. 
T Consensus       118 G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er-i~~ia~~~g~~~~~~l~nI~~~~~~~~e  196 (337)
T PTZ00035        118 GSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERFGLDPEDVLDNIAYARAYNHE  196 (337)
T ss_pred             CeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH-HHHHHHHhCCChHhHhhceEEEccCCHH
Confidence            468899999999999999998754331   0 1123567998888777776 44456655543210          011 


Q ss_pred             --HHHHHHHHHHHhcCCeEEEEEeCCCC
Q 044858          237 --SVRAWRLLEQLKKETKILIILDDIWG  262 (426)
Q Consensus       237 --~~~~~~l~~~l~~~k~~LlVlDdv~~  262 (426)
                        ...+..+...+...+--|||+|.+..
T Consensus       197 ~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        197 HQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             HHHHHHHHHHHHhhccCccEEEEECcHH
Confidence              11222233334445567999999853

>PRK06547 hypothetical protein; Provisional

Probab=96.81  E-value=0.002  Score=55.04  Aligned_cols=35  Identities=26%  Similarity=0.322  Sum_probs=28.1

Q ss_pred             HHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          163 ILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       163 l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +...+......+|.|.|++|+||||+|+.+.+...
T Consensus         6 ~~~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~~~~   40 (172)
T PRK06547          6 IAARLCGGGMITVLIDGRSGSGKTTLAGALAARTG   40 (172)
T ss_pred             HHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            33444566778999999999999999999988643

>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=96.78  E-value=0.0085  Score=53.43  Aligned_cols=24  Identities=25%  Similarity=0.423  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|+|.|+.|+||||+|+.+.....
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHh
Confidence            589999999999999999998765

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=96.78  E-value=0.0097  Score=53.04  Aligned_cols=93  Identities=19%  Similarity=0.299  Sum_probs=59.8

Q ss_pred             CcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          149 DFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      .+.++-|..++++++.+-..             -+.++-|.++|++|.|||-+|+.|.|+....  |     +.|-.   
T Consensus       175 ty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdac--f-----irvig---  244 (435)
T KOG0729|consen  175 TYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDAC--F-----IRVIG---  244 (435)
T ss_pred             ccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCce--E-----Eeehh---
Confidence            45566778888887766543             1345678899999999999999999876532  3     32211   


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                       .++.+...   +      .....+..+++.....|-|+|+||+++
T Consensus       245 -selvqkyv---g------egarmvrelf~martkkaciiffdeid  280 (435)
T KOG0729|consen  245 -SELVQKYV---G------EGARMVRELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             -HHHHHHHh---h------hhHHHHHHHHHHhcccceEEEEeeccc
Confidence             11221111   1      112345566666666788999999985

>cd01394 radB RadB

Probab=96.78  E-value=0.0075  Score=53.73  Aligned_cols=42  Identities=21%  Similarity=0.230  Sum_probs=31.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      -.++.|.|++|+||||++.++.......  -..++|++....++
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~--g~~v~yi~~e~~~~   60 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQ--GKKVAYIDTEGLSS   60 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCCCCH
Confidence            4688999999999999999998776432  33567777655443

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.78  E-value=0.12  Score=50.51  Aligned_cols=28  Identities=29%  Similarity=0.354  Sum_probs=24.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+.+|.++|+.|+||||++..+......
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~  126 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQR  126 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4679999999999999999999876653

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.77  E-value=0.0039  Score=58.91  Aligned_cols=101  Identities=18%  Similarity=0.202  Sum_probs=55.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.++|+.|+|||.||..+.+....++  ..++++++      .+++..+...-.   +...+   ....++.+.+  -
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g--~~V~y~t~------~~l~~~l~~~~~---~~~~~---~~~~~~~l~~--~  247 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRG--KSVIYRTA------DELIEILREIRF---NNDKE---LEEVYDLLIN--C  247 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCC--CeEEEEEH------HHHHHHHHHHHh---ccchh---HHHHHHHhcc--C
Confidence            6799999999999999999999876542  24556554      334444432211   11111   1112344432  3


Q ss_pred             EEEEEeCCCCc--cChhh--hcCCCCC-CCCCeEEEEeecch
Q 044858          253 ILIILDDIWGS--LDLEA--IGIPLAD-DNGGCKVLLTARSQ  289 (426)
Q Consensus       253 ~LlVlDdv~~~--~~~~~--l~~~l~~-~~~~s~iivTtr~~  289 (426)
                      =||||||+...  ..|..  +...+.. ...+-.+||||...
T Consensus       248 DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~  289 (329)
T PRK06835        248 DLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNLS  289 (329)
T ss_pred             CEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            48999999543  23322  2222211 12244588888653

>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=96.77  E-value=0.0073  Score=52.26  Aligned_cols=45  Identities=18%  Similarity=0.094  Sum_probs=31.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      ++.|.|++|+|||+|+.++.......  -..++|++...  +..++.+.
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~--g~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHC--CCcEEEEECCC--CHHHHHHH
Confidence            36799999999999999987765432  23466776543  45555444

A related protein is found in archaea.

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

Probab=96.76  E-value=0.021  Score=54.52  Aligned_cols=99  Identities=22%  Similarity=0.242  Sum_probs=58.4

Q ss_pred             HHHHHHHhccC----CccEEEEEcCCCCcHHH-HHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCCccc
Q 044858          160 LKGILDALSNR----NFNMIGVYGMGGIGKTT-LVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLKIDQ  233 (426)
Q Consensus       160 ~~~l~~~l~~~----~~~vi~I~G~~GiGKTt-La~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~~~~  233 (426)
                      ...+..++.++    +.++|+++|+.|+|||| ||+....-....+ =..+..++..... ...+=++..++-++.+...
T Consensus       187 l~~~~~~~~~~~~~~~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~-~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~v  265 (407)
T COG1419         187 LRKLLLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKK-KKKVAIITTDTYRIGAVEQLKTYADIMGVPLEV  265 (407)
T ss_pred             HHHHHHhhccccccccCcEEEEECCCCCcHHHHHHHHHHHHHhhcc-CcceEEEEeccchhhHHHHHHHHHHHhCCceEE
Confidence            34444454443    46899999999999995 4544444331211 2345566554322 3444556667777877766


Q ss_pred             cCcHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          234 ESESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       234 ~~~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                      ..+...+......+..  .=+|.+|-+-
T Consensus       266 v~~~~el~~ai~~l~~--~d~ILVDTaG  291 (407)
T COG1419         266 VYSPKELAEAIEALRD--CDVILVDTAG  291 (407)
T ss_pred             ecCHHHHHHHHHHhhc--CCEEEEeCCC
Confidence            5555556666666653  2466667664

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.75  E-value=0.0085  Score=56.46  Aligned_cols=89  Identities=17%  Similarity=0.135  Sum_probs=54.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh---cC-ccceEEEEEecCCcCHHHHHHHHHHHhCCCccc----------cCcH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE---NN-LFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ----------ESES  237 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~---~~-~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~----------~~~~  237 (426)
                      ..++.|+|++|+|||+|+.+++.....   .+ .-..++|++....++..+ +.++++.++.....          .+..
T Consensus        96 g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R-l~~ia~~~~~~~~~~l~~i~~~~~~~~~  174 (316)
T TIGR02239        96 GSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER-LLAIAERYGLNPEDVLDNVAYARAYNTD  174 (316)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH-HHHHHHHcCCChHHhhccEEEEecCChH
Confidence            468899999999999999998753221   11 123578999888878776 34455555443211          0111


Q ss_pred             ---HHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          238 ---VRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       238 ---~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                         ..+..+...+...+.-|||+|.+-
T Consensus       175 ~~~~~l~~~~~~~~~~~~~LvVIDSI~  201 (316)
T TIGR02239       175 HQLQLLQQAAAMMSESRFALLIVDSAT  201 (316)
T ss_pred             HHHHHHHHHHHhhccCCccEEEEECcH
Confidence               122223333334456789999874

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).

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.72  E-value=0.015  Score=55.49  Aligned_cols=90  Identities=20%  Similarity=0.216  Sum_probs=55.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      +.+++.++|+.|+||||++..+......++  ..+.+++..... ...+-++...+.++.+.....+...+....+.+..
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g--~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~~l~~  282 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQN--RTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQYMTY  282 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHHHHHh
Confidence            357899999999999999999987664432  345566654322 23445666667676654333333344444555542


Q ss_pred             -CCeEEEEEeCCCC
Q 044858          250 -ETKILIILDDIWG  262 (426)
Q Consensus       250 -~k~~LlVlDdv~~  262 (426)
                       +..=+|++|-.-.
T Consensus       283 ~~~~D~VLIDTAGr  296 (407)
T PRK12726        283 VNCVDHILIDTVGR  296 (407)
T ss_pred             cCCCCEEEEECCCC
Confidence             2345788888743

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.72  E-value=0.0021  Score=64.12  Aligned_cols=49  Identities=16%  Similarity=0.295  Sum_probs=41.8

Q ss_pred             cccccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          150 FMHFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +.+++|-++.++.+++.+.      +.+.+++.++||+|+||||||+.+.+-...
T Consensus        75 F~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455         75 FEEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             hhcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            4468899999999999883      456689999999999999999999987654

>PRK04328 hypothetical protein; Provisional

Probab=96.72  E-value=0.011  Score=53.92  Aligned_cols=41  Identities=15%  Similarity=0.118  Sum_probs=30.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT  213 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  213 (426)
                      .-.++.|.|++|+|||+|+.++......+  -...+|++....
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee~   62 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGVYVALEEH   62 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEEeeCC
Confidence            34689999999999999999987664322  345678877653

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.71  E-value=0.0081  Score=57.04  Aligned_cols=89  Identities=18%  Similarity=0.152  Sum_probs=55.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh---cC-ccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc---------CcHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE---NN-LFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE---------SESV  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~---~~-~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~---------~~~~  238 (426)
                      -.++-|+|++|+|||+|+..++-....   .+ .-..++|++....+++.++ .+|++.++...+..         ...+
T Consensus       123 g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~~~~~~l~~i~~~~~~~~e  201 (342)
T PLN03186        123 GSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGLNGADVLENVAYARAYNTD  201 (342)
T ss_pred             ceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCCChhhhccceEEEecCCHH
Confidence            467889999999999999988754321   11 1126899999999988776 45666665433210         1111


Q ss_pred             H----HHHHHHHHhcCCeEEEEEeCCC
Q 044858          239 R----AWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       239 ~----~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                      .    +..+...+...+.-|||+|.+-
T Consensus       202 ~~~~ll~~~~~~~~~~~~~LIVIDSI~  228 (342)
T PLN03186        202 HQSELLLEAASMMAETRFALMIVDSAT  228 (342)
T ss_pred             HHHHHHHHHHHHhhccCCCEEEEeCcH
Confidence            1    2222223344456789999874

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.70  E-value=0.051  Score=57.25  Aligned_cols=48  Identities=15%  Similarity=0.295  Sum_probs=35.5

Q ss_pred             cccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          150 FMHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..++|+...+..+.+.+.  ......|.|+|..|+|||++|+.+++...
T Consensus       375 ~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~  424 (686)
T PRK15429        375 FGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSG  424 (686)
T ss_pred             ccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcC
Confidence            3457888777777665544  22334588999999999999999988654

>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=96.69  E-value=0.0041  Score=51.06  Aligned_cols=42  Identities=26%  Similarity=0.320  Sum_probs=31.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~  221 (426)
                      |.++|++|+|||+||+.+++....     ...-+.++...+..++..
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~~~-----~~~~i~~~~~~~~~dl~g   43 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALLGR-----PVIRINCSSDTTEEDLIG   43 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHTC-----EEEEEE-TTTSTHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhc-----ceEEEEecccccccccee
Confidence            679999999999999999988732     234567777777777654

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.67  E-value=0.0032  Score=55.25  Aligned_cols=110  Identities=15%  Similarity=0.157  Sum_probs=56.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHH-HHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIK-EIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~-~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      .+|.|+|+.|+||||++..+.......  ....++. +..+.... .-...+..+-....   ........+...+.. .
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~--~~~~i~t-~e~~~E~~~~~~~~~i~q~~vg~---~~~~~~~~i~~aLr~-~   74 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKN--KTHHILT-IEDPIEFVHESKRSLINQREVGL---DTLSFENALKAALRQ-D   74 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhc--CCcEEEE-EcCCccccccCccceeeecccCC---CccCHHHHHHHHhcC-C
Confidence            478999999999999999887765432  2233332 21111100 00001111111111   111122334444543 4


Q ss_pred             eEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhh
Q 044858          252 KILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVL  292 (426)
Q Consensus       252 ~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va  292 (426)
                      +=++++|++.+.+....+...   ...|..++.|+....+.
T Consensus        75 pd~ii~gEird~e~~~~~l~~---a~~G~~v~~t~Ha~~~~  112 (198)
T cd01131          75 PDVILVGEMRDLETIRLALTA---AETGHLVMSTLHTNSAA  112 (198)
T ss_pred             cCEEEEcCCCCHHHHHHHHHH---HHcCCEEEEEecCCcHH
Confidence            679999999877655443222   12355577777766543

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.

>PRK07667 uridine kinase; Provisional

Probab=96.66  E-value=0.0029  Score=55.23  Aligned_cols=37  Identities=24%  Similarity=0.485  Sum_probs=28.5

Q ss_pred             HHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          162 GILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       162 ~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+.+.+.  .++..+|+|.|.+|+||||+|+.+......
T Consensus         5 ~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l~~   43 (193)
T PRK07667          5 ELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENMKQ   43 (193)
T ss_pred             HHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3444443  344579999999999999999999987754

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.66  E-value=0.0093  Score=49.87  Aligned_cols=117  Identities=21%  Similarity=0.182  Sum_probs=62.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEE--EEEecCCcCHHHHHHHHH----HHhCCC--ccccCcHH------
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVI--SSRVSQTPQIKEIQREIA----EKLGLK--IDQESESV------  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~--wv~v~~~~~~~~il~~i~----~~l~~~--~~~~~~~~------  238 (426)
                      ..|-|++..|.||||+|.-..-+....+ +...+  |+..........+++.+-    .+.+..  ....+...      
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~~~g-~~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a~   81 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRALGHG-YRVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAAA   81 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCC-CeEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHHH
Confidence            4678888889999999998887765432 33222  233222344444444431    000110  00011111      


Q ss_pred             -HHHHHHHHHhcCCeEEEEEeCCCCc-----cChhhhcCCCCCCCCCeEEEEeecchh
Q 044858          239 -RAWRLLEQLKKETKILIILDDIWGS-----LDLEAIGIPLADDNGGCKVLLTARSQD  290 (426)
Q Consensus       239 -~~~~l~~~l~~~k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~s~iivTtr~~~  290 (426)
                       ......+.+..+.-=|||||++-..     ...+.+...+.....+.-+|+|.|+..
T Consensus        82 ~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          82 EGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence             1122333444455569999998533     233444444444445778999999965

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.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.66  E-value=0.017  Score=56.76  Aligned_cols=59  Identities=27%  Similarity=0.380  Sum_probs=38.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKI  231 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~  231 (426)
                      ++.+|.++|+.|+||||++..++......+ + .+..++... .+...+.++.+..+++.+.
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~g-~-kV~lV~~D~~R~aa~eQL~~la~~~gvp~  153 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKG-L-KVGLVAADTYRPAAYDQLKQLAEKIGVPF  153 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHcC-C-eEEEecCCCCCHHHHHHHHHHHHHcCCcE
Confidence            467899999999999999999998776532 2 333343322 1223455666667766543

>CHL00206 ycf2 Ycf2; Provisional

Probab=96.66  E-value=0.025  Score=63.67  Aligned_cols=29  Identities=28%  Similarity=0.208  Sum_probs=24.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .++=|.++|++|+|||.||+.++.+..+.
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~es~VP 1657 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATNSYVP 1657 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHhcCCc
Confidence            35568899999999999999999987653

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.66  E-value=0.0027  Score=52.26  Aligned_cols=28  Identities=36%  Similarity=0.507  Sum_probs=24.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENN  200 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~  200 (426)
                      .-|.|+|++|+||||++..+.+..+..+
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g   33 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKG   33 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHHHhcC
Confidence            4589999999999999999998887643

>PRK05439 pantothenate kinase; Provisional

Probab=96.66  E-value=0.016  Score=54.13  Aligned_cols=81  Identities=16%  Similarity=0.152  Sum_probs=43.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH--HHHHhCCCccccCcHHHHHHHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE--IAEKLGLKIDQESESVRAWRLLEQL  247 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~--i~~~l~~~~~~~~~~~~~~~l~~~l  247 (426)
                      +.+-+|+|.|.+|+||||+|+.+............+.-++...-......+..  ++..-+  .+..-+...+...+..+
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~~~~~~~~v~vi~~DdFy~~~~~l~~~~l~~~kg--~Pes~D~~~l~~~L~~L  161 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLSRWPEHPKVELVTTDGFLYPNAVLEERGLMKRKG--FPESYDMRALLRFLSDV  161 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHhhCCCCceEEEeccccccCHHHHhhhhccccCC--CcccccHHHHHHHHHHH
Confidence            45678999999999999999998876543211122334444433333322221  111111  12223444555666666


Q ss_pred             hcCCe
Q 044858          248 KKETK  252 (426)
Q Consensus       248 ~~~k~  252 (426)
                      ..++.
T Consensus       162 k~G~~  166 (311)
T PRK05439        162 KSGKP  166 (311)
T ss_pred             HcCCC
Confidence            66654

>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=96.66  E-value=0.0016  Score=52.39  Aligned_cols=22  Identities=45%  Similarity=0.782  Sum_probs=20.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.|.|..|+||||+|+.+.+..
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            6899999999999999999884

...

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.65  E-value=0.021  Score=58.25  Aligned_cols=50  Identities=14%  Similarity=0.213  Sum_probs=38.2

Q ss_pred             CCcccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          148 QDFMHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .....++|....+.++.+.+.  ......|.|+|..|+|||++|+.+++...
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~  244 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSP  244 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCC
Confidence            345678898888887777665  22234578999999999999999998654

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.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.64  E-value=0.003  Score=55.99  Aligned_cols=24  Identities=21%  Similarity=0.293  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+++.|+|+.|.||||+.+.+...
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~   52 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALI   52 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHH
Confidence            478999999999999999998743

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

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.64  E-value=0.017  Score=52.04  Aligned_cols=86  Identities=21%  Similarity=0.217  Sum_probs=53.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----------------
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----------------  233 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----------------  233 (426)
                      ...++.|.|.+|+|||+|+.++......+  -..++|++....  +.++.+++ .+++.....                 
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~   98 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ--GKKVYVITTENT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGF   98 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC--CCEEEEEEcCCC--HHHHHHHH-HHCCCChhHHHhCCCceEEecccccc
Confidence            34689999999999999999996554322  346778887654  45555553 334322110                 


Q ss_pred             ----cCcHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          234 ----ESESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       234 ----~~~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                          .........+.+.+.+.+.-++|+|.+-
T Consensus        99 ~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         99 EWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             ccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence                1112344455555554456789999975

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.64  E-value=0.013  Score=56.52  Aligned_cols=90  Identities=14%  Similarity=0.111  Sum_probs=54.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC--ccceEEEEEecCC-cCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENN--LFEKVISSRVSQT-PQIKEIQREIAEKLGLKIDQESESVRAWRLLEQL  247 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~--~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l  247 (426)
                      .+.+|.++|+.|+||||.+..+........  .-..+..++.... ....+-++...+.++.+.........+...+..+
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~  252 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQS  252 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHh
Confidence            457899999999999999999987655321  1224445555432 1223336666666776654433333333333333


Q ss_pred             hcCCeEEEEEeCCCC
Q 044858          248 KKETKILIILDDIWG  262 (426)
Q Consensus       248 ~~~k~~LlVlDdv~~  262 (426)
                        .+.=++++|....
T Consensus       253 --~~~DlVLIDTaGr  265 (388)
T PRK12723        253 --KDFDLVLVDTIGK  265 (388)
T ss_pred             --CCCCEEEEcCCCC
Confidence              2345888998853

>PRK14974 cell division protein FtsY; Provisional

Probab=96.64  E-value=0.021  Score=54.03  Aligned_cols=90  Identities=26%  Similarity=0.285  Sum_probs=50.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc--CHHHHHHHHHHHhCCCcccc----CcHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP--QIKEIQREIAEKLGLKIDQE----SESVRAWRLL  244 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~--~~~~il~~i~~~l~~~~~~~----~~~~~~~~l~  244 (426)
                      ++.+|.++|+.|+||||++..++...... .+. ++.+.. ..+  ...+-++.....++.+....    +....+....
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~~-g~~-V~li~~-Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai  215 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKN-GFS-VVIAAG-DTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAI  215 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc-CCe-EEEecC-CcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHH
Confidence            46799999999999999999888776543 232 333332 222  22334556667776543211    1112222222


Q ss_pred             HHHhcCCeEEEEEeCCCCc
Q 044858          245 EQLKKETKILIILDDIWGS  263 (426)
Q Consensus       245 ~~l~~~k~~LlVlDdv~~~  263 (426)
                      +.......=++++|-....
T Consensus       216 ~~~~~~~~DvVLIDTaGr~  234 (336)
T PRK14974        216 EHAKARGIDVVLIDTAGRM  234 (336)
T ss_pred             HHHHhCCCCEEEEECCCcc
Confidence            2222222238999988543

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.63  E-value=0.0071  Score=58.21  Aligned_cols=86  Identities=23%  Similarity=0.275  Sum_probs=53.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc--CcHHHHHHHHHHHhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE--SESVRAWRLLEQLKK  249 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~--~~~~~~~~l~~~l~~  249 (426)
                      -.++.|.|.+|+|||||+.++.......  -..++|++...  +..++. .-+..++...+..  .....+..+.+.+..
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~--g~~VlYvs~EE--s~~qi~-~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~  156 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKR--GGKVLYVSGEE--SPEQIK-LRADRLGISTENLYLLAETNLEDILASIEE  156 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCc--CHHHHH-HHHHHcCCCcccEEEEccCcHHHHHHHHHh
Confidence            3589999999999999999998776543  24567776543  333332 2234555432221  011123455555555


Q ss_pred             CCeEEEEEeCCCC
Q 044858          250 ETKILIILDDIWG  262 (426)
Q Consensus       250 ~k~~LlVlDdv~~  262 (426)
                      .+.-+||+|.+..
T Consensus       157 ~~~~lVVIDSIq~  169 (372)
T cd01121         157 LKPDLVIIDSIQT  169 (372)
T ss_pred             cCCcEEEEcchHH
Confidence            5778999999853

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.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.63  E-value=0.025  Score=51.03  Aligned_cols=143  Identities=20%  Similarity=0.176  Sum_probs=75.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-----CcCHHHHHHHHHHHhCCCccc-------cCcHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-----TPQIKEIQREIAEKLGLKIDQ-------ESESV  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-----~~~~~~il~~i~~~l~~~~~~-------~~~~~  238 (426)
                      +-.+++|+|.+|+|||||++.+..-.+..  . ..++....+     .....+-..+++..++.+.+.       .+...
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~pt--~-G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQ  114 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEEPT--S-GEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQ  114 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcCCC--C-ceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchh
Confidence            34689999999999999999998776532  2 222222111     222334455666666644321       11111


Q ss_pred             HHH-HHHHHHhcCCeEEEEEeCCCCccCh---hhhcCCCC--CCCCCeEEEEeecchhhhhccCCceeeEEccC-CCHHH
Q 044858          239 RAW-RLLEQLKKETKILIILDDIWGSLDL---EAIGIPLA--DDNGGCKVLLTARSQDVLSCEMDCQQNFVVDV-LNDKE  311 (426)
Q Consensus       239 ~~~-~l~~~l~~~k~~LlVlDdv~~~~~~---~~l~~~l~--~~~~~s~iivTtr~~~va~~~~~~~~~~~l~~-L~~~e  311 (426)
                      ... .+.+.+ .-++-++|.|+.-+..+.   ..+...+.  ....|...+..|.+-.++........+..+.. .+...
T Consensus       115 rQRi~IARAL-al~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~isdri~VMy~G~iVE~g~  193 (268)
T COG4608         115 RQRIGIARAL-ALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYISDRIAVMYLGKIVEIGP  193 (268)
T ss_pred             hhhHHHHHHH-hhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhhhcccEEEEecCceeEecC
Confidence            222 223333 347899999998655332   11111111  12236678888888877643333333333333 23344


Q ss_pred             HHHHHH
Q 044858          312 AWSLFK  317 (426)
Q Consensus       312 ~~~Lf~  317 (426)
                      ..++|.
T Consensus       194 ~~~~~~  199 (268)
T COG4608         194 TEEVFS  199 (268)
T ss_pred             HHHHhh
Confidence            445554

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.61  E-value=0.0059  Score=52.71  Aligned_cols=24  Identities=25%  Similarity=0.239  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.|+|++|+||||+|+.+.....
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~~   24 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENFG   24 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHcC
Confidence            578999999999999999988653

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.

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

Probab=96.61  E-value=0.011  Score=51.42  Aligned_cols=50  Identities=22%  Similarity=0.331  Sum_probs=32.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCcc--------ceEEEEEecCCcCHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLF--------EKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f--------~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .+..|.|++|+|||+++.++.........|        ..++|++....  ..++.+.+.
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~--~~~~~~rl~   90 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS--ESQIARRLR   90 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS---HHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC--HHHHHHHHH
Confidence            478899999999999999998876643333        24667766554  334444443

>TIGR00959 ffh signal recognition particle protein

Probab=96.60  E-value=0.017  Score=56.51  Aligned_cols=27  Identities=30%  Similarity=0.311  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++.++.++|+.|+||||++..++....
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~  124 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLK  124 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            467899999999999999988887754

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.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=96.60  E-value=0.16  Score=47.45  Aligned_cols=164  Identities=13%  Similarity=0.040  Sum_probs=88.9

Q ss_pred             HHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHh--------hhcCccceEEEEEe-cCCcCHHHHHHHHHHHhCCCc
Q 044858          162 GILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQA--------KENNLFEKVISSRV-SQTPQIKEIQREIAEKLGLKI  231 (426)
Q Consensus       162 ~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~--------~~~~~f~~~~wv~v-~~~~~~~~il~~i~~~l~~~~  231 (426)
                      .+...+..++ .++..++|..|.||+++|..+.+..        ....|-+...++.. +...+..++. ++.+.+....
T Consensus         7 ~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir-~l~~~~~~~~   85 (299)
T PRK07132          7 FLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFL-SAINKLYFSS   85 (299)
T ss_pred             HHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHH-HHHHHhccCC
Confidence            3444444444 4567799999999999999998875        11222222333321 1222333322 2332221110


Q ss_pred             cccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecc-hhhhhccCCceeeEEccCCC
Q 044858          232 DQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARS-QDVLSCEMDCQQNFVVDVLN  308 (426)
Q Consensus       232 ~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~~~~~~~~~l~~L~  308 (426)
                                     ...+.+=++|+|++....  ..+.+...+..-..++.+|++|.+ ..+.....+....+++.+++
T Consensus        86 ---------------~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~  150 (299)
T PRK07132         86 ---------------FVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPD  150 (299)
T ss_pred             ---------------cccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCC
Confidence                           011467788899986542  234444344333346666665543 44433234556899999999


Q ss_pred             HHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHH
Q 044858          309 DKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       309 ~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                      +++..+.+... +   .+   .+.+..++...+|.=-|+.
T Consensus       151 ~~~l~~~l~~~-~---~~---~~~a~~~a~~~~~~~~a~~  183 (299)
T PRK07132        151 QQKILAKLLSK-N---KE---KEYNWFYAYIFSNFEQAEK  183 (299)
T ss_pred             HHHHHHHHHHc-C---CC---hhHHHHHHHHcCCHHHHHH
Confidence            99998877654 1   11   1235556666666323443

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

Probab=96.59  E-value=0.0012  Score=54.20  Aligned_cols=27  Identities=22%  Similarity=0.313  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...|.|+|..|+||+++|+.++.....
T Consensus        21 ~~pvli~GE~GtGK~~~A~~lh~~~~~   47 (138)
T PF14532_consen   21 SSPVLITGEPGTGKSLLARALHRYSGR   47 (138)
T ss_dssp             SS-EEEECCTTSSHHHHHHCCHHTTTT
T ss_pred             CCcEEEEcCCCCCHHHHHHHHHhhcCc
Confidence            345789999999999999999886553

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

Probab=96.59  E-value=0.0022  Score=56.10  Aligned_cols=25  Identities=40%  Similarity=0.648  Sum_probs=23.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ||+|.|++|+||||+|+.+......
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~   25 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNK   25 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCc
Confidence            6999999999999999999988764

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 ....

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.59  E-value=0.011  Score=50.36  Aligned_cols=80  Identities=16%  Similarity=0.121  Sum_probs=46.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC-CeE
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE-TKI  253 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~-k~~  253 (426)
                      +.|.|.+|+|||++|.++....     ....+++.-...++. ++.+.|.+.-..........+....+.+.+.+. +.-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~-----~~~~~y~at~~~~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~   75 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAEL-----GGPVTYIATAEAFDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGD   75 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhc-----CCCeEEEEccCcCCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCC
Confidence            6799999999999999997651     235667766666653 355554442222222222222223344444221 234


Q ss_pred             EEEEeCC
Q 044858          254 LIILDDI  260 (426)
Q Consensus       254 LlVlDdv  260 (426)
                      .+++|.+
T Consensus        76 ~VLIDcl   82 (169)
T cd00544          76 VVLIDCL   82 (169)
T ss_pred             EEEEEcH
Confidence            7999987

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.

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

Probab=96.59  E-value=0.024  Score=53.00  Aligned_cols=135  Identities=20%  Similarity=0.295  Sum_probs=73.3

Q ss_pred             ccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHH-HHhhhcCccceEEE----EEecCCc---------CHHH
Q 044858          153 FESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVG-RQAKENNLFEKVIS----SRVSQTP---------QIKE  218 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~-~~~~~~~~f~~~~w----v~v~~~~---------~~~~  218 (426)
                      +-+|..+-.--++.|.++....|.+.|.+|+|||.||-... ....++..|..++-    +.++++.         .+.-
T Consensus       226 i~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG~eEeKm~P  305 (436)
T COG1875         226 IRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPGTEEEKMGP  305 (436)
T ss_pred             cCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCCchhhhccc
Confidence            44577777777888889999999999999999998886643 22223344554332    1222211         1111


Q ss_pred             HHHHHHH---HhCCCccccCcHHHHHHHH----------HHHhcCC---eEEEEEeCCCCccChhhhcCCCCCCCCCeEE
Q 044858          219 IQREIAE---KLGLKIDQESESVRAWRLL----------EQLKKET---KILIILDDIWGSLDLEAIGIPLADDNGGCKV  282 (426)
Q Consensus       219 il~~i~~---~l~~~~~~~~~~~~~~~l~----------~~l~~~k---~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~i  282 (426)
                      .++.|..   .+..... .. ...+..+.          .++ +|+   .-++++|+..+... ..++..+...+.||||
T Consensus       306 Wmq~i~DnLE~L~~~~~-~~-~~~l~~~l~~~~iev~alt~I-RGRSl~~~FiIIDEaQNLTp-heikTiltR~G~GsKI  381 (436)
T COG1875         306 WMQAIFDNLEVLFSPNE-PG-DRALEEILSRGRIEVEALTYI-RGRSLPDSFIIIDEAQNLTP-HELKTILTRAGEGSKI  381 (436)
T ss_pred             hHHHHHhHHHHHhcccc-cc-hHHHHHHHhccceeeeeeeee-cccccccceEEEehhhccCH-HHHHHHHHhccCCCEE
Confidence            2223322   2221111 11 11222211          111 122   35899999987632 2233334456789999


Q ss_pred             EEeecchhh
Q 044858          283 LLTARSQDV  291 (426)
Q Consensus       283 ivTtr~~~v  291 (426)
                      +.|.-..++
T Consensus       382 Vl~gd~aQi  390 (436)
T COG1875         382 VLTGDPAQI  390 (436)
T ss_pred             EEcCCHHHc
Confidence            998765543

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=96.58  E-value=0.013  Score=49.69  Aligned_cols=25  Identities=36%  Similarity=0.432  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...+.|.||+|+|||||++.++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3578999999999999999999876

>PRK10867 signal recognition particle protein; Provisional

Probab=96.58  E-value=0.016  Score=56.84  Aligned_cols=29  Identities=28%  Similarity=0.409  Sum_probs=23.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..+.+|.++|++|+||||++..+......
T Consensus        98 ~~p~vI~~vG~~GsGKTTtaakLA~~l~~  126 (433)
T PRK10867         98 KPPTVIMMVGLQGAGKTTTAGKLAKYLKK  126 (433)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHH
Confidence            34679999999999999988888766543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.58  E-value=0.011  Score=57.95  Aligned_cols=87  Identities=20%  Similarity=0.225  Sum_probs=49.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh-hcCccceEEEEEecCCc-CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK-ENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~-~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      .+++.++|++|+||||++..+..... ... -..+..++..... ...+-++...+.++.+.............+..+. 
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~-g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~-  298 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYG-KKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLR-  298 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhC-
Confidence            35899999999999999998877654 222 2345556553321 1223344445555555433222233333333332 


Q ss_pred             CCeEEEEEeCCC
Q 044858          250 ETKILIILDDIW  261 (426)
Q Consensus       250 ~k~~LlVlDdv~  261 (426)
                       ..=+|++|..-
T Consensus       299 -~~DlVlIDt~G  309 (424)
T PRK05703        299 -DCDVILIDTAG  309 (424)
T ss_pred             -CCCEEEEeCCC
Confidence             24588889763

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=96.56  E-value=0.13  Score=45.76  Aligned_cols=180  Identities=15%  Similarity=0.191  Sum_probs=95.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      .+++-+.++|++|.|||-||+.|++...       +.|+.||..    ++.+..+..         ....+..++--...
T Consensus       179 aQPKGvlLygppgtGktLlaraVahht~-------c~firvsgs----elvqk~ige---------gsrmvrelfvmare  238 (404)
T KOG0728|consen  179 AQPKGVLLYGPPGTGKTLLARAVAHHTD-------CTFIRVSGS----ELVQKYIGE---------GSRMVRELFVMARE  238 (404)
T ss_pred             CCCcceEEecCCCCchhHHHHHHHhhcc-------eEEEEechH----HHHHHHhhh---------hHHHHHHHHHHHHh
Confidence            3667788999999999999999987543       346667653    222222110         11223334333344


Q ss_pred             CCeEEEEEeCCCCccC----------------hhhhcCCCC--CCCCCeEEEEeecchhhhh----ccCCceeeEEccCC
Q 044858          250 ETKILIILDDIWGSLD----------------LEAIGIPLA--DDNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVL  307 (426)
Q Consensus       250 ~k~~LlVlDdv~~~~~----------------~~~l~~~l~--~~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L  307 (426)
                      .-+.+|++|++++...                .-++...+.  ...++.+||..|..-++..    ....-...++..+=
T Consensus       239 hapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p  318 (404)
T KOG0728|consen  239 HAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPP  318 (404)
T ss_pred             cCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCC
Confidence            5688999999865410                011112221  2235678888776655431    12223456777776


Q ss_pred             CHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhh--cC----CHHHHHHHHHHH
Q 044858          308 NDKEAWSLFKKMTG--DCIENGELKSVVTEVVKECAGLPIAIVPIAKALK--NK----SPYEWRNALRQL  369 (426)
Q Consensus       308 ~~~e~~~Lf~~~~~--~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~--~~----~~~~w~~~l~~l  369 (426)
                      +++.-.++++-+..  +-..--++..+++++.-..|.--.++-.=|+..+  .+    +.++++-+....
T Consensus       319 ~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~vcteagm~alrerrvhvtqedfemav~kv  388 (404)
T KOG0728|consen  319 NEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKV  388 (404)
T ss_pred             CHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhhhhhhhhHHHHHHhhccccHHHHHHHHHHH
Confidence            66666666654432  2222344555555554433333333333344332  22    566666555543

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.54  E-value=0.0024  Score=56.52  Aligned_cols=27  Identities=30%  Similarity=0.444  Sum_probs=24.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+..+|+|.|++|+|||||++.+....
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            356799999999999999999999876

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.53  E-value=0.0045  Score=60.86  Aligned_cols=50  Identities=18%  Similarity=0.211  Sum_probs=40.3

Q ss_pred             cccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc
Q 044858          152 HFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE  203 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~  203 (426)
                      .++||++.++.+...+..+.  -+.|.|++|+|||+||+.+.........|.
T Consensus        21 ~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~~~~~~F~   70 (498)
T PRK13531         21 GLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQNARAFE   70 (498)
T ss_pred             hccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHhcccCcce
Confidence            47899999999988887654  488999999999999999998765433343

>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=96.53  E-value=0.011  Score=52.18  Aligned_cols=85  Identities=22%  Similarity=0.469  Sum_probs=52.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCC-------CccccCcHH------
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGL-------KIDQESESV------  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~-------~~~~~~~~~------  238 (426)
                      .-+.|.|.+|+|||+|+.++.+....    +..+++.+++. ..+.++.+++...-..       ....++...      
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~~~----d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~   91 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQDA----DVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPY   91 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHCTT----TEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhcccc----cceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhc
Confidence            56899999999999999999988753    34477777654 4566666666443111       111111111      


Q ss_pred             HHHHHHHHHh-cCCeEEEEEeCCC
Q 044858          239 RAWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       239 ~~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                      ..-.+-+++. ++++.|+++||+-
T Consensus        92 ~a~t~AEyfrd~G~dVlli~Dslt  115 (215)
T PF00006_consen   92 TALTIAEYFRDQGKDVLLIIDSLT  115 (215)
T ss_dssp             HHHHHHHHHHHTTSEEEEEEETHH
T ss_pred             cchhhhHHHhhcCCceeehhhhhH
Confidence            1112223332 5899999999984

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 ....

>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=96.51  E-value=0.0023  Score=58.89  Aligned_cols=88  Identities=22%  Similarity=0.309  Sum_probs=47.4

Q ss_pred             HHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH-hCCCccccCcHHH
Q 044858          161 KGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK-LGLKIDQESESVR  239 (426)
Q Consensus       161 ~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~-l~~~~~~~~~~~~  239 (426)
                      ..+++.+...+ +-+.++|+.|+|||++++...+...... | ...-++.+...+...++ .++++ +.......     
T Consensus        23 ~~ll~~l~~~~-~pvLl~G~~GtGKT~li~~~l~~l~~~~-~-~~~~~~~s~~Tts~~~q-~~ie~~l~k~~~~~-----   93 (272)
T PF12775_consen   23 SYLLDLLLSNG-RPVLLVGPSGTGKTSLIQNFLSSLDSDK-Y-LVITINFSAQTTSNQLQ-KIIESKLEKRRGRV-----   93 (272)
T ss_dssp             HHHHHHHHHCT-EEEEEESSTTSSHHHHHHHHHHCSTTCC-E-EEEEEES-TTHHHHHHH-HCCCTTECECTTEE-----
T ss_pred             HHHHHHHHHcC-CcEEEECCCCCchhHHHHhhhccCCccc-c-ceeEeeccCCCCHHHHH-HHHhhcEEcCCCCC-----
Confidence            34555555444 3468999999999999999887654322 2 13344555544444333 33221 11000000     


Q ss_pred             HHHHHHHHhcCCeEEEEEeCCCC
Q 044858          240 AWRLLEQLKKETKILIILDDIWG  262 (426)
Q Consensus       240 ~~~l~~~l~~~k~~LlVlDdv~~  262 (426)
                          + .-..+|++++++||+.-
T Consensus        94 ----~-gP~~~k~lv~fiDDlN~  111 (272)
T PF12775_consen   94 ----Y-GPPGGKKLVLFIDDLNM  111 (272)
T ss_dssp             ----E-EEESSSEEEEEEETTT-
T ss_pred             ----C-CCCCCcEEEEEecccCC
Confidence                0 00136899999999953

>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=96.51  E-value=0.004  Score=51.83  Aligned_cols=28  Identities=32%  Similarity=0.387  Sum_probs=24.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ..+|.|+|.+|+||||||+.+.+.....
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~   29 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFAR   29 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4689999999999999999999998764

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 ....

>PRK08233 hypothetical protein; Provisional

Probab=96.50  E-value=0.0024  Score=55.07  Aligned_cols=26  Identities=31%  Similarity=0.446  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|+|.|.+|+||||||..+.....
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            46899999999999999999998764

>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=96.50  E-value=0.0025  Score=45.30  Aligned_cols=23  Identities=35%  Similarity=0.592  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +|.|.|..|+||||+++.+.+..
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999885

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.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=96.49  E-value=0.017  Score=61.21  Aligned_cols=180  Identities=20%  Similarity=0.256  Sum_probs=89.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh--hcCccc-----------eEEEEEecCCcCHHHHHHHHHHHhCCCccccCcH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK--ENNLFE-----------KVISSRVSQTPQIKEIQREIAEKLGLKIDQESES  237 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~--~~~~f~-----------~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~  237 (426)
                      +.+++.|+|+.+.||||+.+.+.-..-  ..+.|-           ..++..++...++..-+.....          ..
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~~i~~~ig~~~si~~~lStfS~----------~m  395 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSG----------HM  395 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccceEEEecCCccchhhchhHHHH----------HH
Confidence            456889999999999999999864421  111110           1122333322222211111110          01


Q ss_pred             HHHHHHHHHHhcCCeEEEEEeCCCCccChh---hh----cCCCCCCCCCeEEEEeecchhhhhccCCce--eeEEccCCC
Q 044858          238 VRAWRLLEQLKKETKILIILDDIWGSLDLE---AI----GIPLADDNGGCKVLLTARSQDVLSCEMDCQ--QNFVVDVLN  308 (426)
Q Consensus       238 ~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~---~l----~~~l~~~~~~s~iivTtr~~~va~~~~~~~--~~~~l~~L~  308 (426)
                      .....+...+  ..+-|+++|++-...+..   .+    ...+  ...|+.+|+||.............  ....+. ++
T Consensus       396 ~~~~~Il~~~--~~~sLvLlDE~~~GtDp~eg~ala~aile~l--~~~~~~vIitTH~~el~~~~~~~~~v~~~~~~-~d  470 (782)
T PRK00409        396 TNIVRILEKA--DKNSLVLFDELGAGTDPDEGAALAISILEYL--RKRGAKIIATTHYKELKALMYNREGVENASVE-FD  470 (782)
T ss_pred             HHHHHHHHhC--CcCcEEEecCCCCCCCHHHHHHHHHHHHHHH--HHCCCEEEEECChHHHHHHHhcCCCeEEEEEE-Ee
Confidence            1122233333  357899999997543321   22    1122  124788999999977652111111  111111 11


Q ss_pred             HHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHHHhh
Q 044858          309 DKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKR  371 (426)
Q Consensus       309 ~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~l~~  371 (426)
                      .+ ......+...+...    ...|-.|++.+ |+|-.|..-|..+.......++.++..+..
T Consensus       471 ~~-~l~~~Ykl~~G~~g----~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~l~~  527 (782)
T PRK00409        471 EE-TLRPTYRLLIGIPG----KSNAFEIAKRL-GLPENIIEEAKKLIGEDKEKLNELIASLEE  527 (782)
T ss_pred             cC-cCcEEEEEeeCCCC----CcHHHHHHHHh-CcCHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            11 11110111111111    23466777777 899999888888876555566666666543

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.49  E-value=0.034  Score=56.15  Aligned_cols=95  Identities=27%  Similarity=0.320  Sum_probs=58.9

Q ss_pred             CcccccchHH---HHHHHHHHhccCC---------ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          149 DFMHFESRKS---TLKGILDALSNRN---------FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       149 ~~~~~~gR~~---~~~~l~~~l~~~~---------~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .+.+..|.++   ++.++++.|.++.         ++=+.++|++|.|||.||+.+.....+.  |     .+.|...- 
T Consensus       148 ~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VP--F-----f~iSGS~F-  219 (596)
T COG0465         148 TFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP--F-----FSISGSDF-  219 (596)
T ss_pred             ChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCC--c-----eeccchhh-
Confidence            3455667654   5556777776442         4567899999999999999999988775  2     22222110 


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      .+    +.    ..    -....+..++..-++.-+|++++|.++..
T Consensus       220 Ve----mf----VG----vGAsRVRdLF~qAkk~aP~IIFIDEiDAv  254 (596)
T COG0465         220 VE----MF----VG----VGASRVRDLFEQAKKNAPCIIFIDEIDAV  254 (596)
T ss_pred             hh----hh----cC----CCcHHHHHHHHHhhccCCCeEEEehhhhc
Confidence            00    00    00    01234555666655566899999998643

>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=96.48  E-value=0.0069  Score=54.28  Aligned_cols=61  Identities=23%  Similarity=0.285  Sum_probs=37.8

Q ss_pred             HHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHH
Q 044858          160 LKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQ  220 (426)
Q Consensus       160 ~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il  220 (426)
                      ..++++.+.  .++..+|+|+|++|+|||||...+......+++=-.++-|.-|.+++-..++
T Consensus        15 ~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tGGAlL   77 (266)
T PF03308_consen   15 ARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTGGALL   77 (266)
T ss_dssp             HHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC---SS
T ss_pred             HHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCCCccc
Confidence            344555444  3466799999999999999999999888765444445555556666544443

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.

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

Probab=96.48  E-value=0.35  Score=45.47  Aligned_cols=47  Identities=19%  Similarity=0.181  Sum_probs=35.0

Q ss_pred             eEEccCCCHHHHHHHHHHhhCCCCC--CCchHHHHHHHHHHcCCchHHH
Q 044858          301 NFVVDVLNDKEAWSLFKKMTGDCIE--NGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       301 ~~~l~~L~~~e~~~Lf~~~~~~~~~--~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      ++++++++.+|+..++.........  ....+...+++.-..+|+|.-+
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            7899999999999999888752221  1344556777788889999654

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).

>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=96.46  E-value=0.0028  Score=52.23  Aligned_cols=24  Identities=33%  Similarity=0.510  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.++|++|+||||+|+.+.....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Confidence            588999999999999999986654

...

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.46  E-value=0.006  Score=52.31  Aligned_cols=25  Identities=32%  Similarity=0.442  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|.|.|++|+||||+|+.+.+....
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i   26 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGL   26 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4789999999999999999998543

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.46  E-value=0.032  Score=52.27  Aligned_cols=29  Identities=38%  Similarity=0.489  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .++-|.++||+|.|||-||+.+..+....
T Consensus       126 p~kGiLL~GPpG~GKTmlAKA~Akeaga~  154 (386)
T KOG0737|consen  126 PPKGILLYGPPGTGKTMLAKAIAKEAGAN  154 (386)
T ss_pred             CCccceecCCCCchHHHHHHHHHHHcCCC
Confidence            45678899999999999999999887644

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=96.45  E-value=0.0053  Score=55.81  Aligned_cols=62  Identities=29%  Similarity=0.419  Sum_probs=46.4

Q ss_pred             HHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          161 KGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       161 ~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .+++..+.  .++..+|+|+|.+|+|||||...+......+++=..++-|.-|.+++-..++-+
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiLGD  101 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILGD  101 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCcccccc
Confidence            34444443  456789999999999999999999999887766566667777777765555543

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.44  E-value=0.027  Score=51.34  Aligned_cols=97  Identities=20%  Similarity=0.241  Sum_probs=59.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh--cCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE--NNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~--~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      +-+.|.|..|+|||+|+.++.+....  ++.-+.++++-+.+.. +..++..++...-...       ...++...    
T Consensus        70 QR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a  149 (276)
T cd01135          70 QKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIIT  149 (276)
T ss_pred             CEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHH
Confidence            46899999999999999998877541  1224677888887654 5667777665542211       11111111    


Q ss_pred             --HHHHHHHHHh-c-CCeEEEEEeCCCCc-cChhhh
Q 044858          239 --RAWRLLEQLK-K-ETKILIILDDIWGS-LDLEAI  269 (426)
Q Consensus       239 --~~~~l~~~l~-~-~k~~LlVlDdv~~~-~~~~~l  269 (426)
                        ....+-+++. + ++++|+++||+-.. ....++
T Consensus       150 ~~~a~aiAEyfrd~~g~~VLl~~D~ltr~A~A~rEi  185 (276)
T cd01135         150 PRMALTTAEYLAYEKGKHVLVILTDMTNYAEALREI  185 (276)
T ss_pred             HHHHHHHHHHHHhccCCeEEEEEcChhHHHHHHHHH
Confidence              1223445554 2 68999999998543 334443

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.

>PTZ00301 uridine kinase; Provisional

Probab=96.43  E-value=0.003  Score=55.76  Aligned_cols=26  Identities=27%  Similarity=0.510  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|+|.|.+|+||||||+.+.+...
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l~   28 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSELM   28 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHHH
Confidence            46899999999999999999987764

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.43  E-value=0.011  Score=50.87  Aligned_cols=26  Identities=31%  Similarity=0.406  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|.|+.|+|||||++.+.....
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGDLK   53 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccCC
Confidence            35799999999999999999987643

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.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.42  E-value=0.069  Score=54.25  Aligned_cols=152  Identities=14%  Similarity=0.200  Sum_probs=83.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .-|.++|++|+|||-||..+......+       +++|-.+    +++...+   |.      ...-+..++.....-++
T Consensus       702 ~giLLyGppGcGKT~la~a~a~~~~~~-------fisvKGP----ElL~KyI---Ga------SEq~vR~lF~rA~~a~P  761 (952)
T KOG0735|consen  702 TGILLYGPPGCGKTLLASAIASNSNLR-------FISVKGP----ELLSKYI---GA------SEQNVRDLFERAQSAKP  761 (952)
T ss_pred             cceEEECCCCCcHHHHHHHHHhhCCee-------EEEecCH----HHHHHHh---cc------cHHHHHHHHHHhhccCC
Confidence            358899999999999999998776543       5555443    3333322   21      12345567777777899


Q ss_pred             EEEEEeCCCCccC-------------hhhhcCCCC--CCCCCeEEEE-eecchhhhh---ccCCceeeEEccCCCHHHHH
Q 044858          253 ILIILDDIWGSLD-------------LEAIGIPLA--DDNGGCKVLL-TARSQDVLS---CEMDCQQNFVVDVLNDKEAW  313 (426)
Q Consensus       253 ~LlVlDdv~~~~~-------------~~~l~~~l~--~~~~~s~iiv-Ttr~~~va~---~~~~~~~~~~l~~L~~~e~~  313 (426)
                      |+|.||+.++...             .+.+...+.  .+-.|..|+- |||..-+-+   +...-.+.+.-+.=++.+-.
T Consensus       762 CiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl  841 (952)
T KOG0735|consen  762 CILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERL  841 (952)
T ss_pred             eEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHH
Confidence            9999999976511             222322221  1224555554 555543321   11111223333333556666


Q ss_pred             HHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH
Q 044858          314 SLFKKMTGDCIENGELKSVVTEVVKECAGLPIA  346 (426)
Q Consensus       314 ~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla  346 (426)
                      ++|+........+.  ....+.++.+++|.--|
T Consensus       842 ~il~~ls~s~~~~~--~vdl~~~a~~T~g~tgA  872 (952)
T KOG0735|consen  842 EILQVLSNSLLKDT--DVDLECLAQKTDGFTGA  872 (952)
T ss_pred             HHHHHHhhccCCcc--ccchHHHhhhcCCCchh
Confidence            77776654211111  11245677788876543

>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=96.40  E-value=0.02  Score=48.54  Aligned_cols=26  Identities=19%  Similarity=0.266  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|.|||||++.+.....
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGLWP   52 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            35799999999999999999987643

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

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.40  E-value=0.032  Score=53.03  Aligned_cols=44  Identities=16%  Similarity=0.191  Sum_probs=29.0

Q ss_pred             cchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          154 ESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       154 ~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|+...+.++.+.+.  .....-|.|+|..|+||+++|+.+++...
T Consensus         2 iG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~   47 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSK   47 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcC
Confidence            344444444444433  12234478999999999999999987654

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

>PRK06762 hypothetical protein; Provisional

Probab=96.40  E-value=0.0031  Score=53.53  Aligned_cols=25  Identities=32%  Similarity=0.476  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +.+|.|+|++|+||||+|+.+.+..
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998876

>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=96.39  E-value=0.022  Score=49.07  Aligned_cols=116  Identities=22%  Similarity=0.227  Sum_probs=60.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec--CCcCHHHHH------HHHHHHhCCCcc------ccCcH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS--QTPQIKEIQ------REIAEKLGLKID------QESES  237 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~--~~~~~~~il------~~i~~~l~~~~~------~~~~~  237 (426)
                      -.+++|.|+.|+|||||.+.+......   ....+++.-.  ...+.....      .++++.++....      ..+..
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~~~~---~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G  101 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGLLKP---SSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSGG  101 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC---CCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHH
Confidence            358999999999999999999876432   2333333211  111222211      124455543211      11111


Q ss_pred             -HHHHHHHHHHhcCCeEEEEEeCCCCccC---hhhhcCCCCC--CCCCeEEEEeecchhh
Q 044858          238 -VRAWRLLEQLKKETKILIILDDIWGSLD---LEAIGIPLAD--DNGGCKVLLTARSQDV  291 (426)
Q Consensus       238 -~~~~~l~~~l~~~k~~LlVlDdv~~~~~---~~~l~~~l~~--~~~~s~iivTtr~~~v  291 (426)
                       ...-.+.+.+.. .+-++++|+.-..-+   ...+...+..  ...+..||++|.+...
T Consensus       102 ~~qrl~laral~~-~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~  160 (180)
T cd03214         102 ERQRVLLARALAQ-EPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNL  160 (180)
T ss_pred             HHHHHHHHHHHhc-CCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH
Confidence             112234444443 678999999864422   2222222211  1125678888887654

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.

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.39  E-value=0.03  Score=51.35  Aligned_cols=87  Identities=17%  Similarity=0.165  Sum_probs=54.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH-hCC-CccccCcHHH----HHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK-LGL-KIDQESESVR----AWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~-l~~-~~~~~~~~~~----~~~l~~  245 (426)
                      -+++=|+|+.|+||||+|.+++-.....  -...+|++....+++..+.. +... +.. -.......+.    +..+..
T Consensus        60 g~ItEiyG~~gsGKT~lal~~~~~aq~~--g~~a~fIDtE~~l~p~r~~~-l~~~~~d~l~v~~~~~~e~q~~i~~~~~~  136 (279)
T COG0468          60 GRITEIYGPESSGKTTLALQLVANAQKP--GGKAAFIDTEHALDPERAKQ-LGVDLLDNLLVSQPDTGEQQLEIAEKLAR  136 (279)
T ss_pred             ceEEEEecCCCcchhhHHHHHHHHhhcC--CCeEEEEeCCCCCCHHHHHH-HHHhhhcceeEecCCCHHHHHHHHHHHHH
Confidence            3578899999999999999987665433  33789999999999877544 3333 211 1111112222    223333


Q ss_pred             HHhcCCeEEEEEeCCCC
Q 044858          246 QLKKETKILIILDDIWG  262 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~~  262 (426)
                      ...+ +--|+|+|.+-.
T Consensus       137 ~~~~-~i~LvVVDSvaa  152 (279)
T COG0468         137 SGAE-KIDLLVVDSVAA  152 (279)
T ss_pred             hccC-CCCEEEEecCcc
Confidence            2222 356999999853

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.36  E-value=0.029  Score=47.56  Aligned_cols=118  Identities=20%  Similarity=0.166  Sum_probs=64.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccce-EE-EEEecCCcCHHHHHHHHH---HHhCCC--ccccC---cHHH--
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEK-VI-SSRVSQTPQIKEIQREIA---EKLGLK--IDQES---ESVR--  239 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~-wv~v~~~~~~~~il~~i~---~~l~~~--~~~~~---~~~~--  239 (426)
                      ...|-|++..|.||||.|.-+.-+....+ +.+ ++ |+..........++....   .+++..  ....+   +...  
T Consensus         5 ~Gli~v~~g~GkGKtt~a~g~a~ra~~~g-~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~   83 (173)
T TIGR00708         5 RGIIIVHTGNGKGKTTAAFGMALRALGHG-KKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAK   83 (173)
T ss_pred             ccEEEEECCCCCChHHHHHHHHHHHHHCC-CeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHH
Confidence            35788888899999999998887766433 332 22 333332344444554430   001111  11111   1111  


Q ss_pred             --HHHHHHHHhcCCeEEEEEeCCCCc-----cChhhhcCCCCCCCCCeEEEEeecchh
Q 044858          240 --AWRLLEQLKKETKILIILDDIWGS-----LDLEAIGIPLADDNGGCKVLLTARSQD  290 (426)
Q Consensus       240 --~~~l~~~l~~~k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~s~iivTtr~~~  290 (426)
                        .....+.+..+.-=|||||++-..     -+.+.+...+.....+.-||+|.|+..
T Consensus        84 ~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p  141 (173)
T TIGR00708        84 AAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCP  141 (173)
T ss_pred             HHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCC
Confidence              223344444555569999998532     233444444444445778999999874

Alternate name: corrinoid adenosyltransferase.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.35  E-value=0.041  Score=57.35  Aligned_cols=59  Identities=17%  Similarity=0.167  Sum_probs=35.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLK  230 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~  230 (426)
                      ..++.++|+.|+||||++..+............+..++.... ....+-++...+.++.+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvp  244 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVP  244 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCC
Confidence            469999999999999999999876643221223444443221 11334444445555543

>TIGR00235 udk uridine kinase

Probab=96.34  E-value=0.0035  Score=55.40  Aligned_cols=27  Identities=33%  Similarity=0.418  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+|+|+|++|+|||||++.+.....
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            456899999999999999999987654

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

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.31  E-value=0.037  Score=53.94  Aligned_cols=87  Identities=20%  Similarity=0.237  Sum_probs=45.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      ..+++++|+.|+||||++..+............+..++... .....+-+....+.++.+.............+..+. +
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~~~v~~~~dl~~al~~l~-~  269 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVRSIKDIADLQLMLHELR-G  269 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCceecCCCHHHHHHHHHHhc-C
Confidence            46899999999999999998876543222123333443322 112333344555555655433222222223333332 1


Q ss_pred             CeEEEEEeCC
Q 044858          251 TKILIILDDI  260 (426)
Q Consensus       251 k~~LlVlDdv  260 (426)
                       .-++++|-.
T Consensus       270 -~d~VLIDTa  278 (420)
T PRK14721        270 -KHMVLIDTV  278 (420)
T ss_pred             -CCEEEecCC
Confidence             235556654

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=96.29  E-value=0.76  Score=44.45  Aligned_cols=58  Identities=22%  Similarity=0.323  Sum_probs=37.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe-cCCcCHHHHHHHHHHHhCCC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV-SQTPQIKEIQREIAEKLGLK  230 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v-~~~~~~~~il~~i~~~l~~~  230 (426)
                      .+.+|..+|.-|+||||.+-.+.+..+.++ +.. .-|++ -..+..-+=++.+..+.+.+
T Consensus        99 ~P~vImmvGLQGsGKTTt~~KLA~~lkk~~-~kv-llVaaD~~RpAA~eQL~~La~q~~v~  157 (451)
T COG0541          99 PPTVILMVGLQGSGKTTTAGKLAKYLKKKG-KKV-LLVAADTYRPAAIEQLKQLAEQVGVP  157 (451)
T ss_pred             CCeEEEEEeccCCChHhHHHHHHHHHHHcC-Cce-EEEecccCChHHHHHHHHHHHHcCCc
Confidence            467899999999999999999988887632 222 22222 12223344566666666544

>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=96.28  E-value=0.061  Score=50.43  Aligned_cols=85  Identities=22%  Similarity=0.274  Sum_probs=50.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~~~l~~~  246 (426)
                      -+++-|+|+.|+||||||.++.......  -..++|+.....+++.     .+..+|.+.+.     .+..+..-.+.+.
T Consensus        53 G~ivEi~G~~ssGKttLaL~~ia~~q~~--g~~~a~ID~e~~ld~~-----~a~~lGvdl~rllv~~P~~~E~al~~~e~  125 (322)
T PF00154_consen   53 GRIVEIYGPESSGKTTLALHAIAEAQKQ--GGICAFIDAEHALDPE-----YAESLGVDLDRLLVVQPDTGEQALWIAEQ  125 (322)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT--T-EEEEEESSS---HH-----HHHHTT--GGGEEEEE-SSHHHHHHHHHH
T ss_pred             CceEEEeCCCCCchhhhHHHHHHhhhcc--cceeEEecCcccchhh-----HHHhcCccccceEEecCCcHHHHHHHHHH
Confidence            4689999999999999999998776443  3457899988776653     34455554332     1112222233333


Q ss_pred             H-hcCCeEEEEEeCCCCc
Q 044858          247 L-KKETKILIILDDIWGS  263 (426)
Q Consensus       247 l-~~~k~~LlVlDdv~~~  263 (426)
                      + ..+.--++|+|-|-..
T Consensus       126 lirsg~~~lVVvDSv~al  143 (322)
T PF00154_consen  126 LIRSGAVDLVVVDSVAAL  143 (322)
T ss_dssp             HHHTTSESEEEEE-CTT-
T ss_pred             HhhcccccEEEEecCccc
Confidence            3 4455569999998654

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 ....

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=96.28  E-value=0.026  Score=50.96  Aligned_cols=26  Identities=35%  Similarity=0.491  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|.|+.|+|||||.+.++.-.+
T Consensus        28 G~i~~iiGpNG~GKSTLLk~l~g~l~   53 (258)
T COG1120          28 GEITGILGPNGSGKSTLLKCLAGLLK   53 (258)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCC
Confidence            46899999999999999999987544

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

Probab=96.28  E-value=0.011  Score=52.94  Aligned_cols=87  Identities=17%  Similarity=0.222  Sum_probs=50.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcc------------------
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID------------------  232 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~------------------  232 (426)
                      ...++.|.|++|+|||+|+.++......+ .=..++|++...+  ..++.+.+. .++.+..                  
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~-~ge~vlyvs~ee~--~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~   93 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKN-FGEKVLYVSFEEP--PEELIENMK-SFGWDLEEYEDSGKLKIIDAFPERI   93 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH-HT--EEEEESSS---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGS
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhh-cCCcEEEEEecCC--HHHHHHHHH-HcCCcHHHHhhcCCEEEEecccccc
Confidence            34689999999999999999977554322 0124667776544  355554433 3332110                  


Q ss_pred             ---ccCcHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          233 ---QESESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       233 ---~~~~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                         ..+.......+.+.+...+...+|+|.+.
T Consensus        94 ~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls  125 (226)
T PF06745_consen   94 GWSPNDLEELLSKIREAIEELKPDRVVIDSLS  125 (226)
T ss_dssp             T-TSCCHHHHHHHHHHHHHHHTSSEEEEETHH
T ss_pred             cccccCHHHHHHHHHHHHHhcCCCEEEEECHH
Confidence               11223344555555554455799999874

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 ....

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.28  E-value=0.028  Score=51.51  Aligned_cols=39  Identities=18%  Similarity=0.343  Sum_probs=29.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      -.++.|.|++|+|||+++.++......+  -..++|++...
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~--Ge~vlyis~Ee   74 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASR--GNPVLFVTVES   74 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecC
Confidence            4689999999999999999987654332  34567787764

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=96.27  E-value=0.0049  Score=50.68  Aligned_cols=39  Identities=21%  Similarity=0.324  Sum_probs=28.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      ++|.|+|+.|+|||||++.+.+....+ .+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~-g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRR-GYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHc-CCceEEEEEccC
Confidence            579999999999999999999998764 355554555544

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=96.27  E-value=0.024  Score=50.17  Aligned_cols=72  Identities=25%  Similarity=0.293  Sum_probs=46.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .++-+.++|++|+|||.||+.|.+.....       |+.|-.    .++.+.   .+|..      ...+..+++..+++
T Consensus       188 pprgvllygppg~gktml~kava~~t~a~-------firvvg----sefvqk---ylgeg------prmvrdvfrlaken  247 (408)
T KOG0727|consen  188 PPRGVLLYGPPGTGKTMLAKAVANHTTAA-------FIRVVG----SEFVQK---YLGEG------PRMVRDVFRLAKEN  247 (408)
T ss_pred             CCcceEEeCCCCCcHHHHHHHHhhccchh-------eeeecc----HHHHHH---HhccC------cHHHHHHHHHHhcc
Confidence            46678899999999999999999886643       333322    122222   22211      12445556666667


Q ss_pred             CeEEEEEeCCCC
Q 044858          251 TKILIILDDIWG  262 (426)
Q Consensus       251 k~~LlVlDdv~~  262 (426)
                      -+.++++|+++.
T Consensus       248 apsiifideida  259 (408)
T KOG0727|consen  248 APSIIFIDEIDA  259 (408)
T ss_pred             CCcEEEeehhhh
Confidence            789999999864

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=96.26  E-value=0.0099  Score=52.19  Aligned_cols=43  Identities=21%  Similarity=0.382  Sum_probs=31.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIK  217 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  217 (426)
                      .|+|+|-||+||||+|..+......++.| .+.-|+...++++.
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~~~-~VLvVDaDpd~nL~   44 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKGGY-NVLVVDADPDSNLP   44 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhcCCc-eEEEEeCCCCCChH
Confidence            58999999999999999977766654433 34456666666544

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.26  E-value=0.031  Score=51.49  Aligned_cols=89  Identities=20%  Similarity=0.287  Sum_probs=48.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH--HHHHHHHHHHhCCCcc---cc-CcHHHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI--KEIQREIAEKLGLKID---QE-SESVRAWRL  243 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~--~~il~~i~~~l~~~~~---~~-~~~~~~~~l  243 (426)
                      .+++++.++|++|+||||++..+.......  -..+..++... +..  .+-+....+..+.+..   .. +........
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~~--g~~V~li~~D~-~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~  146 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQ--GKSVLLAAGDT-FRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDA  146 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhc--CCEEEEEeCCC-CCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHH
Confidence            346789999999999999999998776543  23455555432 222  2333444555553321   11 111222222


Q ss_pred             HHHHhcCCeEEEEEeCCC
Q 044858          244 LEQLKKETKILIILDDIW  261 (426)
Q Consensus       244 ~~~l~~~k~~LlVlDdv~  261 (426)
                      .........=++++|-.-
T Consensus       147 l~~~~~~~~D~ViIDT~G  164 (272)
T TIGR00064       147 IQKAKARNIDVVLIDTAG  164 (272)
T ss_pred             HHHHHHCCCCEEEEeCCC
Confidence            222222234578888764

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.

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=96.23  E-value=0.028  Score=55.32  Aligned_cols=89  Identities=21%  Similarity=0.323  Sum_probs=57.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcH------
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESES------  237 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~------  237 (426)
                      -+-++|.|.+|+|||||+.++.+....+ +-+.++++-+... ....++..++...-...       ....+..      
T Consensus       143 GQR~gIfa~~G~GKt~Ll~~~~~~~~~~-~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~  221 (461)
T PRK12597        143 GGKTGLFGGAGVGKTVLMMELIFNISKQ-HSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVV  221 (461)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhh-CCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHH
Confidence            3568999999999999999998877653 5677777777654 45666777665432211       1111111      


Q ss_pred             HHHHHHHHHHh-c-CCeEEEEEeCCC
Q 044858          238 VRAWRLLEQLK-K-ETKILIILDDIW  261 (426)
Q Consensus       238 ~~~~~l~~~l~-~-~k~~LlVlDdv~  261 (426)
                      .....+-+++. + ++++||++|++-
T Consensus       222 ~~a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        222 LTGLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHHhcCCceEEEeccch
Confidence            12234455553 2 799999999984

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=96.23  E-value=0.011  Score=60.71  Aligned_cols=78  Identities=14%  Similarity=0.163  Sum_probs=57.7

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .....+.|.++.++.|...+..+  +.+.++|++|+||||+|+.+.+.... .+++..+|..- ...+...+++.+..++
T Consensus        28 ~~~~~vigq~~a~~~L~~~~~~~--~~~l~~G~~G~GKttla~~l~~~l~~-~~~~~~~~~~n-p~~~~~~~~~~v~~~~  103 (637)
T PRK13765         28 RLIDQVIGQEHAVEVIKKAAKQR--RHVMMIGSPGTGKSMLAKAMAELLPK-EELQDILVYPN-PEDPNNPKIRTVPAGK  103 (637)
T ss_pred             ccHHHcCChHHHHHHHHHHHHhC--CeEEEECCCCCcHHHHHHHHHHHcCh-HhHHHheEeeC-CCcchHHHHHHHHHhc
Confidence            34567889888888877766654  46889999999999999999987543 34677777554 4446777777777666


Q ss_pred             CC
Q 044858          228 GL  229 (426)
Q Consensus       228 ~~  229 (426)
                      +.
T Consensus       104 G~  105 (637)
T PRK13765        104 GK  105 (637)
T ss_pred             CH
Confidence            53

>PRK01184 hypothetical protein; Provisional

Probab=96.23  E-value=0.026  Score=48.78  Aligned_cols=21  Identities=48%  Similarity=0.816  Sum_probs=17.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+|.|+|++|+||||+++ +..
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~   22 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IAR   22 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHH
Confidence            479999999999999987 443

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.22  E-value=0.032  Score=55.31  Aligned_cols=60  Identities=20%  Similarity=0.181  Sum_probs=37.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKI  231 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~  231 (426)
                      ..+++++|+.|+||||++.++......+.....+..++... .....+-++...+.++.+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv  316 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPV  316 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCCe
Confidence            46999999999999999999998764332122344444332 1223344455556655544

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.21  E-value=0.0034  Score=54.38  Aligned_cols=22  Identities=27%  Similarity=0.363  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ++.|+|+.|.||||+.+.+.-.
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~~   22 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGLI   22 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHHH
Confidence            4679999999999999999843

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

Probab=96.20  E-value=0.068  Score=42.54  Aligned_cols=38  Identities=21%  Similarity=0.334  Sum_probs=28.2

Q ss_pred             HHHHHHHHhcc---CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          159 TLKGILDALSN---RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       159 ~~~~l~~~l~~---~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .++.|...+.+   +++-|++.+|.+|+|||.+++.+.+..
T Consensus        37 v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   37 VVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            34444444442   356689999999999999999998874

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

>PF13245 AAA_19: Part of AAA domain

Probab=96.20  E-value=0.017  Score=41.92  Aligned_cols=26  Identities=27%  Similarity=0.304  Sum_probs=18.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHH-HHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKE-VGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~-v~~~~  196 (426)
                      +.+++.|.|++|.|||+++.. +.+-.
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            346788899999999955544 44444

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.20  E-value=0.0047  Score=53.51  Aligned_cols=26  Identities=23%  Similarity=0.282  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +.++|.|.|++|+||||+++.+....
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            35789999999999999999998764

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.

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=96.19  E-value=0.01  Score=51.40  Aligned_cols=47  Identities=23%  Similarity=0.279  Sum_probs=32.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ..+|+|-||-|+||||||+.+.+.....     .++-.+.+++-+..+..++
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~~~-----~~~E~vednp~L~~FY~d~   50 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLGFK-----VFYELVEDNPFLDLFYEDP   50 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhCCc-----eeeecccCChHHHHHHHhH
Confidence            4689999999999999999999987643     2334444554444444433

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.19  E-value=0.019  Score=55.99  Aligned_cols=88  Identities=19%  Similarity=0.321  Sum_probs=53.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      +-..++|.|..|+|||||++.+.....    .+.++.+-+++.. .+.++..+++..-+..       ...++...    
T Consensus       161 ~GqrigI~G~sG~GKSTLL~~I~~~~~----~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a  236 (444)
T PRK08972        161 KGQRMGLFAGSGVGKSVLLGMMTRGTT----ADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKG  236 (444)
T ss_pred             CCCEEEEECCCCCChhHHHHHhccCCC----CCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHH
Confidence            346789999999999999999986432    3455556665543 4566666665442211       11111111    


Q ss_pred             --HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 --RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 --~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                        ....+-+++ .+++++||++||+-.
T Consensus       237 ~~~A~tiAEyfrd~G~~VLl~~DslTR  263 (444)
T PRK08972        237 CETATTIAEYFRDQGLNVLLLMDSLTR  263 (444)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEEcChHH
Confidence              112334444 258999999999853

>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=96.18  E-value=0.025  Score=46.79  Aligned_cols=26  Identities=35%  Similarity=0.539  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|.|+.|.|||||++.+.....
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~   51 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELE   51 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCC
Confidence            36799999999999999999987653

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.16  E-value=0.031  Score=56.18  Aligned_cols=86  Identities=19%  Similarity=0.179  Sum_probs=57.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc----------------c
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ----------------E  234 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~----------------~  234 (426)
                      .-.++.|.|++|+|||||+.++......+  -..+++++...  +..++.... +.++.+...                .
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~~~--ge~~~y~s~eE--s~~~i~~~~-~~lg~~~~~~~~~g~l~~~~~~p~~~  336 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENACAN--KERAILFAYEE--SRAQLLRNA-YSWGIDFEEMEQQGLLKIICAYPESA  336 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEEeeC--CHHHHHHHH-HHcCCChHHHhhCCcEEEEEcccccC
Confidence            34689999999999999999998876543  34456665443  455665554 455543211                1


Q ss_pred             CcHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          235 SESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       235 ~~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                      +..+.+..+.+.+.+.+.-++|+|.+.
T Consensus       337 ~~~~~~~~i~~~i~~~~~~~vvIDsi~  363 (484)
T TIGR02655       337 GLEDHLQIIKSEIADFKPARIAIDSLS  363 (484)
T ss_pred             ChHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            124566677777766667799999985

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.

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.15  E-value=0.005  Score=53.84  Aligned_cols=28  Identities=39%  Similarity=0.536  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ++.+|+|.|.+|+||||+|+.+++....
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~~~~~   34 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSEQLGV   34 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHhCc
Confidence            3468999999999999999999998774

>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=96.15  E-value=0.0096  Score=54.66  Aligned_cols=26  Identities=35%  Similarity=0.405  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +.|.|+|.+|+||||+|+++......
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHh
Confidence            57899999999999999999988765

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.13  E-value=0.0056  Score=52.24  Aligned_cols=27  Identities=22%  Similarity=0.276  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +...|.|+|++|+||||+|+.+.+...
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            346899999999999999999998864

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.12  E-value=0.027  Score=58.87  Aligned_cols=83  Identities=17%  Similarity=0.162  Sum_probs=54.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc------cCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ------ESESVRAWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~------~~~~~~~~~l~~  245 (426)
                      -+++-|+|++|+|||||+.+++......  -..++|+.....++.     ..+++++.+.+.      .+.......+..
T Consensus        60 GsiteI~G~~GsGKTtLal~~~~~a~~~--G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i~~  132 (790)
T PRK09519         60 GRVIEIYGPESSGKTTVALHAVANAQAA--GGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIADM  132 (790)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHHHH
Confidence            4688899999999999998876654332  345789988777774     366777765321      122223333333


Q ss_pred             HHhcCCeEEEEEeCCC
Q 044858          246 QLKKETKILIILDDIW  261 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~  261 (426)
                      .+.+++.-|||+|.+.
T Consensus       133 lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        133 LIRSGALDIVVIDSVA  148 (790)
T ss_pred             HhhcCCCeEEEEcchh
Confidence            3445567799999975

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

Probab=96.12  E-value=0.024  Score=50.96  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|.|||||.+.+..-.
T Consensus        31 ~~~~iiGPNGaGKSTLlK~iLGll   54 (254)
T COG1121          31 EITALIGPNGAGKSTLLKAILGLL   54 (254)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC
Confidence            689999999999999999998743

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=96.12  E-value=0.16  Score=47.02  Aligned_cols=125  Identities=9%  Similarity=-0.008  Sum_probs=67.4

Q ss_pred             HHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhc------------CccceEEEEE-ecCC--cCHHHHHHHHH
Q 044858          161 KGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKEN------------NLFEKVISSR-VSQT--PQIKEIQREIA  224 (426)
Q Consensus       161 ~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~------------~~f~~~~wv~-v~~~--~~~~~il~~i~  224 (426)
                      +.+...+..++ .....++|+.|+||+++|..+....-..            .|.|.. ++. ....  ..         
T Consensus         7 ~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~-~i~p~~~~~~I~---------   76 (290)
T PRK05917          7 EALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIH-EFSPQGKGRLHS---------   76 (290)
T ss_pred             HHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEE-EEecCCCCCcCc---------
Confidence            45566666555 4567899999999999999887765321            122222 221 1110  11         


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc-hhhhhccCC
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS-QDVLSCEMD  297 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~-~~va~~~~~  297 (426)
                                  .+.+..+.+.+.    .++.-++|+|+++..  ..++.+...+-.-..++.+|++|.+ ..+.+...+
T Consensus        77 ------------idqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~S  144 (290)
T PRK05917         77 ------------IETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRS  144 (290)
T ss_pred             ------------HHHHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHh
Confidence                        122223333331    245568899999754  4555554444333345666665555 444332233


Q ss_pred             ceeeEEccCC
Q 044858          298 CQQNFVVDVL  307 (426)
Q Consensus       298 ~~~~~~l~~L  307 (426)
                      ....+.+.++
T Consensus       145 Rcq~~~~~~~  154 (290)
T PRK05917        145 RSLSIHIPME  154 (290)
T ss_pred             cceEEEccch
Confidence            4556666654

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.11  E-value=0.017  Score=57.27  Aligned_cols=85  Identities=26%  Similarity=0.316  Sum_probs=52.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc--CcHHHHHHHHHHHhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE--SESVRAWRLLEQLKK  249 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~--~~~~~~~~l~~~l~~  249 (426)
                      -.++.|.|.+|+|||||+.++.......  -..++|++...  +...+... ++.++...+..  ........+.+.+.+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~--g~~vlYvs~Ee--s~~qi~~r-a~rlg~~~~~l~~~~e~~l~~i~~~i~~  154 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAA--GGKVLYVSGEE--SASQIKLR-AERLGLPSDNLYLLAETNLEAILATIEE  154 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccc--cHHHHHHH-HHHcCCChhcEEEeCCCCHHHHHHHHHh
Confidence            3588999999999999999998876532  23567777543  33443322 45555432210  001123455555555


Q ss_pred             CCeEEEEEeCCC
Q 044858          250 ETKILIILDDIW  261 (426)
Q Consensus       250 ~k~~LlVlDdv~  261 (426)
                      .+.-++|+|.+.
T Consensus       155 ~~~~lVVIDSIq  166 (446)
T PRK11823        155 EKPDLVVIDSIQ  166 (446)
T ss_pred             hCCCEEEEechh
Confidence            567799999985

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.11  E-value=0.0044  Score=48.40  Aligned_cols=24  Identities=46%  Similarity=0.731  Sum_probs=20.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      |.|+|++|+|||+||+.+..+...
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~   24 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLK   24 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHH
Confidence            468999999999999998887653

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

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=96.10  E-value=0.0092  Score=56.69  Aligned_cols=50  Identities=12%  Similarity=0.175  Sum_probs=43.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -++..++|.++.+..|+..+.++...-+.|.|..|+||||+|+.+++-..
T Consensus        14 ~pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~   63 (350)
T CHL00081         14 FPFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLP   63 (350)
T ss_pred             CCHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHh
Confidence            35677899999999998888888888888999999999999999987654

>PRK03839 putative kinase; Provisional

Probab=96.09  E-value=0.0054  Score=52.87  Aligned_cols=24  Identities=33%  Similarity=0.559  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|.|++|+||||+++.+++...
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999998865

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=96.07  E-value=0.0054  Score=49.75  Aligned_cols=34  Identities=26%  Similarity=0.290  Sum_probs=26.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      .+.|.|.|.+|+|||||+..+.....-.       |+++|.
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~-------~i~isd   40 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLE-------YIEISD   40 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCc-------eEehhh
Confidence            4568999999999999999999655432       666664

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.07  E-value=0.011  Score=49.98  Aligned_cols=112  Identities=20%  Similarity=0.202  Sum_probs=56.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC--CcCHHHHHHHHHHHhCCCccccCcHH-HHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ--TPQIKEIQREIAEKLGLKIDQESESV-RAWRLLEQLK  248 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~--~~~~~~il~~i~~~l~~~~~~~~~~~-~~~~l~~~l~  248 (426)
                      -.+++|.|+.|+|||||.+.+......   ....+++.-..  ..+..+..+   +.++.- ...+..+ ..-.+.+.+.
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~~~~---~~G~v~~~g~~~~~~~~~~~~~---~~i~~~-~qLS~G~~qrl~laral~   98 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGLYKP---DSGEILVDGKEVSFASPRDARR---AGIAMV-YQLSVGERQMVEIARALA   98 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC---CCeEEEECCEECCcCCHHHHHh---cCeEEE-EecCHHHHHHHHHHHHHh
Confidence            357999999999999999999876432   23344432211  111111111   111110 0011111 1223344444


Q ss_pred             cCCeEEEEEeCCCCccC---hhhhcCCCCC-CCCCeEEEEeecchhh
Q 044858          249 KETKILIILDDIWGSLD---LEAIGIPLAD-DNGGCKVLLTARSQDV  291 (426)
Q Consensus       249 ~~k~~LlVlDdv~~~~~---~~~l~~~l~~-~~~~s~iivTtr~~~v  291 (426)
                      . ++-++++|+.-..-+   ...+...+.. ...+..||++|.+...
T Consensus        99 ~-~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~  144 (163)
T cd03216          99 R-NARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDE  144 (163)
T ss_pred             c-CCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHH
Confidence            3 578999999865422   2222222211 1236678888888653

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.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.07  E-value=0.015  Score=55.14  Aligned_cols=46  Identities=13%  Similarity=0.170  Sum_probs=33.5

Q ss_pred             ccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          151 MHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..++|+...+..+.+.+.  .....-|.|+|..|+||+++|+.++...
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s   53 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLS   53 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhC
Confidence            346777777766666554  1223457899999999999999998654

>COG4240 Predicted kinase [General function prediction only]

Probab=96.06  E-value=0.047  Score=47.75  Aligned_cols=83  Identities=14%  Similarity=0.199  Sum_probs=53.8

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC-----CCccccCcHHHHHHH
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG-----LKIDQESESVRAWRL  243 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~-----~~~~~~~~~~~~~~l  243 (426)
                      .+++-+++|.|+-|+||||++..+++....+.. ..+...++..-+-...-.-.++++..     ...+...+......+
T Consensus        47 ~grPli~gisGpQGSGKStls~~i~~~L~~kg~-ert~~lSLDDlYlthadrl~La~q~npllq~RGlpGTHD~tlglnV  125 (300)
T COG4240          47 RGRPLIVGISGPQGSGKSTLSALIVRLLAAKGL-ERTATLSLDDLYLTHADRLRLARQVNPLLQTRGLPGTHDPTLGLNV  125 (300)
T ss_pred             cCCceEEEeecCCCCchhhHHHHHHHHHHHhcc-cceEEeehhhhhcchHHHHHHHHhcCchhcccCCCCCCchHHHHHH
Confidence            345778999999999999999999998876543 35555555443333333344455532     122334556677778


Q ss_pred             HHHHhcCCe
Q 044858          244 LEQLKKETK  252 (426)
Q Consensus       244 ~~~l~~~k~  252 (426)
                      ++.+.+++.
T Consensus       126 Lnai~~g~~  134 (300)
T COG4240         126 LNAIARGGP  134 (300)
T ss_pred             HHHHhcCCC
Confidence            888876653

>PRK04040 adenylate kinase; Provisional

Probab=96.05  E-value=0.006  Score=52.91  Aligned_cols=26  Identities=31%  Similarity=0.534  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.+|.|+|++|+||||+++.+.+...
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            35799999999999999999988764

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.04  E-value=0.0094  Score=53.35  Aligned_cols=24  Identities=25%  Similarity=0.545  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -|.|.|++|+||||+|+.+.+...
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g   31 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKEN   31 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999988764

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=96.01  E-value=0.039  Score=54.36  Aligned_cols=90  Identities=19%  Similarity=0.282  Sum_probs=56.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccc--eEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcH-----
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFE--KVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESES-----  237 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~--~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~-----  237 (426)
                      +-++|.|..|+|||+|+.++.+.....+.+.  .++++-+++. ..+.+++..+...-...       ..+.+..     
T Consensus       142 QR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a  221 (458)
T TIGR01041       142 QKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVT  221 (458)
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHH
Confidence            5689999999999999999988765321121  4556666544 45667777776432211       0111111     


Q ss_pred             -HHHHHHHHHHh--cCCeEEEEEeCCCC
Q 044858          238 -VRAWRLLEQLK--KETKILIILDDIWG  262 (426)
Q Consensus       238 -~~~~~l~~~l~--~~k~~LlVlDdv~~  262 (426)
                       -....+-+++.  +++++||++||+-.
T Consensus       222 ~~~a~tiAEyfr~d~G~~VLli~DslTR  249 (458)
T TIGR01041       222 PRMALTAAEYLAFEKDMHVLVILTDMTN  249 (458)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcChhH
Confidence             12234556665  58999999999853

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.98  E-value=0.0078  Score=51.10  Aligned_cols=28  Identities=25%  Similarity=0.335  Sum_probs=25.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..++++|+|..|+|||||++.+......
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~   32 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALCA   32 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHhh
Confidence            4679999999999999999999988764

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.97  E-value=0.04  Score=53.97  Aligned_cols=89  Identities=22%  Similarity=0.337  Sum_probs=57.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcH------H
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESES------V  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~------~  238 (426)
                      +-++|.|.+|+|||+|+.++....... +-+.++++-+.... ...++..++...-...       ....+..      .
T Consensus       139 Qr~~Ifg~~G~GKt~l~~~~~~~~~~~-~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~  217 (449)
T TIGR03305       139 GKAGLFGGAGVGKTVLLTEMIHNMVGQ-HQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGH  217 (449)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhc-CCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHH
Confidence            568999999999999999998775532 34677788776544 5666777665432111       1111111      1


Q ss_pred             HHHHHHHHHh--cCCeEEEEEeCCCC
Q 044858          239 RAWRLLEQLK--KETKILIILDDIWG  262 (426)
Q Consensus       239 ~~~~l~~~l~--~~k~~LlVlDdv~~  262 (426)
                      ....+-+++.  +++++||++||+-.
T Consensus       218 ~a~tiAEyfrd~~G~~VLl~~DslTR  243 (449)
T TIGR03305       218 TALTMAEYFRDDEKQDVLLLIDNIFR  243 (449)
T ss_pred             HHHHHHHHHHHhcCCceEEEecChHH
Confidence            2234555665  47999999999853

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.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.97  E-value=0.019  Score=51.38  Aligned_cols=64  Identities=22%  Similarity=0.197  Sum_probs=33.7

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh-----hcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK-----ENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~-----~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .+.+...+..+.  +..|+|++|+|||+++..+.....     ....-...+-++...+..+..++..+.+
T Consensus         7 ~~Ai~~~~~~~~--~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    7 REAIQSALSSNG--ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             HHHHHHHCTSSE---EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             HHHHHHHHcCCC--CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            344444443332  688999999999987777766651     1122333444444444445555554443

>TIGR00416 sms DNA repair protein RadA

Probab=95.97  E-value=0.03  Score=55.58  Aligned_cols=86  Identities=24%  Similarity=0.280  Sum_probs=51.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc--CcHHHHHHHHHHHhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE--SESVRAWRLLEQLKK  249 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~--~~~~~~~~l~~~l~~  249 (426)
                      -.++.|.|.+|+|||||+.++.......+  ..++|++...  +..++... +..++...+..  ........+.+.+.+
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~g--~kvlYvs~EE--s~~qi~~r-a~rlg~~~~~l~~~~e~~~~~I~~~i~~  168 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKNQ--MKVLYVSGEE--SLQQIKMR-AIRLGLPEPNLYVLSETNWEQICANIEE  168 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhcC--CcEEEEECcC--CHHHHHHH-HHHcCCChHHeEEcCCCCHHHHHHHHHh
Confidence            36899999999999999999977665432  3467776543  33333322 33444332210  001123455555555


Q ss_pred             CCeEEEEEeCCCC
Q 044858          250 ETKILIILDDIWG  262 (426)
Q Consensus       250 ~k~~LlVlDdv~~  262 (426)
                      .+.-++|+|.+..
T Consensus       169 ~~~~~vVIDSIq~  181 (454)
T TIGR00416       169 ENPQACVIDSIQT  181 (454)
T ss_pred             cCCcEEEEecchh
Confidence            5677999999853

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)).

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.96  E-value=0.028  Score=54.95  Aligned_cols=88  Identities=20%  Similarity=0.261  Sum_probs=49.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCC------CccccCcHH------H
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGL------KIDQESESV------R  239 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~------~~~~~~~~~------~  239 (426)
                      -..++|+|+.|+|||||++.+......   ...+++.......++.++....+.....      ....++...      .
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~~p---d~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~  241 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARADAF---DTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLT  241 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC---CeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHH
Confidence            357999999999999999988765432   2234444333444555554444333210      011111111      1


Q ss_pred             HHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          240 AWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       240 ~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                      ...+-+++ .+++++|+++||+-.
T Consensus       242 a~~iAEyfrd~G~~Vll~~DslTr  265 (450)
T PRK06002        242 ATAIAEYFRDRGENVLLIVDSVTR  265 (450)
T ss_pred             HHHHHHHHHHcCCCEEEeccchHH
Confidence            12233444 248999999999843

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.96  E-value=0.057  Score=44.88  Aligned_cols=24  Identities=25%  Similarity=0.472  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.|+|.+|+||||+|+.+.....
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~   24 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLF   24 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            578999999999999999998765

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=95.94  E-value=0.0055  Score=53.73  Aligned_cols=23  Identities=43%  Similarity=0.642  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +|+|.|+.|+|||||++.+....
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.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=95.94  E-value=0.059  Score=52.71  Aligned_cols=88  Identities=16%  Similarity=0.327  Sum_probs=53.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      +-..++|+|..|+|||||++++.+....    +.++++-++... .+.++..+.+..-+..       ....+...    
T Consensus       157 ~Gqri~I~G~sG~GKTtLL~~I~~~~~~----d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a  232 (442)
T PRK08927        157 RGQRMGIFAGSGVGKSVLLSMLARNADA----DVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQA  232 (442)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccCC----CEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHH
Confidence            4467899999999999999999876542    344555555443 4556665555432211       11111111    


Q ss_pred             --HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 --RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 --~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                        ....+-+++ .+++++|+++||+-.
T Consensus       233 ~~~a~tiAEyfrd~G~~Vll~~DslTr  259 (442)
T PRK08927        233 AYLTLAIAEYFRDQGKDVLCLMDSVTR  259 (442)
T ss_pred             HHHHHHHHHHHHHCCCcEEEEEeCcHH
Confidence              122344444 358999999999843

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=95.94  E-value=0.064  Score=52.76  Aligned_cols=89  Identities=20%  Similarity=0.323  Sum_probs=56.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcHH-----
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESESV-----  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~~-----  238 (426)
                      -+-++|.|.+|+|||||+.++......+. -+.++++-+... ..+.+++.++...-...       ....+...     
T Consensus       144 GQR~gIfa~~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~  222 (463)
T PRK09280        144 GGKIGLFGGAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVA  222 (463)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            35689999999999999999887765432 245667766544 45667777776542211       11111111     


Q ss_pred             -HHHHHHHHH--hcCCeEEEEEeCCC
Q 044858          239 -RAWRLLEQL--KKETKILIILDDIW  261 (426)
Q Consensus       239 -~~~~l~~~l--~~~k~~LlVlDdv~  261 (426)
                       ....+-+++  .+++++||++|++-
T Consensus       223 ~~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        223 LTGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHHhcCCceEEEecchH
Confidence             122344555  25899999999985

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.93  E-value=0.04  Score=52.11  Aligned_cols=38  Identities=37%  Similarity=0.601  Sum_probs=29.4

Q ss_pred             HHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          162 GILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       162 ~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .+++.+.  .++..+|+|.|++|+|||||+..+.......
T Consensus        44 ~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l~~~   83 (332)
T PRK09435         44 ELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLIEQ   83 (332)
T ss_pred             HHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            3444433  3567799999999999999999988877653

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.92  E-value=0.026  Score=48.13  Aligned_cols=26  Identities=31%  Similarity=0.362  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|.|+.|.|||||.+.+.....
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~~~   53 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRLYD   53 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCCC
Confidence            36899999999999999999987654

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.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=95.91  E-value=0.013  Score=50.72  Aligned_cols=38  Identities=29%  Similarity=0.371  Sum_probs=29.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      .++|.|+|+.|+|||||+..+......  .|...+..+-.
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~--~~~~~v~~TTR   39 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPD--KFGRVVSHTTR   39 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTT--TEEEEEEEESS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhccc--ccccceeeccc
Confidence            478999999999999999999998763  37544444443

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 ....

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.91  E-value=0.035  Score=52.06  Aligned_cols=30  Identities=30%  Similarity=0.584  Sum_probs=25.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      +...+|.|+|++|+|||||+..+.......
T Consensus        32 ~~~~~i~i~G~~G~GKttl~~~l~~~~~~~   61 (300)
T TIGR00750        32 GNAHRVGITGTPGAGKSTLLEALGMELRRR   61 (300)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            457899999999999999999998876543

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.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=95.91  E-value=0.014  Score=55.31  Aligned_cols=48  Identities=19%  Similarity=0.236  Sum_probs=40.4

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++..++|.++.+..++-.+.++...-+.|.|..|+|||||++.+..-.
T Consensus         2 pf~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             CccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            345678999999888877777767778899999999999999998665

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.

>PRK15453 phosphoribulokinase; Provisional

Probab=95.90  E-value=0.061  Score=49.22  Aligned_cols=28  Identities=25%  Similarity=0.407  Sum_probs=24.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..+|+|.|.+|+||||+++.+.+...
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~if~   30 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKIFR   30 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3567999999999999999999987654

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

Probab=95.90  E-value=0.024  Score=55.32  Aligned_cols=46  Identities=22%  Similarity=0.164  Sum_probs=33.1

Q ss_pred             cccchHHHHHHHHHHhc-------cC---------CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALS-------NR---------NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~-------~~---------~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|.+..++.+...+.       ..         ....+.++|++|+|||+||+.+.....
T Consensus        72 ~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~  133 (412)
T PRK05342         72 YVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILD  133 (412)
T ss_pred             HeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhC
Confidence            36788877776644431       10         135689999999999999999987654

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.89  E-value=0.11  Score=50.43  Aligned_cols=72  Identities=22%  Similarity=0.244  Sum_probs=44.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKET  251 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k  251 (426)
                      ++-+.+.|++|.|||.|++.|+-.....       +.+++..            .+...+..+. ...+..++..-+...
T Consensus       186 ~rglLLfGPpgtGKtmL~~aiAsE~~at-------ff~iSas------------sLtsK~~Ge~-eK~vralf~vAr~~q  245 (428)
T KOG0740|consen  186 VRGLLLFGPPGTGKTMLAKAIATESGAT-------FFNISAS------------SLTSKYVGES-EKLVRALFKVARSLQ  245 (428)
T ss_pred             cchhheecCCCCchHHHHHHHHhhhcce-------EeeccHH------------HhhhhccChH-HHHHHHHHHHHHhcC
Confidence            4456699999999999999999887653       2222211            1111222222 233444454445567


Q ss_pred             eEEEEEeCCCCc
Q 044858          252 KILIILDDIWGS  263 (426)
Q Consensus       252 ~~LlVlDdv~~~  263 (426)
                      +.++++|+++..
T Consensus       246 PsvifidEidsl  257 (428)
T KOG0740|consen  246 PSVIFIDEIDSL  257 (428)
T ss_pred             CeEEEechhHHH
Confidence            889999998643

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=95.88  E-value=0.0092  Score=53.04  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .++.|+|+.|.||||+.+.+..
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            7899999999999999999864

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

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.88  E-value=0.098  Score=46.92  Aligned_cols=39  Identities=21%  Similarity=0.205  Sum_probs=29.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      -.++.|.|++|+|||+|+.++......+  -...+|++...
T Consensus        20 G~~~~i~G~~G~GKT~l~~~~~~~~~~~--g~~~~~is~e~   58 (229)
T TIGR03881        20 GFFVAVTGEPGTGKTIFCLHFAYKGLRD--GDPVIYVTTEE   58 (229)
T ss_pred             CeEEEEECCCCCChHHHHHHHHHHHHhc--CCeEEEEEccC
Confidence            4689999999999999999977554322  34567777643

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.88  E-value=0.0073  Score=51.97  Aligned_cols=25  Identities=32%  Similarity=0.402  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|+|+.|+|||||++.+.....
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLA   26 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            4689999999999999999987654

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.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=95.87  E-value=0.0083  Score=51.46  Aligned_cols=25  Identities=16%  Similarity=0.291  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++|.+.|++|+||||+|+.+.....
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~   27 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhC
Confidence            5899999999999999999987753

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.87  E-value=0.055  Score=50.94  Aligned_cols=87  Identities=20%  Similarity=0.359  Sum_probs=51.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec-CCcCHHHHHHHHHHHhCCC-------ccccCcHH-----
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS-QTPQIKEIQREIAEKLGLK-------IDQESESV-----  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~il~~i~~~l~~~-------~~~~~~~~-----  238 (426)
                      -..++|.|..|+|||||.+.+......    +......+. ...++.++.......-+..       ...++...     
T Consensus        69 Gqri~I~G~sG~GKTtLl~~Ia~~~~~----~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~  144 (326)
T cd01136          69 GQRLGIFAGSGVGKSTLLGMIARGTTA----DVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAA  144 (326)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCCC----CEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHH
Confidence            357899999999999999998876542    233333333 3445666666665543221       11111111     


Q ss_pred             -HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 -RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 -~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                       ....+-+++ .+++.+||++||+-.
T Consensus       145 ~~a~~~AEyfr~~g~~Vll~~Dsltr  170 (326)
T cd01136         145 YTATAIAEYFRDQGKDVLLLMDSLTR  170 (326)
T ss_pred             HHHHHHHHHHHHcCCCeEEEeccchH
Confidence             112233333 358999999999843

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.

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=95.84  E-value=0.0056  Score=54.67  Aligned_cols=25  Identities=20%  Similarity=0.309  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +.+++.|+|+.|.||||+.+.+...
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~~   53 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGVI   53 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHH
Confidence            4578999999999999999997743

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

>PRK00625 shikimate kinase; Provisional

Probab=95.84  E-value=0.0083  Score=51.24  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.++|++|+||||+++.+.+...
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999988764

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=95.83  E-value=0.024  Score=48.52  Aligned_cols=26  Identities=23%  Similarity=0.319  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|.|+.|+|||||.+.+.....
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGLLR   53 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccC
Confidence            35799999999999999999987643

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

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.83  E-value=0.0076  Score=51.75  Aligned_cols=27  Identities=33%  Similarity=0.561  Sum_probs=23.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      +.|.+.|.+|+||||+|+++.......
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHh
Confidence            467899999999999999999887653

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.82  E-value=0.007  Score=52.25  Aligned_cols=23  Identities=39%  Similarity=0.592  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +|+|.|.+|+||||+|+.+....
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999875

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.

>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=95.82  E-value=0.015  Score=50.74  Aligned_cols=122  Identities=24%  Similarity=0.289  Sum_probs=57.9

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC--c----CHHH-------HHHHHHHH
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT--P----QIKE-------IQREIAEK  226 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~----~~~~-------il~~i~~~  226 (426)
                      -...++.+.  ...++.+.|++|+|||.||....-+.-..+.|+.++++.-.-.  .    -+.+       .+.-+...
T Consensus         9 Q~~~~~al~--~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~   86 (205)
T PF02562_consen    9 QKFALDALL--NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDA   86 (205)
T ss_dssp             HHHHHHHHH--H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHH
T ss_pred             HHHHHHHHH--hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHH
Confidence            334445555  3468999999999999999998876655577888777642211  0    0111       11111222


Q ss_pred             hCCCccccCcHHHHHHHHH----------HHhcC---CeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          227 LGLKIDQESESVRAWRLLE----------QLKKE---TKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       227 l~~~~~~~~~~~~~~~l~~----------~l~~~---k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                      +..-.....    ...+.+          ++ +|   ...+|++|++.+.  .++..+...   .+.+|++|++--..+.
T Consensus        87 l~~~~~~~~----~~~~~~~~~Ie~~~~~~i-RGrt~~~~~iIvDEaQN~t~~~~k~ilTR---~g~~skii~~GD~~Q~  158 (205)
T PF02562_consen   87 LEELFGKEK----LEELIQNGKIEIEPLAFI-RGRTFDNAFIIVDEAQNLTPEELKMILTR---IGEGSKIIITGDPSQI  158 (205)
T ss_dssp             HTTTS-TTC----HHHHHHTTSEEEEEGGGG-TT--B-SEEEEE-SGGG--HHHHHHHHTT---B-TT-EEEEEE-----
T ss_pred             HHHHhChHh----HHHHhhcCeEEEEehhhh-cCccccceEEEEecccCCCHHHHHHHHcc---cCCCcEEEEecCceee
Confidence            211111111    111111          11 12   2479999999765  456655444   4568999998876543

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

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.80  E-value=0.036  Score=51.02  Aligned_cols=27  Identities=30%  Similarity=0.375  Sum_probs=24.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .++|.++||+|.|||+|.+.+++...+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSI  203 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSI  203 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhhee
Confidence            478999999999999999999998754

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=95.79  E-value=0.019  Score=46.45  Aligned_cols=27  Identities=30%  Similarity=0.201  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..+|.+.|.-|+||||+++.+.+....
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            358999999999999999999988653

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.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=95.78  E-value=0.0075  Score=50.21  Aligned_cols=23  Identities=35%  Similarity=0.556  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++.|+|++|+||||+|+.+....
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            47899999999999999998764

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=95.78  E-value=0.064  Score=47.86  Aligned_cols=53  Identities=21%  Similarity=0.370  Sum_probs=40.6

Q ss_pred             cccCCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          145 KSTQDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       145 ~~~~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|+..+.++-|-+..++++++.+.             -..++-+..+|++|.|||-+|+.......
T Consensus       165 kPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~  230 (424)
T KOG0652|consen  165 KPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTN  230 (424)
T ss_pred             CCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhcc
Confidence            344556778888999999888764             12456688999999999999998876544

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.77  E-value=0.011  Score=50.70  Aligned_cols=28  Identities=25%  Similarity=0.417  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+|.|+|++|+||||+|+.+......
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~   30 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLRE   30 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3468999999999999999999988754

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=95.76  E-value=0.014  Score=52.07  Aligned_cols=23  Identities=17%  Similarity=0.088  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      ..++.|.|+.|.||||+.+.+.-
T Consensus        31 g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999999876

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

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.75  E-value=0.042  Score=54.99  Aligned_cols=89  Identities=17%  Similarity=0.178  Sum_probs=49.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceE-EEEEecCCc-CHHHHHHHHHHHhCCCccccCc------HHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKV-ISSRVSQTP-QIKEIQREIAEKLGLKIDQESE------SVRAWRL  243 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~-~wv~v~~~~-~~~~il~~i~~~l~~~~~~~~~------~~~~~~l  243 (426)
                      -.-..|+|++|+|||||++.+.+..... +-++. +.+-+...+ .+.++.+.+-..+-...-..+.      ......+
T Consensus       416 GQR~LIvgpp~aGKTtLL~~IAn~i~~n-~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~~  494 (672)
T PRK12678        416 GQRGLIVSPPKAGKTTILQNIANAITTN-NPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIER  494 (672)
T ss_pred             CCEeEEeCCCCCCHHHHHHHHHHHHhhc-CCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHHH
Confidence            3457899999999999999999876542 23333 344555444 3333433321111111111111      1112233


Q ss_pred             HHHH-hcCCeEEEEEeCCC
Q 044858          244 LEQL-KKETKILIILDDIW  261 (426)
Q Consensus       244 ~~~l-~~~k~~LlVlDdv~  261 (426)
                      -+++ ..++.+||++|++-
T Consensus       495 Ae~fre~G~dVlillDSlT  513 (672)
T PRK12678        495 AKRLVELGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHcCCCEEEEEeCch
Confidence            3444 35899999999985

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.75  E-value=0.011  Score=52.25  Aligned_cols=31  Identities=26%  Similarity=0.399  Sum_probs=26.8

Q ss_pred             hccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          167 LSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       167 l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+++++|+++|+.|+|||||...+.+...
T Consensus        17 ~~~~~~~~i~~~G~~gsGKTTli~~l~~~~~   47 (207)
T TIGR00073        17 LDKHGLVVLNFMSSPGSGKTTLIEKLIDNLK   47 (207)
T ss_pred             hhhcCcEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3467899999999999999999999988753

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>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=95.74  E-value=0.056  Score=49.06  Aligned_cols=76  Identities=16%  Similarity=0.087  Sum_probs=42.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC--cCHHHHHHHHHHH----hCCCc--cccCcHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT--PQIKEIQREIAEK----LGLKI--DQESESVRAWRLLE  245 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~il~~i~~~----l~~~~--~~~~~~~~~~~l~~  245 (426)
                      +|+|.|.+|+||||+++.+.+.....+  ..+..++...-  .+-...-..+...    .+...  +...+.+.+...++
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~~~g--~~v~vI~~D~yyr~~r~~~~~~~~~a~~~~~nfdHf~PeAnd~dlL~~~l~   78 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFAREG--IHPAVVEGDSFHRYERMEMKMAIAEALDAGRNFSHFGPEANLFDLLEELFR   78 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhcC--CceEEEeccccccCCchhHHHHHHHHhhcCCCCCCCCcccccHHHHHHHHH
Confidence            589999999999999999988765432  12333333222  1222222222221    12222  34455666667777


Q ss_pred             HHhcCC
Q 044858          246 QLKKET  251 (426)
Q Consensus       246 ~l~~~k  251 (426)
                      .+.+++
T Consensus        79 ~L~~g~   84 (277)
T cd02029          79 TYGETG   84 (277)
T ss_pred             HHHcCC
Confidence            776543

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.

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=95.74  E-value=0.027  Score=51.51  Aligned_cols=102  Identities=20%  Similarity=0.219  Sum_probs=58.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .+..+.|||++|.|||-+|+.|+....+.  |     +.++..    .+..        . ........+.+.++...+.
T Consensus       165 ~Pkg~ll~GppGtGKTlla~~Vaa~mg~n--f-----l~v~ss----~lv~--------k-yiGEsaRlIRemf~yA~~~  224 (388)
T KOG0651|consen  165 PPKGLLLYGPPGTGKTLLARAVAATMGVN--F-----LKVVSS----ALVD--------K-YIGESARLIRDMFRYAREV  224 (388)
T ss_pred             CCceeEEeCCCCCchhHHHHHHHHhcCCc--e-----EEeeHh----hhhh--------h-hcccHHHHHHHHHHHHhhh
Confidence            45688999999999999999999988765  3     222111    0000        0 0011123344444555555


Q ss_pred             CeEEEEEeCCCCcc----------------ChhhhcCCCC--CCCCCeEEEEeecchhhh
Q 044858          251 TKILIILDDIWGSL----------------DLEAIGIPLA--DDNGGCKVLLTARSQDVL  292 (426)
Q Consensus       251 k~~LlVlDdv~~~~----------------~~~~l~~~l~--~~~~~s~iivTtr~~~va  292 (426)
                      .+|.|.+||++-..                .+-++...+-  +..+..++|+||...+..
T Consensus       225 ~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l~rVk~ImatNrpdtL  284 (388)
T KOG0651|consen  225 IPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTLHRVKTIMATNRPDTL  284 (388)
T ss_pred             CceEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccchhcccccEEEecCCcccc
Confidence            67999999986320                0111111111  223567899999887654

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=95.74  E-value=0.03  Score=57.64  Aligned_cols=75  Identities=15%  Similarity=0.185  Sum_probs=50.5

Q ss_pred             cccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC
Q 044858          150 FMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG  228 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~  228 (426)
                      ...++|.++.++.+...+..+.  .+.++|++|+||||+++.+.+..... .|...+++. ....+..++++.+..+++
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~--~~ll~G~pG~GKT~la~~la~~l~~~-~~~~~~~~~-n~~~~~~~~~~~v~~~~g   91 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKR--NVLLIGEPGVGKSMLAKAMAELLPDE-ELEDILVYP-NPEDPNMPRIVEVPAGEG   91 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCC--CEEEECCCCCCHHHHHHHHHHHcCch-hheeEEEEe-CCCCCchHHHHHHHHhhc
Confidence            4567888888777777666543  56699999999999999999877543 333333332 233355566666666554

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

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=95.74  E-value=0.04  Score=53.84  Aligned_cols=89  Identities=17%  Similarity=0.237  Sum_probs=57.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh------c-----CccceEEEEEecCCcCHHHHHHHHHHHhC-CC-------ccc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE------N-----NLFEKVISSRVSQTPQIKEIQREIAEKLG-LK-------IDQ  233 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~------~-----~~f~~~~wv~v~~~~~~~~il~~i~~~l~-~~-------~~~  233 (426)
                      +-++|.|.+|+|||||+.++.+....      .     +.=..++++-+++.....+.+.+.+..-+ ..       ...
T Consensus       142 QRigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~atsd  221 (466)
T TIGR01040       142 QKIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLAN  221 (466)
T ss_pred             CeeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEECCC
Confidence            46899999999999999999877641      0     00015667777777777776666666544 21       111


Q ss_pred             cCcHH------HHHHHHHHHh--cCCeEEEEEeCCC
Q 044858          234 ESESV------RAWRLLEQLK--KETKILIILDDIW  261 (426)
Q Consensus       234 ~~~~~------~~~~l~~~l~--~~k~~LlVlDdv~  261 (426)
                      .+...      ....+-+++.  +++++||++||+-
T Consensus       222 ~p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslT  257 (466)
T TIGR01040       222 DPTIERIITPRLALTTAEYLAYQCEKHVLVILTDMS  257 (466)
T ss_pred             CCHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChH
Confidence            11111      1224555665  4799999999984

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK08149 ATP synthase SpaL; Validated

Probab=95.74  E-value=0.064  Score=52.37  Aligned_cols=87  Identities=13%  Similarity=0.246  Sum_probs=51.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec-CCcCHHHHHHHHHHHhCCC-------ccccCcH------
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS-QTPQIKEIQREIAEKLGLK-------IDQESES------  237 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~il~~i~~~l~~~-------~~~~~~~------  237 (426)
                      -..++|+|..|+|||||+..+.....    -+.++...+. ...++.++..+........       ....+..      
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~~----~dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~  226 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHSE----ADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAA  226 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCCC----CCeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHH
Confidence            45789999999999999999987543    2333344444 3345666666666543211       1111111      


Q ss_pred             HHHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          238 VRAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       238 ~~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                      .....+-+++ .+++++||++||+-.
T Consensus       227 ~~a~tiAE~fr~~G~~Vll~~DslTr  252 (428)
T PRK08149        227 LVATTVAEYFRDQGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHHHHHHHHHcCCCEEEEccchHH
Confidence            1122333444 358999999999853

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=95.74  E-value=0.042  Score=57.41  Aligned_cols=26  Identities=31%  Similarity=0.332  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -..|+|+|..|+|||||++.+..-..
T Consensus       499 Ge~vaIvG~SGsGKSTL~KLL~gly~  524 (709)
T COG2274         499 GEKVAIVGRSGSGKSTLLKLLLGLYK  524 (709)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            35799999999999999999876543

>PRK06217 hypothetical protein; Validated

Probab=95.74  E-value=0.0085  Score=51.82  Aligned_cols=25  Identities=28%  Similarity=0.348  Sum_probs=22.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|.|.|.+|+||||+|+.+......
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~   27 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDI   27 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCC
Confidence            4899999999999999999987653

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

Probab=95.74  E-value=0.11  Score=48.04  Aligned_cols=51  Identities=18%  Similarity=0.217  Sum_probs=35.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .++.|.|++|+||||++.++....... +-..++|++...  +..++...+...
T Consensus        31 ~~~~i~g~~G~GKT~l~~~~~~~~~~~-~g~~vl~iS~E~--~~~~~~~r~~~~   81 (271)
T cd01122          31 ELIILTAGTGVGKTTFLREYALDLITQ-HGVRVGTISLEE--PVVRTARRLLGQ   81 (271)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHHh-cCceEEEEEccc--CHHHHHHHHHHH
Confidence            578899999999999999988765432 123567777654  345566665544

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

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.74  E-value=0.034  Score=47.35  Aligned_cols=80  Identities=19%  Similarity=0.173  Sum_probs=42.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc---cCcHHHHHHHHHHHhcC
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ---ESESVRAWRLLEQLKKE  250 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~---~~~~~~~~~l~~~l~~~  250 (426)
                      ++.|.|.+|+||||+|..+......     ..+++.-... .-.+..+.|..........   -.....+..+.+.... 
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~-----~~~~iat~~~-~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~-   75 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGL-----QVLYIATAQP-FDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAA-   75 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCC-----CcEeCcCCCC-ChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcC-
Confidence            6899999999999999999876422     1334433333 3345555654443322111   1111123333333222 


Q ss_pred             CeEEEEEeCC
Q 044858          251 TKILIILDDI  260 (426)
Q Consensus       251 k~~LlVlDdv  260 (426)
                      +.-++++|.+
T Consensus        76 ~~~~VlID~L   85 (170)
T PRK05800         76 PGRCVLVDCL   85 (170)
T ss_pred             CCCEEEehhH
Confidence            2337888986

>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=95.73  E-value=0.0085  Score=49.49  Aligned_cols=24  Identities=29%  Similarity=0.516  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.|.|+.|+||||+|+.+.....
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~~   24 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLG   24 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999998754

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

Probab=95.72  E-value=0.013  Score=52.48  Aligned_cols=60  Identities=20%  Similarity=0.287  Sum_probs=38.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe---------cCCcCHHHH--HHHHHHHhCCCcc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV---------SQTPQIKEI--QREIAEKLGLKID  232 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v---------~~~~~~~~i--l~~i~~~l~~~~~  232 (426)
                      ++..|.++||+|+||||..+.++.....+..-.  .-+++         +.+.++++.  .++.+++.++..+
T Consensus        18 ~p~~ilVvGMAGSGKTTF~QrL~~hl~~~~~pp--YviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPN   88 (366)
T KOG1532|consen   18 RPVIILVVGMAGSGKTTFMQRLNSHLHAKKTPP--YVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPN   88 (366)
T ss_pred             CCcEEEEEecCCCCchhHHHHHHHHHhhccCCC--eEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCC
Confidence            466889999999999999999998876543222  22222         223355543  3566777655443

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=95.71  E-value=0.032  Score=45.05  Aligned_cols=36  Identities=14%  Similarity=-0.104  Sum_probs=26.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEE
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSR  209 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~  209 (426)
                      .+.|.|+.|+|||+.+..+............+++++
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~   37 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLA   37 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEc
Confidence            467999999999999988887765433345566654

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

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.70  E-value=0.009  Score=51.42  Aligned_cols=25  Identities=36%  Similarity=0.636  Sum_probs=22.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +|+|.|.+|+||||||+.+......
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~~   25 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLRV   25 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH
Confidence            5899999999999999999988653

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK14527 adenylate kinase; Provisional

Probab=95.70  E-value=0.011  Score=51.42  Aligned_cols=28  Identities=18%  Similarity=0.258  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..+|.|+|++|+||||+|+.+.+...
T Consensus         4 ~~~~~i~i~G~pGsGKsT~a~~La~~~~   31 (191)
T PRK14527          4 TKNKVVIFLGPPGAGKGTQAERLAQELG   31 (191)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3567899999999999999999987764

>PTZ00185 ATPase alpha subunit; Provisional

Probab=95.67  E-value=0.081  Score=52.36  Aligned_cols=90  Identities=16%  Similarity=0.139  Sum_probs=52.5

Q ss_pred             cEEEEEcCCCCcHHHHH-HHHHHHhhh-----cCccceEEEEEecCCcCHHHHHHHHHHHhC-CCc-------cccCcHH
Q 044858          173 NMIGVYGMGGIGKTTLV-KEVGRQAKE-----NNLFEKVISSRVSQTPQIKEIQREIAEKLG-LKI-------DQESESV  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa-~~v~~~~~~-----~~~f~~~~wv~v~~~~~~~~il~~i~~~l~-~~~-------~~~~~~~  238 (426)
                      +-+.|.|..|+|||+|| ..+.+....     .+.-+.++++-+++..+...-+.+.++.-+ ...       ..++...
T Consensus       190 QR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~~  269 (574)
T PTZ00185        190 QRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGL  269 (574)
T ss_pred             CEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHHH
Confidence            46889999999999996 666666522     123456788888876643333444444433 110       1111111


Q ss_pred             ------HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 ------RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 ------~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                            ....+-+++ .+++++|+|+||+-.
T Consensus       270 r~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr  300 (574)
T PTZ00185        270 QYLAPYSGVTMGEYFMNRGRHCLCVYDDLSK  300 (574)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCEEEEEcCchH
Confidence                  112233333 357999999999853

>PRK13975 thymidylate kinase; Provisional

Probab=95.67  E-value=0.024  Score=49.46  Aligned_cols=26  Identities=31%  Similarity=0.412  Sum_probs=23.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+|+|.|+.|+||||+++.+.+....
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            47999999999999999999988753

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.66  E-value=0.019  Score=52.69  Aligned_cols=42  Identities=19%  Similarity=0.227  Sum_probs=35.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..+++.|+|.+|+|||+++.++.......  ...++||+....+
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~--ge~vlyvs~~e~~   63 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGARE--GEPVLYVSTEESP   63 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhc--CCcEEEEEecCCH
Confidence            45789999999999999999999887754  7788999887653

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.66  E-value=0.018  Score=50.50  Aligned_cols=30  Identities=20%  Similarity=0.295  Sum_probs=25.6

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .++..+|.|+|++|+||||||+.+......
T Consensus        21 ~~~~~~i~i~G~~GsGKSTla~~l~~~l~~   50 (198)
T PRK03846         21 GHKGVVLWFTGLSGSGKSTVAGALEEALHE   50 (198)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            346679999999999999999999987643

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

Probab=95.66  E-value=0.033  Score=53.04  Aligned_cols=63  Identities=16%  Similarity=0.159  Sum_probs=46.3

Q ss_pred             ccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          153 FESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      ++|+++.+..+...+..++  -+.+.|++|+|||+||+.+.......     .+++.+.......++...
T Consensus        26 ~~g~~~~~~~~l~a~~~~~--~vll~G~PG~gKT~la~~lA~~l~~~-----~~~i~~t~~l~p~d~~G~   88 (329)
T COG0714          26 VVGDEEVIELALLALLAGG--HVLLEGPPGVGKTLLARALARALGLP-----FVRIQCTPDLLPSDLLGT   88 (329)
T ss_pred             eeccHHHHHHHHHHHHcCC--CEEEECCCCccHHHHHHHHHHHhCCC-----eEEEecCCCCCHHHhcCc
Confidence            6778888877777766553  37899999999999999999887632     345666666666665443

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.66  E-value=0.069  Score=52.21  Aligned_cols=88  Identities=17%  Similarity=0.325  Sum_probs=53.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      +-..++|.|..|+|||||...+++...    .+.++++-++.. ..+.++....+..-+..       ...++...    
T Consensus       161 ~Gq~~~I~G~sG~GKStLl~~Ia~~~~----~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a  236 (439)
T PRK06936        161 EGQRMGIFAAAGGGKSTLLASLIRSAE----VDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKA  236 (439)
T ss_pred             CCCEEEEECCCCCChHHHHHHHhcCCC----CCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHH
Confidence            345789999999999999999988754    345667766654 35555555544332111       11111111    


Q ss_pred             --HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 --RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 --~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                        ....+-+++ .+++++|+++||+-.
T Consensus       237 ~~~a~tiAEyfrd~G~~Vll~~DslTR  263 (439)
T PRK06936        237 GFVATSIAEYFRDQGKRVLLLMDSVTR  263 (439)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchhH
Confidence              122334444 258999999999853

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.65  E-value=0.0091  Score=51.36  Aligned_cols=24  Identities=38%  Similarity=0.551  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++|+|+|+.|+|||||++.+....
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            478999999999999999998854

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.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=95.64  E-value=0.13  Score=53.68  Aligned_cols=47  Identities=15%  Similarity=0.323  Sum_probs=34.1

Q ss_pred             cccccchHHHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          150 FMHFESRKSTLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..++|....+.++.+...   ... .-|.|+|..|+||+++|+.+++...
T Consensus       324 ~~~l~g~s~~~~~~~~~~~~~a~~~-~pvli~Ge~GtGK~~~A~~ih~~s~  373 (638)
T PRK11388        324 FDHMPQDSPQMRRLIHFGRQAAKSS-FPVLLCGEEGVGKALLAQAIHNESE  373 (638)
T ss_pred             ccceEECCHHHHHHHHHHHHHhCcC-CCEEEECCCCcCHHHHHHHHHHhCC
Confidence            4456777766666665554   222 3378999999999999999988653

>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=95.63  E-value=0.011  Score=46.86  Aligned_cols=23  Identities=35%  Similarity=0.527  Sum_probs=20.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |.|+|..|+|||||.+.+.....
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~~   24 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGEF   24 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS-
T ss_pred             EEEECcCCCCHHHHHHHHhcCCC
Confidence            78999999999999999987654

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.

>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=95.62  E-value=0.021  Score=48.53  Aligned_cols=24  Identities=46%  Similarity=0.577  Sum_probs=20.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      |.|+|.+|+|||||++.+++..+.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l~~   25 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEELKK   25 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHhhc
Confidence            689999999999999999988753

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.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=95.62  E-value=0.047  Score=52.53  Aligned_cols=41  Identities=22%  Similarity=0.269  Sum_probs=30.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT  213 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  213 (426)
                      .++.|.|.+|+|||.||-.++.............+++....
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~   42 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHP   42 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecch
Confidence            47899999999999999999998822233455566665543

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.60  E-value=0.012  Score=51.85  Aligned_cols=25  Identities=36%  Similarity=0.388  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+|+|+|+.|+|||||++.+....
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4689999999999999999999864

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=95.60  E-value=0.081  Score=49.92  Aligned_cols=49  Identities=18%  Similarity=0.248  Sum_probs=36.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIA  224 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~  224 (426)
                      -..++|.|..|+|||+|++++.+...    -+.++++-+.+. ..+.+++.++-
T Consensus       157 Gqr~~I~G~~G~GKT~L~~~Iak~~~----~dvvVyv~iGERg~Ev~e~l~ef~  206 (369)
T cd01134         157 GGTAAIPGPFGCGKTVIQQSLSKYSN----SDIVIYVGCGERGNEMTEVLEEFP  206 (369)
T ss_pred             CCEEEEECCCCCChHHHHHHHHhCCC----CCEEEEEEeCCChHHHHHHHHHHH
Confidence            35789999999999999999988643    356777777654 45566666653

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.

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.60  E-value=0.011  Score=51.14  Aligned_cols=26  Identities=15%  Similarity=0.295  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +..+|.|+|++|+|||||++.+....
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            45789999999999999999998764

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=95.60  E-value=0.019  Score=54.42  Aligned_cols=48  Identities=17%  Similarity=0.257  Sum_probs=38.4

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++..++|.++.++.+.-.+.+.+..-+.+.|..|+||||+|+.+..-.
T Consensus         6 ~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          6 PFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             CHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            456788999988887765554444568899999999999999997764

>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=95.59  E-value=0.015  Score=46.37  Aligned_cols=25  Identities=36%  Similarity=0.523  Sum_probs=18.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      |.|+|.+|+||||+|+.+.......
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~~   26 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGLS   26 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT--
T ss_pred             EeeECCCccHHHHHHHHHHHHcCCc
Confidence            6799999999999999999887643

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.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.59  E-value=0.025  Score=52.09  Aligned_cols=94  Identities=13%  Similarity=0.131  Sum_probs=52.9

Q ss_pred             HHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-------cC
Q 044858          163 ILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-------ES  235 (426)
Q Consensus       163 l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-------~~  235 (426)
                      ....+...+..++.|.|.+|+|||||+..+.+.....  .. .+.+ .....+..+  .+.++..+.+.-.       ..
T Consensus        95 ~r~~~~~~~~~~v~l~G~pGsGKTTLl~~l~~~l~~~--~~-~~VI-~gD~~t~~D--a~rI~~~g~pvvqi~tG~~Chl  168 (290)
T PRK10463         95 NRARFAARKQLVLNLVSSPGSGKTTLLTETLMRLKDS--VP-CAVI-EGDQQTVND--AARIRATGTPAIQVNTGKGCHL  168 (290)
T ss_pred             HHHHHHhcCCeEEEEECCCCCCHHHHHHHHHHHhccC--CC-EEEE-CCCcCcHHH--HHHHHhcCCcEEEecCCCCCcC
Confidence            4444456678899999999999999999999886543  22 2222 222222222  2223444433211       11


Q ss_pred             cHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 044858          236 ESVRAWRLLEQLKKETKILIILDDIWG  262 (426)
Q Consensus       236 ~~~~~~~l~~~l~~~k~~LlVlDdv~~  262 (426)
                      +...+......+.....-+++++++-+
T Consensus       169 ~a~mv~~Al~~L~~~~~d~liIEnvGn  195 (290)
T PRK10463        169 DAQMIADAAPRLPLDDNGILFIENVGN  195 (290)
T ss_pred             cHHHHHHHHHHHhhcCCcEEEEECCCC
Confidence            233344445555433346778898854

>TIGR01351 adk adenylate kinases

Probab=95.59  E-value=0.051  Score=48.08  Aligned_cols=23  Identities=26%  Similarity=0.352  Sum_probs=20.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |.|.|++|+||||+|+.+.....
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g   24 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYG   24 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            68999999999999999987653

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.

>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=95.58  E-value=0.024  Score=53.16  Aligned_cols=46  Identities=15%  Similarity=0.322  Sum_probs=31.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQ  220 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il  220 (426)
                      +++.+.|.||+||||+|....-....++  ..+.-++..+..++.+++
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~G--~rtLlvS~Dpa~~L~d~l   47 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARRG--KRTLLVSTDPAHSLSDVL   47 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTT--S-EEEEESSTTTHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhCC--CCeeEeecCCCccHHHHh
Confidence            6789999999999999988876655432  234455555554544444

...

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.58  E-value=0.041  Score=53.21  Aligned_cols=47  Identities=23%  Similarity=0.292  Sum_probs=34.1

Q ss_pred             cccchHHHHHHHHHHhcc--------------CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          152 HFESRKSTLKGILDALSN--------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~--------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .++|.++.++.+.-.+..              ..++.|.++|++|+|||++|+.+......
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~   73 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANA   73 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            356766666665444331              12467899999999999999999988754

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.

>PRK04196 V-type ATP synthase subunit B; Provisional

Probab=95.58  E-value=0.071  Score=52.73  Aligned_cols=89  Identities=21%  Similarity=0.280  Sum_probs=56.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc---CccceEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcH---
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN---NLFEKVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESES---  237 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~---~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~---  237 (426)
                      -+-++|.|..|+|||+|+.++.+....+   ..+ .++++-+++. ..+.+++.++...-...       ....+..   
T Consensus       143 GQR~gIfgg~G~GKs~L~~~ia~~~~~d~~~~~~-v~V~~~iGeRgrEv~e~~~~~~~~~~l~rtvvV~atsd~p~~~R~  221 (460)
T PRK04196        143 GQKLPIFSGSGLPHNELAAQIARQAKVLGEEENF-AVVFAAMGITFEEANFFMEDFEETGALERSVVFLNLADDPAIERI  221 (460)
T ss_pred             CCEEEeeCCCCCCccHHHHHHHHhhhhccCCCce-EEEEEEeccccHHHHHHHHHHHhcCCcceEEEEEEcCCCCHHHHH
Confidence            3568899999999999999998876532   112 4566666544 46677777776542211       1111111   


Q ss_pred             ---HHHHHHHHHHh--cCCeEEEEEeCCC
Q 044858          238 ---VRAWRLLEQLK--KETKILIILDDIW  261 (426)
Q Consensus       238 ---~~~~~l~~~l~--~~k~~LlVlDdv~  261 (426)
                         -....+-+++.  +++++||++||+-
T Consensus       222 ~a~~~a~tiAEyfr~d~G~~VLli~DslT  250 (460)
T PRK04196        222 LTPRMALTAAEYLAFEKGMHVLVILTDMT  250 (460)
T ss_pred             HHHHHHHHHHHHHHHhcCCcEEEEEcChH
Confidence               12234556665  5799999999984

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=95.57  E-value=0.025  Score=47.46  Aligned_cols=31  Identities=19%  Similarity=0.306  Sum_probs=26.9

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .++..+|.++|.+|+||||+|..++......
T Consensus        20 ~~~~~viW~TGLSGsGKSTiA~ale~~L~~~   50 (197)
T COG0529          20 GQKGAVIWFTGLSGSGKSTIANALEEKLFAK   50 (197)
T ss_pred             CCCCeEEEeecCCCCCHHHHHHHHHHHHHHc
Confidence            4566799999999999999999999987654

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.56  E-value=0.084  Score=47.73  Aligned_cols=141  Identities=16%  Similarity=0.142  Sum_probs=71.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCcc----------ceEEEEEecCCc-CHHHHHHHHHHHhCCCc-c---------
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLF----------EKVISSRVSQTP-QIKEIQREIAEKLGLKI-D---------  232 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----------~~~~wv~v~~~~-~~~~il~~i~~~l~~~~-~---------  232 (426)
                      +-.|+|++|+|||+|+.++.-.......|          ..+++++...+. .+.+=+..+...++... .         
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~rl~~~~g~   82 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDSGR   82 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCCCHHHHHHHHHHHHhhcCCcCcccceEEeccC
Confidence            56799999999999999998765422111          134555544432 22333333333332100 0         


Q ss_pred             -------c---cCcHHHHHHHHHHHhcCCeEEEEEeCCCC--------ccChhhhcCCCC--CCCCCeEEEEeecchhhh
Q 044858          233 -------Q---ESESVRAWRLLEQLKKETKILIILDDIWG--------SLDLEAIGIPLA--DDNGGCKVLLTARSQDVL  292 (426)
Q Consensus       233 -------~---~~~~~~~~~l~~~l~~~k~~LlVlDdv~~--------~~~~~~l~~~l~--~~~~~s~iivTtr~~~va  292 (426)
                             .   ......+..+.+.+...+.-+||+|-+..        ......+...+.  ....|+.||+++......
T Consensus        83 ~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~lvviDpl~~~~~~~~~d~~~~~~~~~~L~~~a~~~g~avl~v~H~~K~~  162 (239)
T cd01125          83 IQPISIAREGRIIVVPEFERIIEQLLIRRIDLVVIDPLVSFHGVSENDNGAMDAVIKALRRIAAQTGAAILLVHHVRKGS  162 (239)
T ss_pred             CCceecccCCcccccHHHHHHHHHHHhcCCCEEEECChHHhCCCCcCCHHHHHHHHHHHHHHHHHhCCEEEEEeccCccc
Confidence                   0   01223444555555444678999996532        111222222111  123477788887765321


Q ss_pred             h--------------ccCCceeeEEccCCCHHHHHH
Q 044858          293 S--------------CEMDCQQNFVVDVLNDKEAWS  314 (426)
Q Consensus       293 ~--------------~~~~~~~~~~l~~L~~~e~~~  314 (426)
                      .              ........+.+.+.+++++.+
T Consensus       163 ~~~~~~~~~~rGssal~~~~r~~~~l~~~~~~~~~~  198 (239)
T cd01125         163 AKDGDTQEAARGASALVDGARWVRALTRMTSEEAEK  198 (239)
T ss_pred             ccCcccccccCcHHHHhcccceEEEEeeCCHHHHHh
Confidence            1              001123467777777777766

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.

>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=95.56  E-value=0.024  Score=53.28  Aligned_cols=92  Identities=25%  Similarity=0.361  Sum_probs=60.7

Q ss_pred             ccccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC----c---CHH
Q 044858          151 MHFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT----P---QIK  217 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~----~---~~~  217 (426)
                      ..|+|-++.++++++.+.      +..-+++.++||.|.|||||++.+.+-.+.   |  .+|.-...+    +   =+.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~---y--~~Y~l~~~Pm~e~PL~L~P~  135 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLEE---Y--PIYTLKGCPMHEEPLHLFPK  135 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhhe---E--EEEEecCCccccChhhhCCH
Confidence            368999999999999886      345689999999999999999999887764   3  333322111    1   134


Q ss_pred             HHHHHHHHHhCCCccccCcHHHHHHHHHHH
Q 044858          218 EIQREIAEKLGLKIDQESESVRAWRLLEQL  247 (426)
Q Consensus       218 ~il~~i~~~l~~~~~~~~~~~~~~~l~~~l  247 (426)
                      ++-.++.+.++......-......++.+..
T Consensus       136 ~~r~~~~~~~~~~i~g~l~p~~~~~L~~~y  165 (358)
T PF08298_consen  136 ELRREFEDELGIRIEGELCPWCRKRLLEEY  165 (358)
T ss_pred             hHHHHHHHHhCcccCCCcCHHHHHHHHHHh
Confidence            555566666766554433333334444444

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=95.56  E-value=0.043  Score=51.47  Aligned_cols=61  Identities=16%  Similarity=0.234  Sum_probs=41.4

Q ss_pred             ccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHH
Q 044858          153 FESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQ  220 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il  220 (426)
                      ++-+......++.++..+  +.|.|.|++|+||||+|+.+.......     .+.|..+...+..++.
T Consensus        47 y~f~~~~~~~vl~~l~~~--~~ilL~G~pGtGKTtla~~lA~~l~~~-----~~rV~~~~~l~~~Dli  107 (327)
T TIGR01650        47 YLFDKATTKAICAGFAYD--RRVMVQGYHGTGKSTHIEQIAARLNWP-----CVRVNLDSHVSRIDLV  107 (327)
T ss_pred             ccCCHHHHHHHHHHHhcC--CcEEEEeCCCChHHHHHHHHHHHHCCC-----eEEEEecCCCChhhcC
Confidence            444445566677777543  358999999999999999999887532     2355555555554443

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.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=95.56  E-value=0.067  Score=52.22  Aligned_cols=88  Identities=22%  Similarity=0.335  Sum_probs=50.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCC-------ccccCcHH------
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLK-------IDQESESV------  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~-------~~~~~~~~------  238 (426)
                      -..++|.|..|+|||||++.+......   ...++.....+...+.++....+..-+..       ...++...      
T Consensus       140 Gq~i~I~G~sG~GKTtLl~~I~~~~~~---~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~  216 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARNTDA---DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAY  216 (418)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCCC---CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHH
Confidence            357899999999999999988876542   22233322233445566666554432211       11111111      


Q ss_pred             HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 ~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                      ....+-+++ .+++++||++||+-.
T Consensus       217 ~a~~iAEyfrd~G~~Vll~~DslTr  241 (418)
T TIGR03498       217 TATAIAEYFRDQGKDVLLLMDSVTR  241 (418)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchhH
Confidence            122344444 257899999999853

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.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=95.55  E-value=0.1  Score=51.16  Aligned_cols=90  Identities=19%  Similarity=0.317  Sum_probs=57.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcHH-----
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESESV-----  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~~-----  238 (426)
                      -+-++|.|.+|+|||||+.++......+ +-..++++-++.. ..+.+++.++...-...       ....+...     
T Consensus       143 GQr~~If~~~G~GKt~L~~~~~~~~~~~-~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~  221 (461)
T TIGR01039       143 GGKIGLFGGAGVGKTVLIQELINNIAKE-HGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVA  221 (461)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHHHHhc-CCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            3568999999999999999988776542 2246667777544 45677777775432211       11111111     


Q ss_pred             -HHHHHHHHHh--cCCeEEEEEeCCCC
Q 044858          239 -RAWRLLEQLK--KETKILIILDDIWG  262 (426)
Q Consensus       239 -~~~~l~~~l~--~~k~~LlVlDdv~~  262 (426)
                       ....+-+++.  +++++||++||+-.
T Consensus       222 ~~a~tiAEyfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       222 LTGLTMAEYFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEecchhH
Confidence             2234555563  47899999999853

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.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.54  E-value=0.01  Score=48.62  Aligned_cols=24  Identities=33%  Similarity=0.537  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|+|+|+.|+|||||++.+.....
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~~   24 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEFD   24 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcCC
Confidence            378999999999999999997643

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.

>PRK14531 adenylate kinase; Provisional

Probab=95.53  E-value=0.046  Score=47.22  Aligned_cols=25  Identities=20%  Similarity=0.171  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..|.|+|++|+||||+++.+.....
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g   27 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHG   27 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3588999999999999999988764

>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=95.53  E-value=0.042  Score=47.86  Aligned_cols=25  Identities=32%  Similarity=0.524  Sum_probs=22.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +|+|.|+.|+||||+++.+.+....
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~   26 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEA   26 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            6899999999999999999988753

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.53  E-value=0.077  Score=45.69  Aligned_cols=119  Identities=18%  Similarity=0.122  Sum_probs=65.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEE--EEEecCCcCHHHHHHHHH--H--HhCCC--ccccCc---HHH-
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVI--SSRVSQTPQIKEIQREIA--E--KLGLK--IDQESE---SVR-  239 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~--wv~v~~~~~~~~il~~i~--~--~l~~~--~~~~~~---~~~-  239 (426)
                      ...|.|+|..|-||||.|.-+.-+....+ +.+.+  |..-........++..+-  .  +.+..  ....+.   ... 
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~ra~g~G-~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~  100 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMALRAVGHG-KKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAA  100 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHHHHHHCC-CeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHH
Confidence            46799999999999999998887765433 22222  222222344455554421  0  01111  111111   111 


Q ss_pred             ---HHHHHHHHhcCCeEEEEEeCCCCc-----cChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          240 ---AWRLLEQLKKETKILIILDDIWGS-----LDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       240 ---~~~l~~~l~~~k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                         .....+.+..++-=|||||++-..     -+.+++...+.....+.-||+|-|+..-
T Consensus       101 ~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~  160 (191)
T PRK05986        101 REGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPR  160 (191)
T ss_pred             HHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCH
Confidence               223344444555569999998533     2344444444444457789999998643

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

Probab=95.53  E-value=0.06  Score=45.72  Aligned_cols=44  Identities=14%  Similarity=0.188  Sum_probs=28.7

Q ss_pred             cchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          154 ESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       154 ~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|....+.++++.+.  .....-|.|+|..|+||+.+|+.+++...
T Consensus         2 iG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~   47 (168)
T PF00158_consen    2 IGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSP   47 (168)
T ss_dssp             S--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCST
T ss_pred             EeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhh
Confidence            455555555555443  12224567999999999999999998644

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 ....

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=95.52  E-value=0.066  Score=52.92  Aligned_cols=90  Identities=20%  Similarity=0.310  Sum_probs=56.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCCc--------------cccCc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLKI--------------DQESE  236 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~~--------------~~~~~  236 (426)
                      -+-++|.|.+|+|||+|+.++....... +=+.++++-+++.. ...++...++..-....              ..++.
T Consensus       161 GQR~gIfgg~GvGKs~L~~~~~~~~~~~-~~dv~V~~lIGERgrEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd~p~  239 (494)
T CHL00060        161 GGKIGLFGGAGVGKTVLIMELINNIAKA-HGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPP  239 (494)
T ss_pred             CCEEeeecCCCCChhHHHHHHHHHHHHh-cCCeEEEEEeccCchHHHHHHHHHHhcCccccCcccccceEEEEECCCCCH
Confidence            3568999999999999999988774321 12677787776554 56777777765211110              01111


Q ss_pred             H------HHHHHHHHHHhc-C-CeEEEEEeCCCC
Q 044858          237 S------VRAWRLLEQLKK-E-TKILIILDDIWG  262 (426)
Q Consensus       237 ~------~~~~~l~~~l~~-~-k~~LlVlDdv~~  262 (426)
                      .      .....+-+++.. + +++||++||+-.
T Consensus       240 ~~R~~a~~~A~tiAEyfrd~g~~~VLll~DslTR  273 (494)
T CHL00060        240 GARMRVGLTALTMAEYFRDVNKQDVLLFIDNIFR  273 (494)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCEEEEcccchH
Confidence            1      122345566643 4 499999999853

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=95.51  E-value=0.015  Score=48.71  Aligned_cols=29  Identities=31%  Similarity=0.597  Sum_probs=26.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENN  200 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~  200 (426)
                      .++++|+|..|+|||||...+....+.++
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G   30 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARG   30 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHHHhCC
Confidence            47899999999999999999999888754

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=95.51  E-value=0.042  Score=56.49  Aligned_cols=52  Identities=15%  Similarity=0.050  Sum_probs=32.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEEEEecCCcCHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      .++..|.|.+|+||||++..+....... ..-...+.+..+...-...+...+
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~  219 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESL  219 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHH
Confidence            3688999999999999999988765331 111234555554443344444444

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.50  E-value=0.011  Score=49.40  Aligned_cols=20  Identities=40%  Similarity=0.674  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVG  193 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~  193 (426)
                      .|+|+|.+|+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999987

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=95.50  E-value=0.055  Score=52.74  Aligned_cols=86  Identities=22%  Similarity=0.402  Sum_probs=49.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcHH-----
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESESV-----  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~~-----  238 (426)
                      -..++|.|..|+|||||++.+......    +..+...+... ..+.++.......-...       ....+...     
T Consensus       137 Gq~~~I~G~sG~GKTtLl~~I~~~~~~----~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~  212 (411)
T TIGR03496       137 GQRMGIFAGSGVGKSTLLGMMARYTEA----DVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAA  212 (411)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCC----CEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHH
Confidence            357899999999999999988865432    33344445443 34555555554332111       11111111     


Q ss_pred             -HHHHHHHHH-hcCCeEEEEEeCCC
Q 044858          239 -RAWRLLEQL-KKETKILIILDDIW  261 (426)
Q Consensus       239 -~~~~l~~~l-~~~k~~LlVlDdv~  261 (426)
                       ....+-+++ .+++++||++||+-
T Consensus       213 ~~a~tiAEyfr~~G~~Vll~~Dslt  237 (411)
T TIGR03496       213 FYATAIAEYFRDQGKDVLLLMDSLT  237 (411)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEeChH
Confidence             122334444 25789999999984

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.

>PRK05922 type III secretion system ATPase; Validated

Probab=95.50  E-value=0.098  Score=51.13  Aligned_cols=87  Identities=20%  Similarity=0.333  Sum_probs=50.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCc-------cccCcHH-----
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKI-------DQESESV-----  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~-------~~~~~~~-----  238 (426)
                      -..++|.|..|+|||||.+.+.....    .+...++.++. .....+.+.+.........       ..++...     
T Consensus       157 GqrigI~G~nG~GKSTLL~~Ia~~~~----~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~  232 (434)
T PRK05922        157 GQRIGVFSEPGSGKSSLLSTIAKGSK----STINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAG  232 (434)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccCC----CCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHH
Confidence            35689999999999999999987543    23333333333 3344555555544332211       1111111     


Q ss_pred             -HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 -RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 -~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                       ....+-+++ .+++++|+++||+-.
T Consensus       233 ~~a~tiAEyfrd~G~~VLl~~DslTR  258 (434)
T PRK05922        233 RAAMTIAEYFRDQGHRVLFIMDSLSR  258 (434)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchhH
Confidence             122344444 358999999999854

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=95.49  E-value=0.031  Score=52.49  Aligned_cols=48  Identities=21%  Similarity=0.353  Sum_probs=33.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~  221 (426)
                      .+++.+.|.||+||||+|....-.....+  ..+.-|+..+..++.+++.
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~~g--~kvLlvStDPAhsL~d~f~   49 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAESG--KKVLLVSTDPAHSLGDVFD   49 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHHcC--CcEEEEEeCCCCchHhhhc
Confidence            46899999999999999999766655443  3356666655554444433

>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=95.48  E-value=0.023  Score=47.56  Aligned_cols=34  Identities=21%  Similarity=0.431  Sum_probs=27.5

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +++|.+.+.+   ++++++|..|+|||||...+....
T Consensus        26 ~~~l~~~l~~---k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   26 IEELKELLKG---KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             HHHHHHHHTT---SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             HHHHHHHhcC---CEEEEECCCCCCHHHHHHHHHhhc
Confidence            4566666554   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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.48  E-value=0.029  Score=53.65  Aligned_cols=111  Identities=16%  Similarity=0.109  Sum_probs=57.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHH-HHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKE-IQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~-il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      ....|.|.|+.|+||||+.+.+.+....  +....++. +.++..... -...+..+-..   ..........+...+. 
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~--~~~~~i~t-iEdp~E~~~~~~~~~i~q~ev---g~~~~~~~~~l~~~lr-  193 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINK--NAAGHIIT-IEDPIEYVHRNKRSLINQREV---GLDTLSFANALRAALR-  193 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCc--CCCCEEEE-EcCChhhhccCccceEEcccc---CCCCcCHHHHHHHhhc-
Confidence            3478999999999999999998876542  23333332 222211100 00000001000   1111112223334444 


Q ss_pred             CCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          250 ETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       250 ~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                      ..+=+|++|++.+.+.+......   ...|..++.|......
T Consensus       194 ~~pd~i~vgEird~~~~~~~l~a---a~tGh~v~~T~Ha~~~  232 (343)
T TIGR01420       194 EDPDVILIGEMRDLETVELALTA---AETGHLVFGTLHTNSA  232 (343)
T ss_pred             cCCCEEEEeCCCCHHHHHHHHHH---HHcCCcEEEEEcCCCH
Confidence            46889999999887666542221   2335556666665544

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.

>PRK14530 adenylate kinase; Provisional

Probab=95.48  E-value=0.013  Score=52.08  Aligned_cols=25  Identities=24%  Similarity=0.262  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.|.|+|++|+||||+++.+.....
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~   28 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFG   28 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3689999999999999999987764

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.48  E-value=0.11  Score=49.08  Aligned_cols=28  Identities=32%  Similarity=0.451  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..++.++|+.|+||||++..+......
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~  140 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKA  140 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            4679999999999999999999887764

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.48  E-value=0.057  Score=52.99  Aligned_cols=89  Identities=19%  Similarity=0.308  Sum_probs=52.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCC-------ccccCcHH-----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLK-------IDQESESV-----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~-------~~~~~~~~-----  238 (426)
                      +-..++|.|..|+|||||++.+.......   ..++...-.+...+.++.+.+...-+..       ....+...     
T Consensus       162 ~Gq~~~I~G~sG~GKTtLl~~ia~~~~~d---~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~  238 (441)
T PRK09099        162 EGQRMGIFAPAGVGKSTLMGMFARGTQCD---VNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKAA  238 (441)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCCC---eEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHH
Confidence            44679999999999999999998655421   2344433344455666666665442211       11111111     


Q ss_pred             -HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 -RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 -~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                       ....+-+++ .+++++|+++||+-.
T Consensus       239 ~~a~tiAEyfrd~G~~VLl~~DslTr  264 (441)
T PRK09099        239 YVATAIAEYFRDRGLRVLLMMDSLTR  264 (441)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchhH
Confidence             122334444 358999999999853

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=95.47  E-value=0.12  Score=47.03  Aligned_cols=95  Identities=21%  Similarity=0.349  Sum_probs=61.1

Q ss_pred             ccCCcccccchHHHHHHHHHHhc----c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          146 STQDFMHFESRKSTLKGILDALS----N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       146 ~~~~~~~~~gR~~~~~~l~~~l~----~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      |...+.++-|-+..+.+|.+...    .         ..++=|.++|.+|.|||-||+.|+|.....  |-.+       
T Consensus       180 P~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSAT--FlRv-------  250 (440)
T KOG0726|consen  180 PQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSAT--FLRV-------  250 (440)
T ss_pred             chhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchh--hhhh-------
Confidence            33445667778888888777654    1         245667799999999999999999876543  3211       


Q ss_pred             CcCHHHHHHHHHH-HhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          213 TPQIKEIQREIAE-KLGLKIDQESESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       213 ~~~~~~il~~i~~-~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                            +-.++++ ++|.      -..++.++++.....-+.++++|+++
T Consensus       251 ------vGseLiQkylGd------GpklvRqlF~vA~e~apSIvFiDEId  288 (440)
T KOG0726|consen  251 ------VGSELIQKYLGD------GPKLVRELFRVAEEHAPSIVFIDEID  288 (440)
T ss_pred             ------hhHHHHHHHhcc------chHHHHHHHHHHHhcCCceEEeehhh
Confidence                  1112221 2221      12355666666666678899999885

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=95.47  E-value=0.063  Score=52.47  Aligned_cols=90  Identities=23%  Similarity=0.356  Sum_probs=52.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCc-------cccCcHH-----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKI-------DQESESV-----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~-------~~~~~~~-----  238 (426)
                      +-..++|.|..|+|||||+..+....+..   ..++...-.+.....+++...+..-+...       ...+...     
T Consensus       155 ~Gqri~I~G~sG~GKTtLl~~Ia~~~~~~---~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~  231 (432)
T PRK06793        155 IGQKIGIFAGSGVGKSTLLGMIAKNAKAD---INVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAA  231 (432)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhccCCCC---eEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHH
Confidence            34578999999999999999998765431   22333222334667777776665433211       1111111     


Q ss_pred             -HHHHHHHHH-hcCCeEEEEEeCCCCc
Q 044858          239 -RAWRLLEQL-KKETKILIILDDIWGS  263 (426)
Q Consensus       239 -~~~~l~~~l-~~~k~~LlVlDdv~~~  263 (426)
                       ....+.+++ .++++.||++||+-..
T Consensus       232 ~~a~~iAEyfr~~G~~VLlilDslTr~  258 (432)
T PRK06793        232 KLATSIAEYFRDQGNNVLLMMDSVTRF  258 (432)
T ss_pred             HHHHHHHHHHHHcCCcEEEEecchHHH
Confidence             112233333 2478999999999644

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.47  E-value=0.081  Score=48.33  Aligned_cols=94  Identities=15%  Similarity=0.209  Sum_probs=53.6

Q ss_pred             cEEEEEcCCCCcHHHHH-HHHHHHhhhcCccceE-EEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          173 NMIGVYGMGGIGKTTLV-KEVGRQAKENNLFEKV-ISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~~~-~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      +-+.|.|..|+|||+|| ..+.+...    -+.+ +++-+.+. ....++..++...-...       ...++...    
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~~~----~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a  145 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQKG----KKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLA  145 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHhcC----CCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHH
Confidence            56899999999999996 55555432    2333 56666554 45666776666432111       11111111    


Q ss_pred             --HHHHHHHHHh-cCCeEEEEEeCCCCc-cChhhhc
Q 044858          239 --RAWRLLEQLK-KETKILIILDDIWGS-LDLEAIG  270 (426)
Q Consensus       239 --~~~~l~~~l~-~~k~~LlVlDdv~~~-~~~~~l~  270 (426)
                        ....+-+++. +++++||++||+-.. ..++++.
T Consensus       146 ~~~a~aiAE~fr~~G~~Vlvl~DslTr~A~A~rEis  181 (274)
T cd01132         146 PYTGCAMGEYFMDNGKHALIIYDDLSKQAVAYRQMS  181 (274)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEcChHHHHHHHHHHH
Confidence              1123333332 479999999999644 4455543

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.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.45  E-value=0.072  Score=54.38  Aligned_cols=27  Identities=22%  Similarity=0.273  Sum_probs=22.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +-..++|+|+.|+|||||++.+.....
T Consensus       360 ~G~~vaIvG~SGsGKSTLl~lL~g~~~  386 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTLLMLLTGLLD  386 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            446799999999999999999976543

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.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=95.43  E-value=0.047  Score=47.58  Aligned_cols=26  Identities=31%  Similarity=0.418  Sum_probs=23.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..|+|.|..|+||||+++.+.+....
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l~~   29 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLLQE   29 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            57999999999999999999988765

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.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.42  E-value=0.013  Score=50.84  Aligned_cols=26  Identities=23%  Similarity=0.373  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.|++|+|++|+|||||.+.+..-..
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~LE~   53 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGLEE   53 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCcC
Confidence            46899999999999999999876543

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.42  E-value=0.041  Score=51.92  Aligned_cols=26  Identities=31%  Similarity=0.362  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +-|.++|++|.|||-||+.|+.....
T Consensus       246 kgvLm~GPPGTGKTlLAKAvATEc~t  271 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLLAKAVATECGT  271 (491)
T ss_pred             ceeeeeCCCCCcHHHHHHHHHHhhcC
Confidence            56889999999999999999988764

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.42  E-value=0.011  Score=50.01  Aligned_cols=22  Identities=23%  Similarity=0.498  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.|+|++|+||||+|+.+.+..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999998775

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.42  E-value=0.11  Score=52.25  Aligned_cols=86  Identities=15%  Similarity=0.094  Sum_probs=51.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcc------------------
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID------------------  232 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~------------------  232 (426)
                      .-+++.|.|++|+||||||.++...-..+ .=...+|++...  +..++.+.. .+++....                  
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~-~ge~~lyvs~eE--~~~~l~~~~-~~~G~~~~~~~~~g~l~~~~~~~~~~   95 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIH-FDEPGVFVTFEE--SPQDIIKNA-RSFGWDLQKLVDEGKLFILDASPDPE   95 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh-CCCCEEEEEEec--CHHHHHHHH-HHcCCCHHHHhhcCceEEEecCchhc
Confidence            34689999999999999999986553221 013567777753  344444443 33332111                  


Q ss_pred             ------ccCcHHHHHHHHHHHhcCCeEEEEEeCC
Q 044858          233 ------QESESVRAWRLLEQLKKETKILIILDDI  260 (426)
Q Consensus       233 ------~~~~~~~~~~l~~~l~~~k~~LlVlDdv  260 (426)
                            ..+.......+...+..+++-.+|||.+
T Consensus        96 ~~~~~~~~~l~~~l~~i~~~ls~g~~qRVvIDSl  129 (484)
T TIGR02655        96 GQDVVGGFDLSALIERINYAIRKYKAKRVSIDSV  129 (484)
T ss_pred             cccccccCCHHHHHHHHHHHHHHhCCcEEEEeeh
Confidence                  0111234455666666666778888954

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.

>PRK13949 shikimate kinase; Provisional

Probab=95.41  E-value=0.013  Score=49.85  Aligned_cols=24  Identities=42%  Similarity=0.440  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -|.|+|+.|+||||+++.+.+...
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELG   26 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            488999999999999999998765

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=95.41  E-value=0.063  Score=47.14  Aligned_cols=119  Identities=24%  Similarity=0.335  Sum_probs=63.7

Q ss_pred             HHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEEEEecCCcCHHHHHHHHHHHh--------CCCccc
Q 044858          163 ILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQTPQIKEIQREIAEKL--------GLKIDQ  233 (426)
Q Consensus       163 l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~~~~il~~i~~~l--------~~~~~~  233 (426)
                      ++..+-+..-....|.|++|+|||||.+.+..-.... ..|...--+-+....       +|+..+        +...+-
T Consensus       128 li~~ly~~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDers-------EIag~~~gvpq~~~g~R~dV  200 (308)
T COG3854         128 LIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERS-------EIAGCLNGVPQHGRGRRMDV  200 (308)
T ss_pred             HHHHHHhcCceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccc-------hhhccccCCchhhhhhhhhh
Confidence            4444444555557899999999999999998765432 234321111111111       121111        111111


Q ss_pred             cCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          234 ESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       234 ~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                      .+..-..+-+...+.+--+=++|+|++-..++-..+...+   ..|.++|.|..-..+
T Consensus       201 ld~cpk~~gmmmaIrsm~PEViIvDEIGt~~d~~A~~ta~---~~GVkli~TaHG~~i  255 (308)
T COG3854         201 LDPCPKAEGMMMAIRSMSPEVIIVDEIGTEEDALAILTAL---HAGVKLITTAHGNGI  255 (308)
T ss_pred             cccchHHHHHHHHHHhcCCcEEEEeccccHHHHHHHHHHH---hcCcEEEEeeccccH
Confidence            1111112233334444457799999998776655554443   458888887765544

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.41  E-value=0.013  Score=50.87  Aligned_cols=24  Identities=25%  Similarity=0.488  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .++.|+|+.|+|||||++.+....
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQRE   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccC
Confidence            468999999999999999997654

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.41  E-value=0.079  Score=47.04  Aligned_cols=24  Identities=25%  Similarity=0.252  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|.|++|+||||+|+.+.....
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~   25 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYG   25 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            378999999999999999987654

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.40  E-value=0.015  Score=48.75  Aligned_cols=33  Identities=21%  Similarity=0.315  Sum_probs=25.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEE
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVIS  207 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~w  207 (426)
                      +++|+|+.|+|||||+..+....+.+ .+...+.
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~~~-G~~V~vi   33 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALKAR-GYRVATI   33 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEE
Confidence            57899999999999999999987653 3444333

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PRK13947 shikimate kinase; Provisional

Probab=95.40  E-value=0.014  Score=49.79  Aligned_cols=25  Identities=36%  Similarity=0.347  Sum_probs=22.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|.|+|++|+||||+++.+.+....
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~   27 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSF   27 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            4889999999999999999987653

>PRK06851 hypothetical protein; Provisional

Probab=95.40  E-value=0.23  Score=47.62  Aligned_cols=43  Identities=23%  Similarity=0.275  Sum_probs=32.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT  213 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  213 (426)
                      +-.+++.|.|++|+|||||+..++.....++ ++..++-|.+.+
T Consensus       212 ~~~~~~~i~G~pG~GKstl~~~i~~~a~~~G-~~v~~~hC~~dP  254 (367)
T PRK06851        212 GVKNRYFLKGRPGTGKSTMLKKIAKAAEERG-FDVEVYHCGFDP  254 (367)
T ss_pred             ccceEEEEeCCCCCcHHHHHHHHHHHHHhCC-CeEEEEeCCCCC
Confidence            3457899999999999999999999886643 655555554443

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=95.39  E-value=0.044  Score=55.48  Aligned_cols=48  Identities=8%  Similarity=0.156  Sum_probs=36.3

Q ss_pred             cccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          150 FMHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...++|+...+.++.+.+.  ......|.|+|..|+|||++|+.+++...
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~  235 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASP  235 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC
Confidence            3457788777777766665  22334688999999999999999998754

>cd01878 HflX HflX subfamily

Probab=95.38  E-value=0.061  Score=47.24  Aligned_cols=27  Identities=19%  Similarity=0.332  Sum_probs=22.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +....|+|+|.+|+|||||...+....
T Consensus        39 ~~~~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          39 SGIPTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHhcch
Confidence            345689999999999999999988763

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

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

Probab=95.37  E-value=0.1  Score=55.27  Aligned_cols=129  Identities=17%  Similarity=0.224  Sum_probs=73.8

Q ss_pred             HHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcccc---
Q 044858          158 STLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQE---  234 (426)
Q Consensus       158 ~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~---  234 (426)
                      ....+|++.+.++  .|+.|.|+.|+||||-.-+++.+..-  .....+-++=++.-....+-+.+++.++......   
T Consensus        53 ~~~~~i~~ai~~~--~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY  128 (845)
T COG1643          53 AVRDEILKAIEQN--QVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGY  128 (845)
T ss_pred             HHHHHHHHHHHhC--CEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeE
Confidence            3456666666654  67999999999999999888766542  1223444443444456667788888887543211   


Q ss_pred             -----------------CcHHHHHHHH-HHHhcCCeEEEEEeCCCCccChhh-----hcCCCCCCCCCeEEEEeecchhh
Q 044858          235 -----------------SESVRAWRLL-EQLKKETKILIILDDIWGSLDLEA-----IGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       235 -----------------~~~~~~~~l~-~~l~~~k~~LlVlDdv~~~~~~~~-----l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                                       ++..++..+. +.++. +--.||+|++++..--.+     +...+....+.-||||+|=.-+.
T Consensus       129 ~iRfe~~~s~~Trik~mTdGiLlrei~~D~~Ls-~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld~  207 (845)
T COG1643         129 SIRFESKVSPRTRIKVMTDGILLREIQNDPLLS-GYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDA  207 (845)
T ss_pred             EEEeeccCCCCceeEEeccHHHHHHHhhCcccc-cCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccCH
Confidence                             1222233333 22222 345899999986522111     11112222224899999866543

>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=95.37  E-value=0.03  Score=48.78  Aligned_cols=44  Identities=18%  Similarity=0.254  Sum_probs=32.1

Q ss_pred             cccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +.+++|.+..+..+.-.....  .-+.++|++|+|||++|+.+..-
T Consensus         2 f~dI~GQe~aKrAL~iAAaG~--h~lLl~GppGtGKTmlA~~l~~l   45 (206)
T PF01078_consen    2 FSDIVGQEEAKRALEIAAAGG--HHLLLIGPPGTGKTMLARRLPSL   45 (206)
T ss_dssp             TCCSSSTHHHHHHHHHHHHCC----EEEES-CCCTHHHHHHHHHHC
T ss_pred             hhhhcCcHHHHHHHHHHHcCC--CCeEEECCCCCCHHHHHHHHHHh
Confidence            446778887777766655543  56899999999999999998754

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.

>PRK14529 adenylate kinase; Provisional

Probab=95.35  E-value=0.069  Score=47.49  Aligned_cols=83  Identities=20%  Similarity=0.246  Sum_probs=45.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCccce--EEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKENNLFEK--VISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~--~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      |.|.|++|+||||+++.+....... +...  .+.-.+..........++++.+-    ..-++......+.+.+.+...
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~~~-~is~gdllr~~i~~~t~lg~~i~~~i~~G----~lvpdei~~~lv~~~l~~~~~   77 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYDLA-HIESGAIFREHIGGGTELGKKAKEYIDRG----DLVPDDITIPMILETLKQDGK   77 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCC-CcccchhhhhhccCCChHHHHHHHHHhcc----CcchHHHHHHHHHHHHhccCC
Confidence            7889999999999999998877532 2211  11112222223333444444321    112233334445555543224


Q ss_pred             EEEEEeCCCC
Q 044858          253 ILIILDDIWG  262 (426)
Q Consensus       253 ~LlVlDdv~~  262 (426)
                      -=+|||+.-.
T Consensus        78 ~g~iLDGfPR   87 (223)
T PRK14529         78 NGWLLDGFPR   87 (223)
T ss_pred             CcEEEeCCCC
Confidence            4588999853

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=95.35  E-value=0.1  Score=55.16  Aligned_cols=101  Identities=18%  Similarity=0.206  Sum_probs=59.1

Q ss_pred             ccchHHHHHHHHHHhcc-------C-CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          153 FESRKSTLKGILDALSN-------R-NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~-------~-~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ++|.++.+..|.+.+..       . +...+.+.|+.|+|||.||+.+....-.  ..+..+-++.|..      .. +.
T Consensus       564 V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fg--se~~~IriDmse~------~e-vs  634 (898)
T KOG1051|consen  564 VIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFG--SEENFIRLDMSEF------QE-VS  634 (898)
T ss_pred             ccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcC--CccceEEechhhh------hh-hh
Confidence            34555555555555541       1 3446788999999999999999887642  2344444444432      11 22


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      +-.+.+ +.--..+...++.+.+.+.-..+|+||||...
T Consensus       635 kligsp-~gyvG~e~gg~LteavrrrP~sVVLfdeIEkA  672 (898)
T KOG1051|consen  635 KLIGSP-PGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKA  672 (898)
T ss_pred             hccCCC-cccccchhHHHHHHHHhcCCceEEEEechhhc
Confidence            222322 22222234557777787644468889999754

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.35  E-value=0.015  Score=51.27  Aligned_cols=25  Identities=16%  Similarity=0.383  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ....|.|+|++|+|||||++.+.+.
T Consensus        12 ~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         12 KPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhc
Confidence            4678999999999999999999754

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.33  E-value=0.017  Score=50.45  Aligned_cols=25  Identities=24%  Similarity=0.399  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+|.|.|.+|+||||+|+.+....
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998874

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=95.32  E-value=0.011  Score=51.94  Aligned_cols=23  Identities=22%  Similarity=0.365  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+++|+|+.|.||||+.+.+...
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~~   52 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGLA   52 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHHH
Confidence            68999999999999999999843

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>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=95.32  E-value=0.016  Score=48.39  Aligned_cols=23  Identities=35%  Similarity=0.446  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |.|+|++|+||||+|+.+.....
T Consensus         2 i~l~G~~GsGKstla~~la~~l~   24 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALG   24 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhC
Confidence            78999999999999999987764

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.

>PRK00698 tmk thymidylate kinase; Validated

Probab=95.31  E-value=0.052  Score=47.64  Aligned_cols=26  Identities=23%  Similarity=0.419  Sum_probs=23.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+|+|.|+.|+||||+++.+.+....
T Consensus         4 ~~I~ieG~~gsGKsT~~~~L~~~l~~   29 (205)
T PRK00698          4 MFITIEGIDGAGKSTQIELLKELLEQ   29 (205)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            58999999999999999999987754

>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=95.30  E-value=0.016  Score=44.93  Aligned_cols=21  Identities=38%  Similarity=0.381  Sum_probs=19.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVG  193 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~  193 (426)
                      ..++|.|+.|+|||||++.+.
T Consensus        16 e~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          16 VGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             EEEEEEcCCCCCHHHHHHHhh
Confidence            578999999999999999976

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

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.30  E-value=0.18  Score=45.59  Aligned_cols=50  Identities=10%  Similarity=0.189  Sum_probs=34.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .++.|.|.+|+|||+++.++......+. =..++|++...  +..++...++.
T Consensus        14 ~l~lI~G~~G~GKT~~~~~~~~~~~~~~-g~~vly~s~E~--~~~~~~~r~~~   63 (242)
T cd00984          14 DLIIIAARPSMGKTAFALNIAENIAKKQ-GKPVLFFSLEM--SKEQLLQRLLA   63 (242)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhC-CCceEEEeCCC--CHHHHHHHHHH
Confidence            5889999999999999999877665431 22456666544  45566666543

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.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.29  E-value=0.015  Score=51.45  Aligned_cols=25  Identities=28%  Similarity=0.452  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|++|+|||||++.+.--.
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~Gl~   57 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAGLE   57 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhccc
Confidence            3579999999999999999987543

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.29  E-value=0.018  Score=49.21  Aligned_cols=26  Identities=27%  Similarity=0.317  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...|.|+|+.|+||||+++.+.+...
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~   29 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcC
Confidence            34699999999999999999998754

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

Probab=95.27  E-value=0.27  Score=48.74  Aligned_cols=40  Identities=20%  Similarity=0.293  Sum_probs=30.3

Q ss_pred             HHHHHHHHHhc-----cCC--ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          158 STLKGILDALS-----NRN--FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       158 ~~~~~l~~~l~-----~~~--~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .-+.++-.||.     .++  .+++.|+|++|+||||.++.+.....
T Consensus        89 kKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg  135 (634)
T KOG1970|consen   89 KKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELG  135 (634)
T ss_pred             HhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhhC
Confidence            34555666665     333  45999999999999999999987765

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.23  E-value=0.11  Score=46.33  Aligned_cols=47  Identities=28%  Similarity=0.187  Sum_probs=33.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      ..++.|.|.+|+|||+++.++......+  =..++|++...  +..++.+.
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~--g~~~~y~s~e~--~~~~l~~~   62 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKN--GEKAMYISLEE--REERILGY   62 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC--CHHHHHHH
Confidence            4688999999999999999987664332  24566777755  34444444

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.22  E-value=0.087  Score=51.53  Aligned_cols=88  Identities=13%  Similarity=0.211  Sum_probs=51.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      +-..++|.|..|+|||||++.+.+...    .+..++..+.. ...+.+++.+....-...       ....+...    
T Consensus       154 ~GqrigI~G~sG~GKSTLL~~I~~~~~----~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a  229 (433)
T PRK07594        154 EGQRVGIFSAPGVGKSTLLAMLCNAPD----ADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRA  229 (433)
T ss_pred             CCCEEEEECCCCCCccHHHHHhcCCCC----CCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHH
Confidence            345789999999999999999887543    34445555544 445556666554311100       01111111    


Q ss_pred             --HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 --RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 --~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                        ....+-+++ .+++++||++||+-.
T Consensus       230 ~~~a~tiAEyfrd~G~~VLl~~Dsltr  256 (433)
T PRK07594        230 LFVATTIAEFFRDNGKRVVLLADSLTR  256 (433)
T ss_pred             HHHHHHHHHHHHHCCCcEEEEEeCHHH
Confidence              122344444 258899999999853

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.21  E-value=0.016  Score=51.50  Aligned_cols=25  Identities=24%  Similarity=0.462  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --+++|+|++|+|||||.+.+.--.
T Consensus        29 GEfvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          29 GEFVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3579999999999999999997543

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.21  E-value=0.016  Score=49.04  Aligned_cols=21  Identities=33%  Similarity=0.469  Sum_probs=17.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |+|+|..|+|||||++.+...
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            789999999999999999977

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

Probab=95.21  E-value=0.084  Score=51.43  Aligned_cols=46  Identities=22%  Similarity=0.166  Sum_probs=33.2

Q ss_pred             cccchHHHHHHHHHHhc-------c----C-------CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALS-------N----R-------NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~-------~----~-------~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|.++.++.+...+.       .    .       ....+.++|++|+|||+||+.+.....
T Consensus        78 ~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~  141 (413)
T TIGR00382        78 YVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILN  141 (413)
T ss_pred             eecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcC
Confidence            35787777776654441       1    1       124789999999999999999987654

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.

>PHA02774 E1; Provisional

Probab=95.20  E-value=0.051  Score=54.54  Aligned_cols=48  Identities=19%  Similarity=0.169  Sum_probs=33.2

Q ss_pred             HHHHHHHHhcc-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe
Q 044858          159 TLKGILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV  210 (426)
Q Consensus       159 ~~~~l~~~l~~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v  210 (426)
                      -+..+..++.. ++...+.|+|++|+|||.+|..+.+-..    -..+.|++.
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L~----G~vi~fvN~  468 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLK----GKVISFVNS  468 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhC----CCEEEEEEC
Confidence            34455555543 3345899999999999999999998764    223456664

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

Probab=95.20  E-value=0.049  Score=47.62  Aligned_cols=31  Identities=26%  Similarity=0.322  Sum_probs=25.6

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .++-++..|.|++|+||||++..+.......
T Consensus        15 ~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~   45 (196)
T PF13604_consen   15 TSGDRVSVLQGPAGTGKTTLLKALAEALEAA   45 (196)
T ss_dssp             HCTCSEEEEEESTTSTHHHHHHHHHHHHHHT
T ss_pred             hcCCeEEEEEECCCCCHHHHHHHHHHHHHhC
Confidence            3445788999999999999999988877654

>PRK13695 putative NTPase; Provisional

Probab=95.18  E-value=0.03  Score=47.86  Aligned_cols=25  Identities=48%  Similarity=0.693  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|+|+|.+|+|||||++.+++....
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~   26 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKE   26 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3789999999999999999887654

>PLN02200 adenylate kinase family protein

Probab=95.11  E-value=0.021  Score=51.36  Aligned_cols=27  Identities=22%  Similarity=0.111  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.+|.|.|++|+||||+|+.+.+...
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~g   68 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETFG   68 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356889999999999999999987653

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.10  E-value=0.19  Score=46.07  Aligned_cols=90  Identities=17%  Similarity=0.217  Sum_probs=50.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      +..+++++|+.|+||||++..+......+.  ..+.+++..... ....-++...+.++.+.....+...+...++.+.+
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~~~--~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l~~l~~  151 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHGKK--KTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKE  151 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHHcC--CeEEEEecCCCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHHHHHHh
Confidence            447899999999999999999877654321  234455543221 12222333344444443332233334444444542


Q ss_pred             -CCeEEEEEeCCCC
Q 044858          250 -ETKILIILDDIWG  262 (426)
Q Consensus       250 -~k~~LlVlDdv~~  262 (426)
                       .+.=++++|..-.
T Consensus       152 ~~~~D~ViIDt~Gr  165 (270)
T PRK06731        152 EARVDYILIDTAGK  165 (270)
T ss_pred             cCCCCEEEEECCCC
Confidence             2345788898743

>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=95.10  E-value=0.02  Score=51.60  Aligned_cols=34  Identities=29%  Similarity=0.383  Sum_probs=23.0

Q ss_pred             EEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          177 VYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       177 I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      |+||+|+||||+++.+.+.....+  ..++-|+..+
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~--~~~~~vNLDP   34 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNG--RDVYIVNLDP   34 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT---S-EEEEE--T
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcc--CCceEEEcch
Confidence            689999999999999999876543  2344455433

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.07  E-value=0.17  Score=51.37  Aligned_cols=85  Identities=15%  Similarity=0.184  Sum_probs=53.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc----------------cC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ----------------ES  235 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~----------------~~  235 (426)
                      -.++.|.|.+|+|||+|+.++.......  -..++|++....  ..++.+.. .+++.+...                ..
T Consensus       273 g~~~li~G~~G~GKT~l~~~~~~~~~~~--g~~~~yis~e~~--~~~i~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~~  347 (509)
T PRK09302        273 GSIILVSGATGTGKTLLASKFAEAACRR--GERCLLFAFEES--RAQLIRNA-RSWGIDLEKMEEKGLLKIICARPESYG  347 (509)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecCC--HHHHHHHH-HHcCCChHHHhhcCCceeecCCcccCC
Confidence            4688899999999999999998765433  356778876543  44554443 344432110                11


Q ss_pred             cHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          236 ESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       236 ~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                      .......+.+.+...+.-++|+|.+.
T Consensus       348 ~~~~~~~i~~~i~~~~~~~vVIDslt  373 (509)
T PRK09302        348 LEDHLIIIKREIEEFKPSRVAIDPLS  373 (509)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            12334455555555556689999984

>PRK13948 shikimate kinase; Provisional

Probab=95.06  E-value=0.026  Score=48.62  Aligned_cols=28  Identities=25%  Similarity=0.383  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .....|.++|+.|+||||+++.+.+...
T Consensus         8 ~~~~~I~LiG~~GsGKSTvg~~La~~lg   35 (182)
T PRK13948          8 RPVTWVALAGFMGTGKSRIGWELSRALM   35 (182)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcC
Confidence            3457899999999999999999998764

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

Probab=95.05  E-value=0.075  Score=51.46  Aligned_cols=47  Identities=21%  Similarity=0.287  Sum_probs=35.1

Q ss_pred             cccchHHHHHHHHHHhcc--------------CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          152 HFESRKSTLKGILDALSN--------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~--------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .++|.++.++.+..++.+              ..+..|.++|++|+|||+||+.+......
T Consensus        16 ~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~   76 (443)
T PRK05201         16 YIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANA   76 (443)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            366777777776655532              12467899999999999999999887653

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=95.05  E-value=0.034  Score=46.71  Aligned_cols=27  Identities=33%  Similarity=0.519  Sum_probs=24.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      +++.|+|..|+|||||+..+.......
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~l~~~   28 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPALSAR   28 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999887654

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=95.04  E-value=0.077  Score=51.89  Aligned_cols=27  Identities=22%  Similarity=0.422  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +-..++|.|..|+|||||++.+.....
T Consensus       154 ~GQ~igI~G~sGaGKSTLl~~I~g~~~  180 (434)
T PRK07196        154 KGQRVGLMAGSGVGKSVLLGMITRYTQ  180 (434)
T ss_pred             cceEEEEECCCCCCccHHHHHHhcccC
Confidence            346799999999999999999877543

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=95.03  E-value=0.062  Score=55.04  Aligned_cols=25  Identities=32%  Similarity=0.227  Sum_probs=21.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++..|.|.+|+||||++..+.....
T Consensus       161 ~~~vitGgpGTGKTt~v~~ll~~l~  185 (586)
T TIGR01447       161 NFSLITGGPGTGKTTTVARLLLALV  185 (586)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHH
Confidence            6889999999999999999877654

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.02  E-value=0.03  Score=49.24  Aligned_cols=24  Identities=21%  Similarity=0.185  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..++.|.|+.|.||||+.+.+...
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~   52 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALL   52 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999998644

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

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=95.01  E-value=0.12  Score=50.99  Aligned_cols=88  Identities=16%  Similarity=0.310  Sum_probs=48.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC-------CCccccCcHH-----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG-------LKIDQESESV-----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~-------~~~~~~~~~~-----  238 (426)
                      +-..++|+|..|+|||||++.+.......   ...+++.--+..+..++....+..-+       ......+...     
T Consensus       157 ~Gq~i~I~G~sG~GKStLl~~I~~~~~~~---~gvI~~~Gerg~ev~e~~~~~l~~~~l~r~v~vv~~~~~~~~~r~~~~  233 (438)
T PRK07721        157 KGQRVGIFAGSGVGKSTLMGMIARNTSAD---LNVIALIGERGREVREFIERDLGPEGLKRSIVVVATSDQPALMRIKGA  233 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcccCCC---eEEEEEEecCCccHHHHHHhhcChhhhcCeEEEEECCCCCHHHHHHHH
Confidence            44689999999999999999888765431   23344333333345554443222111       0111111111     


Q ss_pred             -HHHHHHHHH-hcCCeEEEEEeCCC
Q 044858          239 -RAWRLLEQL-KKETKILIILDDIW  261 (426)
Q Consensus       239 -~~~~l~~~l-~~~k~~LlVlDdv~  261 (426)
                       ....+-+++ .+++++||++||+-
T Consensus       234 ~~a~~iAEyfr~~g~~Vll~~Dslt  258 (438)
T PRK07721        234 YTATAIAEYFRDQGLNVMLMMDSVT  258 (438)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeChH
Confidence             122334444 35899999999984

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=95.00  E-value=0.17  Score=49.70  Aligned_cols=88  Identities=19%  Similarity=0.362  Sum_probs=51.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCCc-------cccCcHH----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLKI-------DQESESV----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~~-------~~~~~~~----  238 (426)
                      +-..++|+|..|+|||||++.+.....    .+.++...+... .+..++...+...-+...       ...+...    
T Consensus       167 ~GqrigI~G~sG~GKSTLl~~I~g~~~----~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a  242 (451)
T PRK05688        167 RGQRLGLFAGTGVGKSVLLGMMTRFTE----ADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRA  242 (451)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCC----CCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHH
Confidence            345789999999999999999876432    234444444433 345566655554432211       1111111    


Q ss_pred             --HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 --RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 --~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                        ....+-+++ .+++++||++||+-.
T Consensus       243 ~~~a~aiAEyfrd~G~~VLl~~DslTR  269 (451)
T PRK05688        243 AMYCTRIAEYFRDKGKNVLLLMDSLTR  269 (451)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEecchhH
Confidence              122334444 258999999999853

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=95.00  E-value=0.021  Score=50.56  Aligned_cols=24  Identities=29%  Similarity=0.565  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -+++|+|++|+|||||...+.--.
T Consensus        32 e~vaI~GpSGSGKSTLLniig~ld   55 (226)
T COG1136          32 EFVAIVGPSGSGKSTLLNLLGGLD   55 (226)
T ss_pred             CEEEEECCCCCCHHHHHHHHhccc
Confidence            579999999999999999987543

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=95.00  E-value=0.081  Score=51.65  Aligned_cols=88  Identities=18%  Similarity=0.367  Sum_probs=49.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      +-..++|+|..|+|||||++.+......    +..+...+.. .....++..+.+.+-+..       ....+...    
T Consensus       136 ~Gqri~I~G~sG~GKTtLl~~i~~~~~~----~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~  211 (413)
T TIGR03497       136 KGQRVGIFAGSGVGKSTLLGMIARNAKA----DINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKA  211 (413)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCC----CeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHH
Confidence            3467999999999999999988875432    2222233333 334555555544432211       11111111    


Q ss_pred             --HHHHHHHHH-hcCCeEEEEEeCCCC
Q 044858          239 --RAWRLLEQL-KKETKILIILDDIWG  262 (426)
Q Consensus       239 --~~~~l~~~l-~~~k~~LlVlDdv~~  262 (426)
                        ....+-+++ .+++++||++||+-.
T Consensus       212 ~~~a~tiAEyfr~~G~~Vll~~Dsltr  238 (413)
T TIGR03497       212 AFTATAIAEYFRDQGKDVLLMMDSVTR  238 (413)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEcCcHH
Confidence              122334444 358999999999853

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.

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=94.96  E-value=0.11  Score=51.23  Aligned_cols=86  Identities=20%  Similarity=0.367  Sum_probs=47.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCC-------ccccCcHH-----
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLK-------IDQESESV-----  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~-------~~~~~~~~-----  238 (426)
                      -..++|.|..|+|||||++.+......    +......+.. .....++..+.+..-+..       ....+...     
T Consensus       163 Gq~~~I~G~sG~GKStLl~~I~~~~~~----~~~vi~~iG~r~~ev~~~~~~~~~~~~l~~tvvv~~~~d~~p~~r~~~~  238 (440)
T TIGR01026       163 GQRIGIFAGSGVGKSTLLGMIARNTEA----DVNVIALIGERGREVREFIEHDLGEEGLKRSVVVVATSDQSPLLRLKGA  238 (440)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC----CEEEEEEEeecchHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHH
Confidence            457899999999999999988876432    2223333332 334444554443321110       01111111     


Q ss_pred             -HHHHHHHHH-hcCCeEEEEEeCCC
Q 044858          239 -RAWRLLEQL-KKETKILIILDDIW  261 (426)
Q Consensus       239 -~~~~l~~~l-~~~k~~LlVlDdv~  261 (426)
                       ....+-+++ .+++++||++||+-
T Consensus       239 ~~a~t~AE~frd~G~~Vll~~DslT  263 (440)
T TIGR01026       239 YVATAIAEYFRDQGKDVLLLMDSVT  263 (440)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEeChH
Confidence             112233333 35889999999984

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>PRK13946 shikimate kinase; Provisional

Probab=94.96  E-value=0.025  Score=48.94  Aligned_cols=26  Identities=19%  Similarity=0.294  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.|.++|+.|+||||+++.+.+...
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg   35 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLG   35 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            35799999999999999999998874

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=94.96  E-value=0.026  Score=46.87  Aligned_cols=47  Identities=28%  Similarity=0.376  Sum_probs=32.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLK  230 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~  230 (426)
                      .++++|+|.+|+||||+.+.+.... ..  +..         .+..++.-+++...+..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l-~~--~~i---------vNyG~~Mle~A~k~glv   50 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL-VK--HKI---------VNYGDLMLEIAKKKGLV   50 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH-hh--cee---------eeHhHHHHHHHHHhCCc
Confidence            5789999999999999999887766 11  111         13456666666665543

>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=94.93  E-value=0.048  Score=51.52  Aligned_cols=53  Identities=21%  Similarity=0.273  Sum_probs=36.1

Q ss_pred             cccccchHHHHHH---HHHHhccCC--ccEEEEEcCCCCcHHHHHHHHHHHhhhcCcc
Q 044858          150 FMHFESRKSTLKG---ILDALSNRN--FNMIGVYGMGGIGKTTLVKEVGRQAKENNLF  202 (426)
Q Consensus       150 ~~~~~gR~~~~~~---l~~~l~~~~--~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f  202 (426)
                      ..+++|..+..+.   +++...+++  -+.|.+.|++|.|||+||..+.+....+-.|
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF   80 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPF   80 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-E
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCe
Confidence            4578887655443   455555554  4789999999999999999999998765444

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.

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=94.91  E-value=0.034  Score=51.17  Aligned_cols=28  Identities=25%  Similarity=0.419  Sum_probs=25.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENN  200 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~  200 (426)
                      ++|+|+|.+|+|||||+..+......++
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~L~~~G   29 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDRLSGRG   29 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhCC
Confidence            5799999999999999999999987654

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=94.90  E-value=0.038  Score=52.04  Aligned_cols=26  Identities=31%  Similarity=0.302  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+.|+|+.|+|||||++.+.....
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~~~  169 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDEIP  169 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHccCC
Confidence            36899999999999999999887654

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=94.88  E-value=0.025  Score=48.51  Aligned_cols=25  Identities=16%  Similarity=0.259  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++.|+|+.|+|||||++.+.....
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~   28 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFS   28 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4789999999999999999998754

>PRK04182 cytidylate kinase; Provisional

Probab=94.88  E-value=0.025  Score=48.48  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.|.|+.|+||||+++.+.+...
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg   25 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            689999999999999999988754

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=94.85  E-value=0.17  Score=42.69  Aligned_cols=22  Identities=27%  Similarity=0.540  Sum_probs=19.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      ++..|+|+.|.|||++.+.+.-
T Consensus        22 ~~~~i~G~NgsGKS~~l~~i~~   43 (162)
T cd03227          22 SLTIITGPNGSGKSTILDAIGL   43 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999753

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=94.83  E-value=0.024  Score=46.24  Aligned_cols=25  Identities=28%  Similarity=0.522  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|+|+.|+|||||.+.+.....
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~~~   36 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGLLP   36 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTSSH
T ss_pred             CEEEEEccCCCccccceeeeccccc
Confidence            5799999999999999999887654

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 ....

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=94.82  E-value=0.15  Score=47.76  Aligned_cols=55  Identities=20%  Similarity=0.203  Sum_probs=40.6

Q ss_pred             cccccchHHHHHH---HHHHhccCC--ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccce
Q 044858          150 FMHFESRKSTLKG---ILDALSNRN--FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEK  204 (426)
Q Consensus       150 ~~~~~gR~~~~~~---l~~~l~~~~--~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~  204 (426)
                      ..+|+|..+..+.   +++...+++  -+.|.|+|++|.|||+||-.+.+.....-+|..
T Consensus        38 ~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~   97 (450)
T COG1224          38 GDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVA   97 (450)
T ss_pred             CCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCcee
Confidence            4567886654432   455555442  468999999999999999999999887777753

>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]

Probab=94.82  E-value=0.073  Score=51.03  Aligned_cols=25  Identities=32%  Similarity=0.495  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..|+|+|+.|+|||||...+.-...
T Consensus       614 SRiaIVGPNGVGKSTlLkLL~Gkl~  638 (807)
T KOG0066|consen  614 SRIAIVGPNGVGKSTLLKLLIGKLD  638 (807)
T ss_pred             ceeEEECCCCccHHHHHHHHhcCCC
Confidence            4689999999999999999876543

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=94.80  E-value=0.027  Score=47.81  Aligned_cols=24  Identities=33%  Similarity=0.477  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.|.|+.|+||||+|+.+.+...
T Consensus         2 iI~i~G~~GSGKstia~~la~~lg   25 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLS   25 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            689999999999999999987653

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.

>PLN02348 phosphoribulokinase

Probab=94.80  E-value=0.031  Score=53.60  Aligned_cols=28  Identities=21%  Similarity=0.323  Sum_probs=25.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +++.+|+|.|.+|+||||+|+.+.+...
T Consensus        47 ~~p~IIGIaG~SGSGKSTfA~~L~~~Lg   74 (395)
T PLN02348         47 DGTVVIGLAADSGCGKSTFMRRLTSVFG   74 (395)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4567899999999999999999998875

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.79  E-value=0.023  Score=51.76  Aligned_cols=25  Identities=36%  Similarity=0.671  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|.++|++|+||||+|+.+......
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~   25 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSE   25 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3789999999999999999987654

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	426
3sfz_A	1249	Crystal Structure Of Full-Length Murine Apaf-1 Leng		8e-10
3iza_B	1263	Structure Of An Apoptosome-Procaspase-9 Card Comple		4e-09
1z6t_A	591	Structure Of The Apoptotic Protease-activating Fact		4e-09
3shf_A	1256	Crystal Structure Of The R265s Mutant Of Full-Lengt		5e-09

>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1 Length = 1249

Iteration: 1
 Score = 61.6 bits (148), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 103/238 (43%), Gaps = 37/238 (15%)
Query: 153 FESRKSTLKGILDALSNRNF--NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV 210
           F +RK  +  I   L   N     + +YGM G GK+ L  E  R   +++L E   S  V
Sbjct: 126 FVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVR---DHSLLEGCFSGGV 182
Query: 211 SQTPQIKEIQREIAEKLG---LKIDQES-----------ESVRAWRLLEQLKKETKILII 256
                 K+ +  +  KL    +++DQE            E+    R+L  L+K  + L+I
Sbjct: 183 HWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVL-MLRKHPRSLLI 241
Query: 257 LDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEA---- 312
           LDD+W    L+A        +  C++LLT R + V    M  +    V+    +E     
Sbjct: 242 LDDVWDPWVLKAF-------DNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEI 294
Query: 313 WSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLK 370
            SLF  M  +     +L +    ++KEC G P+ +V +  AL    P  W   LRQL+
Sbjct: 295 LSLFVNMKKE-----DLPAEAHSIIKECKGSPL-VVSLIGALLRDFPNRWAYYLRQLQ 346

>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1 Bound To Adp Length = 591

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 104/247 (42%), Gaps = 55/247 (22%)
Query: 153 FESRKSTLKGILDALSNRN--FNMIGVYGMGGIGKTTLVKE------------------- 191
           F +RK  +  I   LS        + ++GM G GK+ L  E                   
Sbjct: 126 FVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWV 185
Query: 192 -VGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK 249
            VG+Q K   L + + + +R+ Q           +++L L I++  + +R    +  L+K
Sbjct: 186 SVGKQDKSGLLMKLQNLCTRLDQ-------DESFSQRLPLNIEEAKDRLR----ILMLRK 234
Query: 250 ETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLND 309
             + L+ILDD+W S  L+A        +  C++LLT R + V    M     +VV V + 
Sbjct: 235 HPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSVMG--PKYVVPVESS 285
Query: 310 ------KEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWR 363
                  E  SLF  M     +  +L      ++KEC G P+ +V +  AL    P  W 
Sbjct: 286 LGKEKGLEILSLFVNM-----KKADLPEQAHSIIKECKGSPL-VVSLIGALLRDFPNRWE 339
Query: 364 NALRQLK 370
             L+QL+
Sbjct: 340 YYLKQLQ 346

>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length Murine Apaf-1 Length = 1256

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 102/238 (42%), Gaps = 37/238 (15%)
Query: 153 FESRKSTLKGILDALSNRNF--NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV 210
           F +RK  +  I   L   N     + +YGM G GK+ L  E  R   +++L E   S  V
Sbjct: 133 FVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVR---DHSLLEGCFSGGV 189
Query: 211 SQTPQIKEIQREIAEKLG---LKIDQES-----------ESVRAWRLLEQLKKETKILII 256
                 K+ +  +  KL    +++DQE            E+    R+L  L+K  + L+I
Sbjct: 190 HWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVL-MLRKHPRSLLI 248
Query: 257 LDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEA---- 312
           LDD+W    L+A        +  C++LLT   + V    M  +    V+    +E     
Sbjct: 249 LDDVWDPWVLKAF-------DNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEI 301
Query: 313 WSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLK 370
            SLF  M  +     +L +    ++KEC G P+ +V +  AL    P  W   LRQL+
Sbjct: 302 LSLFVNMKKE-----DLPAEAHSIIKECKGSPL-VVSLIGALLRDFPNRWAYYLRQLQ 353

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	426
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	3e-46
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-40
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	9e-37
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	4e-22
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	7e-05
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	6e-04
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	7e-04

>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 =  166 bits (422), Expect = 3e-46
 Identities = 42/360 (11%), Positives = 107/360 (29%), Gaps = 28/360 (7%)

Query: 65  QQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGL 124
            + +  +L       +E+  LI     +N   L                A  E + +  +
Sbjct: 51  LERIANFLRIYRRQASELGPLIDFFNYNNQSHLADF------LEDYIDFAINEPDLLRPV 104

Query: 125 HEKGRFDSVSFRTIPEETWLKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIG 184
               +F             +         E     +   LD + + +   + ++G  G G
Sbjct: 105 VIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSG 164

Query: 185 KTTLVKEVGRQAKE--NNLFEKVISSRVSQT--PQIKEIQREIAEKLG--------LKID 232
           K+ +  +   ++ +     ++ ++  + S T      ++  +I   L           ++
Sbjct: 165 KSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVE 224

Query: 233 QESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVL 292
             +  V    +   L      L + DD+     +              + L+T R  ++ 
Sbjct: 225 HVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWA------QELRLRCLVTTRDVEIS 278

Query: 293 SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK 352
           +      +   V  L   E +   +          + + V+ + ++  +G P  ++   K
Sbjct: 279 NAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFK 338

Query: 353 ALKNKSPYEW---RNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG 409
           + + K+  +     N L       +   +     +    +Q     L  +E R       
Sbjct: 339 SCEPKTFEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVL-SDEDRSALAFAV 397

>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 =  153 bits (386), Expect = 2e-40
 Identities = 74/404 (18%), Positives = 136/404 (33%), Gaps = 90/404 (22%)

Query: 50  VQYKVDD------SRIKGDGIQQPVEEWL---IT---VDEAINE----------VETLIA 87
            QY+  D           +   + V++     ++   +D  I              TL++
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73

Query: 88  DKEKSNNRCLKGLCPNLKTRYQ-LSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKS 146
            +E+   + ++ +   L+  Y+ L    + E              +  +    +  +   
Sbjct: 74  KQEEMVQKFVEEV---LRINYKFLMSPIKTEQRQPSM-------MTRMYIEQRDRLY-ND 122

Query: 147 TQDFM-HFESRKSTLKGILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE- 203
            Q F  +  SR      +  AL   R    + + G+ G GKT +  +V    K     + 
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182

Query: 204 KV--ISSRVSQTPQIKEIQREIAEKLGLKIDQ--------------ESESVRAW-RLLEQ 246
           K+  ++ +   +P   E   E+ +KL  +ID                  S++A  R L +
Sbjct: 183 KIFWLNLKNCNSP---ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 247 LKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQ---DVLSCEMDCQ--QN 301
            K     L++L ++  +    A        N  CK+LLT R +   D LS         +
Sbjct: 240 SKPYENCLLVLLNVQNAKAWNAF-------NLSCKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 302 FVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYE 361
                L   E  SL  K         +L   V          P  +  IA+++++     
Sbjct: 293 HHSMTLTPDEVKSLLLKYLD--CRPQDLPREV------LTTNPRRLSIIAESIRDG-LAT 343

Query: 362 WRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTF 405
           W N  + +  + L            + I+ S N L   E RK F
Sbjct: 344 WDN-WKHVNCDKLT-----------TIIESSLNVLEPAEYRKMF 375

>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 = 52.2 bits (124), Expect = 3e-07
 Identities = 66/466 (14%), Positives = 124/466 (26%), Gaps = 163/466 (34%)

Query: 17  APIIRQFTYCCS--YNTN-------------LEKLKNELEKLKIARASVQY------K-- 53
           + + R +       YN N               KL+  L +L+ A+  +        K  
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW 165

Query: 54  -----VDDSRIK---GDGIQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLK 105
                    +++      I      W + +    N  ET++   E       + + PN  
Sbjct: 166 VALDVCLSYKVQCKMDFKIF-----W-LNLKN-CNSPETVL---EMLQKLLYQ-IDPNWT 214

Query: 106 TRYQLSKKAEREANAIVGLHEKGRF-------------DSVSFRTIPEETWLKSTQDFMH 152
           +R   S   +   ++I    E  R               +V               +  +
Sbjct: 215 SRSDHSSNIKLRIHSIQ--AELRRLLKSKPYENCLLVLLNV---------QNAKAWNAFN 263

Query: 153 FESRKSTL-----KGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVIS 207
              +   L     K + D LS      I +         TL  +   + K   L  K + 
Sbjct: 264 LSCK--ILLTTRFKQVTDFLSAATTTHISLDHH----SMTLTPD---EVKS--LLLKYLD 312

Query: 208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRA-------WRLLEQLKKETKILIILDDI 260
            R    P      RE+      ++   +ES+R        W+ +   K  T I   L+  
Sbjct: 313 CRPQDLP------REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN-- 364

Query: 261 WGSLD-------LEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAW 313
              L+        + + +            +      +LS            ++     W
Sbjct: 365 --VLEPAEYRKMFDRLSV-FPPS-----AHIPT---ILLS------------LI-----W 396

Query: 314 SLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNF 373
                +    +           VV +             +L  K P E   ++  +    
Sbjct: 397 F---DVIKSDVM---------VVVNKLH---------KYSLVEKQPKESTISIPSIYLEL 435

Query: 374 LRSFSGTQA-----VAAYSTIQ-LSYNQLGGEELRKTFLLIGYSYI 413
                   A     V  Y+  +    + L    L + F    YS+I
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF----YSHI 477

>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 = 42.9 bits (100), Expect = 2e-04
 Identities = 40/361 (11%), Positives = 106/361 (29%), Gaps = 102/361 (28%)

Query: 30  NTNLEKLKNELEK---LKIARASVQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLI 86
           +   + L  E+      +++  +   +   +           + W        +++ T+I
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLATW---------DNWK---HVNCDKLTTII 359

Query: 87  ADKEKSNNRCLKGLCPN-LKTRYQLSKKAEREANAIVGLHEKGRF-DSVSFRTIPEET-- 142
                     L  L P   +  +        +  ++        F  S     IP     
Sbjct: 360 E-------SSLNVLEPAEYRKMF--------DRLSV--------FPPSAH---IPTILLS 393

Query: 143 --WLKST----QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA 196
             W           ++   + S        L  +         +  I     VK     A
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYS--------LVEKQPKE-STISIPSIYLELKVKLENEYA 444

Query: 197 KENNLFEKVISSRVSQTPQIKEIQRE--IAEKLG--LKIDQESESVRAWRLLEQLKKETK 252
              ++ +     +   +  +     +      +G  LK  +  E +  +R+         
Sbjct: 445 LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM--------- 495

Query: 253 ILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEA 312
             + LD  +    +          N    +L      + L  ++   + ++ D  ND + 
Sbjct: 496 --VFLDFRFLEQKIRHDSTAW---NASGSIL------NTLQ-QLKFYKPYICD--NDPK- 540

Query: 313 WSLFKKMTGDCIENGELKSVVTEVV--KECAGLPIAIVPIAKALKNKSPYEWRNALRQLK 370
              ++++    ++   L  +   ++  K        ++ IA   ++++ +E   A +Q++
Sbjct: 541 ---YERLVNAILDF--LPKIEENLICSKYTD-----LLRIALMAEDEAIFE--EAHKQVQ 588

Query: 371 R 371
           R
Sbjct: 589 R 589

>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 =  140 bits (355), Expect = 9e-37
 Identities = 77/385 (20%), Positives = 125/385 (32%), Gaps = 34/385 (8%)

Query: 34  EKLKNELEKLKIARAS---VQYKVDDSRIKGDGIQQPVEEWLITVDEAINEVETLIADKE 90
            K +N L + + A        Y +D     G  +    EE +            LI    
Sbjct: 3   AKARNCLLQHREALEKDIKTSYIMDHMISDGF-LTISEEEKVRNEPTQQQRAAMLIKMIL 61

Query: 91  KSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETWLKSTQDF 150
           K +N        N          A    + I  +      DSVS  T    T L      
Sbjct: 62  KKDNDSYVSFY-NALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVP 120

Query: 151 ---MHFESRKSTLKGILDAL--SNRNFNMIGVYGMGGIGKTTLVKEV--GRQAKENNLFE 203
              + F +RK  +  I   L         + ++GM G GK+ L  E        E     
Sbjct: 121 QRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPG 180

Query: 204 KVISSRVSQTPQIKEI--QREIAEKLGLKIDQESESVRAWRLL-EQLK-----KETKILI 255
            V    V +  +   +   + +  +L                  ++L+     K  + L+
Sbjct: 181 GVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLL 240

Query: 256 ILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDV-LSCEMDCQQNFVVDVLNDKEAWS 314
           ILDD+W S  L+A        +  C++LLT R + V  S         V   L  ++   
Sbjct: 241 ILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLE 293

Query: 315 LFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRN-- 372
           +            +L      ++KEC G P+ +  I   L++  P  W   L+QL+    
Sbjct: 294 ILSLFVNMK--KADLPEQAHSIIKECKGSPLVVSLIGALLRDF-PNRWEYYLKQLQNKQF 350

Query: 373 -FLRSFSGTQAVAAYSTIQLSYNQL 396
             +R  S     A    + +S   L
Sbjct: 351 KRIRKSSSYDYEALDEAMSISVEML 375

>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 = 98.4 bits (245), Expect = 4e-22
 Identities = 72/377 (19%), Positives = 138/377 (36%), Gaps = 48/377 (12%)

Query: 59  IKGDGIQQP-VEEWLITVDEAINEVETLIADKEKS----NNRCLKGLCPNLKTRYQLSKK 113
           IK   I    +   +++V E   +V++     +++         K  C  +     L  +
Sbjct: 20  IKTSYIMDHMISNGVLSVIE-EEKVKSQATQYQRAAALIKMILNKDNCAYISFYNALLHE 78

Query: 114 AERE-----ANAIVGLHEKGRFDSVSFRTIPEETWLKST---QDFMHFESRKSTLKGILD 165
             ++      + +  +      D+    T    T L      Q  + F +RK  +  I  
Sbjct: 79  GYKDLAALLQSGLPLVSSSSGKDTDGGITSFVRTVLCEGGVPQRPVIFVTRKKLVHAIQQ 138

Query: 166 ALSNRNF--NMIGVYGMGGIGKTTLVKEVGRQAKE-NNLFEKVI-------SSRVSQTPQ 215
            L   N     + +YGM G GK+ L  E  R        F   +         +     +
Sbjct: 139 KLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMK 198

Query: 216 IKEI------QREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAI 269
           ++ +      +   +++L L I++  + +R       L+K  + L+ILDD+W    L+A 
Sbjct: 199 LQNLCMRLDQEESFSQRLPLNIEEAKDRLRVL----MLRKHPRSLLILDDVWDPWVLKAF 254

Query: 270 GIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDV-LNDKEAWSLFKKMTGDCIENGE 328
                     C++LLT R + V    M  +    V+  L  ++   +        ++  +
Sbjct: 255 DNQ-------CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVN--MKKED 305

Query: 329 LKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKR---NFLRSFSGTQAVAA 385
           L +    ++KEC G P+ +  I   L++  P  W   LRQL+      +R  S     A 
Sbjct: 306 LPAEAHSIIKECKGSPLVVSLIGALLRDF-PNRWAYYLRQLQNKQFKRIRKSSSYDYEAL 364

Query: 386 YSTIQLSYNQLGGEELR 402
              + +S   L  +   
Sbjct: 365 DEAMSISVEMLREDIKD 381

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20 Length = 389

 Score = 43.6 bits (102), Expect = 7e-05
 Identities = 18/104 (17%), Positives = 36/104 (34%), Gaps = 4/104 (3%)

Query: 158 STLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIK 217
             L   L    +       + G  G GKT  ++++    K+     + +           
Sbjct: 31  ILLGNWLRNPGHHYPRAT-LLGRPGTGKTVTLRKLWELYKDKTTA-RFVYINGFIYRNFT 88

Query: 218 EIQREIAEKLGLKIDQESESVRAW--RLLEQLKKETKILIILDD 259
            I  EIA  L +   +   S   +   L+E L++    + ++ D
Sbjct: 89  AIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLD 132

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi} Length = 350

 Score = 40.9 bits (95), Expect = 6e-04
 Identities = 17/123 (13%), Positives = 44/123 (35%), Gaps = 20/123 (16%)

Query: 156 RKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK-------------ENNLF 202
           R+   + + ++L N       + G+  +GK++L++    +                +   
Sbjct: 17  REEESRKLEESLENYPL--TLLLGIRRVGKSSLLRAFLNERPGILIDCRELYAERGHITR 74

Query: 203 EKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWR-----LLEQLKKETKILIIL 257
           E++I    S     ++ Q +    L LK         + R     L +  ++  + ++  
Sbjct: 75  EELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAF 134

Query: 258 DDI 260
           D+ 
Sbjct: 135 DEA 137

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae} Length = 318

 Score = 40.3 bits (93), Expect = 7e-04
 Identities = 17/139 (12%), Positives = 47/139 (33%), Gaps = 11/139 (7%)

Query: 131 DSVSFRTIPEETWLKSTQDFMHFESRKSTLKGIL-DALSNRNFNMIGVYGMGGIGKTTLV 189
           D     +I E   L+  +         + +   + D+L +    +  +       K  LV
Sbjct: 5   DINLEESIRES--LQKRELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLV 62

Query: 190 KEVGRQAKENNLFEKVISSRV-----SQTPQIKEIQREIAEKLGLKI---DQESESVRAW 241
            +V  +   ++  +++           +   +  +  +I   +  +    D   E++  +
Sbjct: 63  NDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFY 122

Query: 242 RLLEQLKKETKILIILDDI 260
                  K+ K LI++ + 
Sbjct: 123 ITNVPKAKKRKTLILIQNP 141

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	426
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.7
2fna_A	357	Conserved hypothetical protein; structural genomic	99.67
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.65
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.55
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.53
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.5
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.48
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.48
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.47
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.39
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.29
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.19
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.09
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.07
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.01
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.95
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.93
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.86
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.84
3pvs_A	447	Replication-associated recombination protein A; ma	98.83
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.78
3bos_A	242	Putative DNA replication factor; P-loop containing	98.78
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.77
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.7
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.7
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.68
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.68
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.66
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.66
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.65
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.63
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.62
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.6
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.57
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.55
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.55
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.54
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.54
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.52
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.48
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.47
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.43
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.42
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.4
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.38
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.36
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.36
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.32
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.31
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.27
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.26
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.24
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.19
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.16
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	98.14
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.11
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.1
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.08
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.04
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.98
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.96
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.93
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.91
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.8
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.8
3co5_A	143	Putative two-component system transcriptional RES	97.74
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.72
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.67
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.61
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.58
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.55
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.53
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.5
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.49
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.45
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.35
3io5_A	333	Recombination and repair protein; storage dimer, i	97.34
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	97.3
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.27
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.26
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.17
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.16
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.11
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.11
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.09
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.05
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.04
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.01
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.97
2qgz_A	308	Helicase loader, putative primosome component; str	96.96
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.93
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.93
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.9
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.86
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.78
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.77
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.7
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.67
3ice_A	422	Transcription termination factor RHO; transcriptio	96.61
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.56
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.56
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.55
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.5
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.5
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.39
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.35
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.35
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.31
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	96.29
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.29
2xxa_A	433	Signal recognition particle protein; protein trans	96.28
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.27
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.26
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	96.25
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.22
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.21
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.16
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.15
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.15
2hf9_A	226	Probable hydrogenase nickel incorporation protein	96.13
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.1
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.1
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.07
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.06
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.05
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.04
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.03
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.03
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.0
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.0
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.99
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.98
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.97
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.94
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.92
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	95.9
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.89
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.87
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.87
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.87
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.86
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.86
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.86
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.86
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.85
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.83
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.81
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.79
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.78
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.78
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.78
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.77
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.77
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.75
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.74
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.73
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.73
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.73
1via_A	175	Shikimate kinase; structural genomics, transferase	95.72
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.68
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.68
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.68
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.66
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.65
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.65
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.65
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.64
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.62
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.61
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.61
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.61
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.61
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.6
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.59
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.59
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.58
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.56
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	95.55
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.54
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	95.53
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.53
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.53
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.53
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.52
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.5
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.5
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	95.5
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.5
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.5
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.47
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.47
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.44
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.4
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.38
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.38
3l0o_A	427	Transcription termination factor RHO; helicase, RH	95.38
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.37
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.36
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.34
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.31
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.31
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.3
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.3
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	95.29
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.29
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.28
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.28
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.22
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.2
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.19
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.18
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.16
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.14
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.1
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.1
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.09
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.05
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.02
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.01
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.01
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.0
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.97
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	94.97
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.94
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.93
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.91
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	94.89
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.89
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	94.88
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.87
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.83
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.82
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.82
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.82
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.81
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.8
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.78
1tue_A	212	Replication protein E1; helicase, replication, E1E	94.78
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.78
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	94.77
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	94.75
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.73
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.71
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.71
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.7
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.69
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.69
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	94.68
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.68
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.66
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	94.65
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.65
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.64
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.64
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.62
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.58
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.58
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	94.57
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.57
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.55
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.5
2og2_A	359	Putative signal recognition particle receptor; nuc	94.46
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.45
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.4
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.38
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.37
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.36
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	94.36
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.32
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	94.31
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.31
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	94.29
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.29
3end_A	307	Light-independent protochlorophyllide reductase ir	94.29
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.28
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.28
1g6h_A	257	High-affinity branched-chain amino acid transport	94.26
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.25
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.25
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	94.24
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.23
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.21
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.2
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.19
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.17
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	94.17
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.16
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.16
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.15
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.08
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.04
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.02
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	93.98
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.97
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.97
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.97
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	93.93
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.93
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.93
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	93.92
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.91
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	93.9
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.9
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.86
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	93.84
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.84
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.83
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	93.8
2wji_A	165	Ferrous iron transport protein B homolog; membrane	93.79
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	93.78
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.76
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.76
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.73
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	93.69
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	93.64
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.62
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	93.6
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.58
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	93.56
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.55
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	93.52
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	93.52
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.49
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.49
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.49
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.48
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.44
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	93.43
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	93.42
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	93.4
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	93.35
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.34
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	93.31
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	93.28
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.27
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	93.22
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.22
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.21
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	93.19
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.17
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	93.16
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.15
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.15
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.15
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.14
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.11
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.1
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	93.1
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	93.08
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.06
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	93.05
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.04
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.03
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.01
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.0
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	92.99
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	92.99
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	92.98
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	92.98
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	92.96
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	92.95
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	92.94
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	92.93
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	92.91
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	92.91
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	92.87
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	92.87
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	92.86
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	92.86
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	92.85
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	92.84
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	92.81
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	92.8
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	92.8
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	92.79
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	92.77
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	92.77
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	92.76
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	92.75
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	92.69
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	92.67
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	92.66
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	92.65
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	92.63
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	92.63
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.62
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	92.61
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.61
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	92.55
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	92.53
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	92.51
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	92.51
1p9r_A	418	General secretion pathway protein E; bacterial typ	92.5
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	92.49
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	92.48
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	92.48
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	92.44
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	92.43
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	92.41
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.4
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	92.4
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	92.39
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	92.39
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.37
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.34
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.32
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	92.29
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	92.28
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	92.24
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	92.23
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.22
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	92.21
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	92.21
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.21
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	92.18
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.17
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	92.15
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.15
3cwq_A	209	Para family chromosome partitioning protein; alpha	92.12
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	92.12
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	92.12
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.12
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	92.12
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	92.12
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	92.11
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.09
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	92.06
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	92.01
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	91.99
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	91.95
2fh5_B	214	SR-beta, signal recognition particle receptor beta	91.95
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	91.94
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	91.94
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	91.93
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	91.93
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	91.92
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	91.9
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	91.9
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	91.89
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	91.87
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	91.84
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	91.84
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	91.83
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	91.83
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	91.82
3llu_A	196	RAS-related GTP-binding protein C; structural geno	91.79
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	91.75
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	91.74
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	91.74
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	91.73
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	91.73
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	91.73
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	91.7
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	91.68
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	91.68
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	91.68
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	91.63
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	91.63
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	91.62
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	91.6
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	91.59
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	91.57
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	91.55
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	91.55
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	91.54
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	91.53
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	91.47
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	91.46
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	91.39
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	91.32
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	91.3
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	91.3
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	91.29
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.29
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	91.28
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	91.26
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	91.25
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	91.23
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	91.17
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	91.14
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	91.13
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	91.12
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	91.1
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	91.09
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	91.07
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	91.06
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	91.06
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	91.01
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	91.0
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	90.99
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	90.88
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	90.86
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	90.84
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	90.83
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	90.7
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	90.63

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=1.1e-40  Score=337.58  Aligned_cols=253  Identities=13%  Similarity=0.133  Sum_probs=198.6

Q ss_pred             cchHHHHHHHHHHhccC---CccEEEEEcCCCCcHHHHHHHHHH--HhhhcCccceEEEEEecCCc--CHHHHHHHHHHH
Q 044858          154 ESRKSTLKGILDALSNR---NFNMIGVYGMGGIGKTTLVKEVGR--QAKENNLFEKVISSRVSQTP--QIKEIQREIAEK  226 (426)
Q Consensus       154 ~gR~~~~~~l~~~l~~~---~~~vi~I~G~~GiGKTtLa~~v~~--~~~~~~~f~~~~wv~v~~~~--~~~~il~~i~~~  226 (426)
                      +||+.++++|.++|...   ..++|+|+||||+||||||+++|+  +.....+|++++|+++++.+  ++..++..|+.+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            49999999999999743   578999999999999999999998  56677889999999999885  899999999999


Q ss_pred             hCCCcc--------ccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhccCCc
Q 044858          227 LGLKID--------QESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDC  298 (426)
Q Consensus       227 l~~~~~--------~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~~~~~  298 (426)
                      ++....        ..+.......+.+.+...|||||||||||+..++ .+.     ..+||+||||||+..++......
T Consensus       211 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~-----~~~gs~ilvTTR~~~v~~~~~~~  284 (549)
T 2a5y_B          211 LKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWA-----QELRLRCLVTTRDVEISNAASQT  284 (549)
T ss_dssp             HTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHH-----HHTTCEEEEEESBGGGGGGCCSC
T ss_pred             HhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-ccc-----ccCCCEEEEEcCCHHHHHHcCCC
Confidence            986521        1112233556666665434999999999998754 211     12699999999999997532234


Q ss_pred             eeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHHHhhccccCCC
Q 044858          299 QQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFS  378 (426)
Q Consensus       299 ~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~l~~~~~~~~~  378 (426)
                      ...|+|++|++++||+||.+.++....++++.+++++|+++|+|+||||+++|+.|+.++   |+.+ +.+.+...... 
T Consensus       285 ~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~---w~~~-~~l~~~l~~~~-  359 (549)
T 2a5y_B          285 CEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKT---FEKM-AQLNNKLESRG-  359 (549)
T ss_dssp             EEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSS---HHHH-HHHHHHHHHHC-
T ss_pred             CeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccch---HHHH-HHhHHHhhccc-
Confidence            568999999999999999999876544577888999999999999999999999998764   3333 33322211100 


Q ss_pred             CcchhhhhhhHHhhhcCCCCChhHHHHH-----------Hhhc---CCccChhhHhhhccC
Q 044858          379 GTQAVAAYSTIQLSYNQLGGEELRKTFL-----------LIGY---SYICNVKDLLYRGMG  425 (426)
Q Consensus       379 ~~~~~~~~~~l~~sy~~L~~~~lk~cfl-----------~~s~---~~~i~~~~Li~~Wi~  425 (426)
                        . ..+..++.+||++||++ +|.||+           |||+   ++.|+    +++|++
T Consensus       360 --~-~~i~~~l~~Sy~~L~~~-lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a  412 (549)
T 2a5y_B          360 --L-VGVECITPYSYKSLAMA-LQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSC  412 (549)
T ss_dssp             --S-STTCCCSSSSSSSHHHH-HHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHH
T ss_pred             --H-HHHHHHHhcccccccHH-HHHHHhccchhhhhHhhheeeeCCCCeee----eeeeee
Confidence              1 56889999999999998 999999           9999   67887    778875

>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=5.1e-35  Score=323.81  Aligned_cols=268  Identities=21%  Similarity=0.308  Sum_probs=208.1

Q ss_pred             cCCcccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhh-cCcc-ceEEEEEecCCcC--HHHHH
Q 044858          147 TQDFMHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE-NNLF-EKVISSRVSQTPQ--IKEIQ  220 (426)
Q Consensus       147 ~~~~~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~-~~~f-~~~~wv~v~~~~~--~~~il  220 (426)
                      +.....|+||+.++++|.+.|.  +++.++|+|+||||+||||||+++|++... ..+| +.++|+++++..+  ....+
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            3455679999999999999985  456789999999999999999999988643 3334 5788999988543  44456


Q ss_pred             HHHHHHhCCCcc-----ccCcHHHHHHHHHHHhc-CCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhc
Q 044858          221 REIAEKLGLKID-----QESESVRAWRLLEQLKK-ETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSC  294 (426)
Q Consensus       221 ~~i~~~l~~~~~-----~~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~  294 (426)
                      ..++..+.....     ..........+...+.. ++|+||||||+|+...|..+       .+||+||||||++.++..
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            777777764322     12223334444444432 24999999999998777654       468999999999998743


Q ss_pred             cCCceeeEEccC-CCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHHHhhcc
Q 044858          295 EMDCQQNFVVDV-LNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNF  373 (426)
Q Consensus       295 ~~~~~~~~~l~~-L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~l~~~~  373 (426)
                      .......+.+.+ |+++++++||...++..  .+.+.+.+++|+++|+|+||||..+|++|+.++ ..|+..++.+....
T Consensus       273 ~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~--~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-~~~~~~l~~l~~~~  349 (1249)
T 3sfz_A          273 VMGPKHVVPVESGLGREKGLEILSLFVNMK--KEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQ  349 (1249)
T ss_dssp             CCSCBCCEECCSSCCHHHHHHHHHHHHTSC--STTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-SCHHHHHHHHHSCC
T ss_pred             hcCCceEEEecCCCCHHHHHHHHHHhhCCC--hhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-hHHHHHHHHHhhhh
Confidence            456667899996 99999999999988533  234456799999999999999999999999765 47999999887554


Q ss_pred             ccCC---CCcchhhhhhhHHhhhcCCCCChhHHHHHHhhc---CCccChhhHhhhccC
Q 044858          374 LRSF---SGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGY---SYICNVKDLLYRGMG  425 (426)
Q Consensus       374 ~~~~---~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s~---~~~i~~~~Li~~Wi~  425 (426)
                      ....   ...+.+.+..+|.+||+.||++ +|.||+|||+   ++.|+++.|+.+|.+
T Consensus       350 ~~~~~~~~~~~~~~~~~~l~~s~~~L~~~-~~~~~~~l~~f~~~~~i~~~~~~~~~~~  406 (1249)
T 3sfz_A          350 FKRIRKSSSYDYEALDEAMSISVEMLRED-IKDYYTDLSILQKDVKVPTKVLCVLWDL  406 (1249)
T ss_dssp             CCCSSCTTCTTHHHHHHHHHHHHHTSCTT-THHHHHHGGGSCTTCCEEHHHHHHHHTC
T ss_pred             hhhcccccccchHHHHHHHHHHHHhCCHH-HHHHHHHhCccCCCCeeCHHHHHHHhCC
Confidence            3221   1112367999999999999998 9999999998   789999999999963

>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=1.8e-35  Score=305.42  Aligned_cols=241  Identities=19%  Similarity=0.137  Sum_probs=189.2

Q ss_pred             ccchHHHHHHHHHHhcc-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccce-EEEEEecCCcCHHHHHHHHHHHhCCC
Q 044858          153 FESRKSTLKGILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEK-VISSRVSQTPQIKEIQREIAEKLGLK  230 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~il~~i~~~l~~~  230 (426)
                      .+||+.++++|.++|.+ +..++|+|+||||+||||||+++|++.+...+|+. ++|+++++.++...++..|+..++..
T Consensus       130 ~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i  209 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI  209 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhc
Confidence            48999999999999875 45789999999999999999999998777778996 99999999999888888887754211


Q ss_pred             ---cccc---------CcHHHHHHHHHHH--hcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhccC
Q 044858          231 ---IDQE---------SESVRAWRLLEQL--KKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEM  296 (426)
Q Consensus       231 ---~~~~---------~~~~~~~~l~~~l--~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~~~  296 (426)
                         ....         +.......+.+.+  ..++|+||||||+|+.+.|+.+.       +||+||||||+..++.. .
T Consensus       210 ~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~~Va~~-l  281 (1221)
T 1vt4_I          210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDF-L  281 (1221)
T ss_dssp             CSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCSHHHHH-H
T ss_pred             CcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccChHHHHh-c
Confidence               1000         1112233444444  14689999999999988887652       58999999999988631 1


Q ss_pred             CceeeEEcc------CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcC--CHHHHHHHHHH
Q 044858          297 DCQQNFVVD------VLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNK--SPYEWRNALRQ  368 (426)
Q Consensus       297 ~~~~~~~l~------~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~--~~~~w~~~l~~  368 (426)
                      .....|.++      +|+++|||+||.+.++..  .   .++..+|   |+|+||||.++|+.|+.+  +..+|+..   
T Consensus       282 ~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~--~---eeL~~eI---CgGLPLALkLaGs~Lr~k~~s~eeW~~~---  350 (1221)
T 1vt4_I          282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR--P---QDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKHV---  350 (1221)
T ss_dssp             HHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCC--T---TTHHHHH---CCCCHHHHHHHHHHHHHSCSSHHHHHHC---
T ss_pred             CCCeEEEecCccccCCcCHHHHHHHHHHHcCCC--H---HHHHHHH---hCCCHHHHHHHHHHHhCCCCCHHHHhcC---
Confidence            222356666      899999999999986432  1   2233333   999999999999999976  77788652   


Q ss_pred             HhhccccCCCCcchhhhhhhHHhhhcCCCCChh-HHHHHHhhc---CCccChhhHhhhccC
Q 044858          369 LKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEEL-RKTFLLIGY---SYICNVKDLLYRGMG  425 (426)
Q Consensus       369 l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~l-k~cfl~~s~---~~~i~~~~Li~~Wi~  425 (426)
                             .    . ..+..+|.+||+.||++ . |+||+|||+   ++.|+.+.|+.+|++
T Consensus       351 -------~----~-~~I~aaLelSYd~Lp~e-elK~cFL~LAIFPed~~I~~elLa~LW~a  398 (1221)
T 1vt4_I          351 -------N----C-DKLTTIIESSLNVLEPA-EYRKMFDRLSVFPPSAHIPTILLSLIWFD  398 (1221)
T ss_dssp             -------S----C-HHHHHHHHHHHHHSCTT-HHHHHHHHTTSSCTTSCEEHHHHHHHHCS
T ss_pred             -------C----h-hHHHHHHHHHHHhCCHH-HHHHHHHHHhCCCCCCCCCHHHHHHHhcC
Confidence                   1    2 78999999999999998 8 999999999   689999999999985

>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=2.3e-32  Score=279.84  Aligned_cols=264  Identities=20%  Similarity=0.290  Sum_probs=196.3

Q ss_pred             CcccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhh-cCccc-eEEEEEecCCcCHHHHHHHH-
Q 044858          149 DFMHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE-NNLFE-KVISSRVSQTPQIKEIQREI-  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~-~~~f~-~~~wv~v~~~~~~~~il~~i-  223 (426)
                      ....|+||+.+++.|.+.+.  .++.++|+|+|+||+||||||.+++++... ..+|. .++|++++.. +...++..+ 
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~  200 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQ  200 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHH
T ss_pred             CCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHH
Confidence            45679999999999999987  346789999999999999999999987654 56784 7999999875 334444444 


Q ss_pred             --HHHhCCC-----ccccCcHHHHHHHHHHHhc-CCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhcc
Q 044858          224 --AEKLGLK-----IDQESESVRAWRLLEQLKK-ETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCE  295 (426)
Q Consensus       224 --~~~l~~~-----~~~~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~~  295 (426)
                        +..++..     ....+.......+...+.. .+++||||||+|+...+..+       .++++||||||+..++...
T Consensus       201 ~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l-------~~~~~ilvTsR~~~~~~~~  273 (591)
T 1z6t_A          201 NLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSV  273 (591)
T ss_dssp             HHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTT-------CSSCEEEEEESCGGGGTTC
T ss_pred             HHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHh-------cCCCeEEEECCCcHHHHhc
Confidence              4455421     1112233344555555543 26899999999987655532       3589999999999876422


Q ss_pred             CCceeeEE-ccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHHHhhccc
Q 044858          296 MDCQQNFV-VDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFL  374 (426)
Q Consensus       296 ~~~~~~~~-l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~l~~~~~  374 (426)
                      .+....+. +++|+.+++++||...++..  .+...+.+.+|+++|+|+||||..+|+.|+... ..|...++.+.....
T Consensus       274 ~~~~~~v~~l~~L~~~ea~~L~~~~~~~~--~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~-~~w~~~l~~l~~~~~  350 (591)
T 1z6t_A          274 MGPKYVVPVESSLGKEKGLEILSLFVNMK--KADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQNKQF  350 (591)
T ss_dssp             CSCEEEEECCSSCCHHHHHHHHHHHHTSC--GGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST-TCHHHHHHHHHSCCC
T ss_pred             CCCceEeecCCCCCHHHHHHHHHHHhCCC--cccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc-hhHHHHHHHHHHhHH
Confidence            22222222 35899999999999998742  222345789999999999999999999998663 379999888875432


Q ss_pred             cCCC---CcchhhhhhhHHhhhcCCCCChhHHHHHHhhc---CCccChhhHhhhcc
Q 044858          375 RSFS---GTQAVAAYSTIQLSYNQLGGEELRKTFLLIGY---SYICNVKDLLYRGM  424 (426)
Q Consensus       375 ~~~~---~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s~---~~~i~~~~Li~~Wi  424 (426)
                      ....   ......+..++..||+.||++ .|.||++||+   ++.|+.+.|..+|.
T Consensus       351 ~~~~~~~~~~~~~l~~~l~~s~~~L~~~-~~~~l~~la~f~~~~~i~~~~l~~l~~  405 (591)
T 1z6t_A          351 KRIRKSSSYDYEALDEAMSISVEMLRED-IKDYYTDLSILQKDVKVPTKVLCILWD  405 (591)
T ss_dssp             CCSSCCCSSCCHHHHHHHHHHHHTSCTT-THHHHHHGGGCCTTCCEEHHHHHHHHT
T ss_pred             HHhhhccccchHHHHHHHHHHHHhCCHH-HHHHHHHccccCCCCccCHHHHHHHhc
Confidence            2111   112268899999999999998 9999999999   68899999999986

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.70  E-value=5.1e-16  Score=147.79  Aligned_cols=196  Identities=13%  Similarity=0.123  Sum_probs=129.1

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc------CHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP------QIKEIQRE  222 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~------~~~~il~~  222 (426)
                      .+..|+||+++++.|.+++.++  +++.|+|++|+|||||++++.+...       .+|+++....      +...++..
T Consensus        10 ~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~   80 (350)
T 2qen_A           10 RREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNERP-------GILIDCRELYAERGHITREELIKE   80 (350)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHSS-------EEEEEHHHHHHTTTCBCHHHHHHH
T ss_pred             ChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHcC-------cEEEEeecccccccCCCHHHHHHH
Confidence            4567999999999999988764  7899999999999999999987641       6677765432      56677777


Q ss_pred             HHHHhCC-----------------Ccc--ccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC---------hhhhcCCCC
Q 044858          223 IAEKLGL-----------------KID--QESESVRAWRLLEQLKKETKILIILDDIWGSLD---------LEAIGIPLA  274 (426)
Q Consensus       223 i~~~l~~-----------------~~~--~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~---------~~~l~~~l~  274 (426)
                      +.+.+..                 ..+  ..........+.+.....++++|||||++....         +..+.... 
T Consensus        81 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~-  159 (350)
T 2qen_A           81 LQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAY-  159 (350)
T ss_dssp             HHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHH-
T ss_pred             HHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHH-
Confidence            7666542                 000  011122222333333222389999999976542         12221111 


Q ss_pred             CCCCCeEEEEeecchhh-hh--------c-cC-CceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          275 DDNGGCKVLLTARSQDV-LS--------C-EM-DCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       275 ~~~~~s~iivTtr~~~v-a~--------~-~~-~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                      ...++.++|+|++.... ..        . .. .....+++.||+.+|+.+++.+.+....... -.+.+..|++.|+|+
T Consensus       160 ~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~-~~~~~~~i~~~tgG~  238 (350)
T 2qen_A          160 DSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV-PENEIEEAVELLDGI  238 (350)
T ss_dssp             HHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHHTTC
T ss_pred             HhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHhCCC
Confidence            11247889999887542 11        0 11 1235899999999999999988653221111 145678999999999


Q ss_pred             hHHHHHHHHHhh
Q 044858          344 PIAIVPIAKALK  355 (426)
Q Consensus       344 Plai~~~~~~l~  355 (426)
                      |+++..++..+.
T Consensus       239 P~~l~~~~~~~~  250 (350)
T 2qen_A          239 PGWLVVFGVEYL  250 (350)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999987653

>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=99.67  E-value=1.6e-15  Score=144.74  Aligned_cols=194  Identities=14%  Similarity=0.178  Sum_probs=124.5

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-----cCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-----PQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-----~~~~~il~~i  223 (426)
                      .+..|+||+++++.|.+ +..   +++.|+|++|+|||+|++++.+....     ..+|+++...     .+...++..+
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~l   81 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELNL-----PYIYLDLRKFEERNYISYKDFLLEL   81 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHTC-----CEEEEEGGGGTTCSCCCHHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcCC-----CEEEEEchhhccccCCCHHHHHHHH
Confidence            45679999999999999 765   68999999999999999999987542     2578877642     3445555555


Q ss_pred             HHHhC------------------CCccc---c-C----cHHHHHHHHHHHhc-C-CeEEEEEeCCCCcc-----Chhhhc
Q 044858          224 AEKLG------------------LKIDQ---E-S----ESVRAWRLLEQLKK-E-TKILIILDDIWGSL-----DLEAIG  270 (426)
Q Consensus       224 ~~~l~------------------~~~~~---~-~----~~~~~~~l~~~l~~-~-k~~LlVlDdv~~~~-----~~~~l~  270 (426)
                      .+.+.                  .+.+.   . .    .......+.+.+.+ . ++++|||||++...     ++..+.
T Consensus        82 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~~~~~~l  161 (357)
T 2fna_A           82 QKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPAL  161 (357)
T ss_dssp             HHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHHH
T ss_pred             HHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccCchhHHHHH
Confidence            44331                  00000   0 0    01123344444432 1 48999999997532     222221


Q ss_pred             CCCCCCCCCeEEEEeecchhhhh---------c-cCCc-eeeEEccCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHH
Q 044858          271 IPLADDNGGCKVLLTARSQDVLS---------C-EMDC-QQNFVVDVLNDKEAWSLFKKMTGD-CIENGELKSVVTEVVK  338 (426)
Q Consensus       271 ~~l~~~~~~s~iivTtr~~~va~---------~-~~~~-~~~~~l~~L~~~e~~~Lf~~~~~~-~~~~~~~~~~~~~i~~  338 (426)
                      ..+.....+..+|+|++......         . ..+. ...+.+.+|+.+++.+++...+.. ....+..    ..|++
T Consensus       162 ~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~----~~i~~  237 (357)
T 2fna_A          162 AYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY----EVVYE  237 (357)
T ss_dssp             HHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH----HHHHH
T ss_pred             HHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcH----HHHHH
Confidence            11212224688999998764211         0 1112 368999999999999999886531 1112221    78999


Q ss_pred             HcCCchHHHHHHHHHhh
Q 044858          339 ECAGLPIAIVPIAKALK  355 (426)
Q Consensus       339 ~c~GlPlai~~~~~~l~  355 (426)
                      .|+|+|+++..++..+.
T Consensus       238 ~t~G~P~~l~~~~~~~~  254 (357)
T 2fna_A          238 KIGGIPGWLTYFGFIYL  254 (357)
T ss_dssp             HHCSCHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHHHc
Confidence            99999999999988765

>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=99.65  E-value=5.3e-15  Score=144.13  Aligned_cols=246  Identities=17%  Similarity=0.107  Sum_probs=152.6

Q ss_pred             cccccchHHHHHHHHHHh-c----c--CCccEEEE--EcCCCCcHHHHHHHHHHHhhhc---Cccc-eEEEEEecCCcCH
Q 044858          150 FMHFESRKSTLKGILDAL-S----N--RNFNMIGV--YGMGGIGKTTLVKEVGRQAKEN---NLFE-KVISSRVSQTPQI  216 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l-~----~--~~~~vi~I--~G~~GiGKTtLa~~v~~~~~~~---~~f~-~~~wv~v~~~~~~  216 (426)
                      +..|+||+.+++.+.+.+ .    .  .....+.|  +|++|+|||||++.+++.....   ..|. .++|+.+....+.
T Consensus        21 p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (412)
T 1w5s_A           21 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNL  100 (412)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSH
T ss_pred             CCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCH
Confidence            367999999999998888 4    2  34567777  9999999999999999876542   1123 3567777777889


Q ss_pred             HHHHHHHHHHhCCCccc--cCcHHHHHHHHHHHh-cCCeEEEEEeCCCCccC--------hhhhcCCC---CCCC--CCe
Q 044858          217 KEIQREIAEKLGLKIDQ--ESESVRAWRLLEQLK-KETKILIILDDIWGSLD--------LEAIGIPL---ADDN--GGC  280 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~--~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~~--------~~~l~~~l---~~~~--~~s  280 (426)
                      ..++..++.+++...+.  .+.......+.+.+. .+++++|||||++....        +..+...+   +...  ...
T Consensus       101 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v  180 (412)
T 1w5s_A          101 YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRI  180 (412)
T ss_dssp             HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBE
T ss_pred             HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceE
Confidence            99999999999765432  122333445555553 35799999999976421        22221111   1112  345


Q ss_pred             EEEEeecchhhhh--------ccCCceeeEEccCCCHHHHHHHHHHhhCCC-CCCCchHHHHHHHHHHcC------CchH
Q 044858          281 KVLLTARSQDVLS--------CEMDCQQNFVVDVLNDKEAWSLFKKMTGDC-IENGELKSVVTEVVKECA------GLPI  345 (426)
Q Consensus       281 ~iivTtr~~~va~--------~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~-~~~~~~~~~~~~i~~~c~------GlPl  345 (426)
                      .+|+||+......        ........+.+.+|+.++.+++|...+... .....-.+....|++.|+      |+|.
T Consensus       181 ~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G~p~  260 (412)
T 1w5s_A          181 GFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSAR  260 (412)
T ss_dssp             EEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHH
T ss_pred             EEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCCcHH
Confidence            6888887554210        001111239999999999999998765310 011122457888999999      9997


Q ss_pred             HHHHHHHHhh------cC---CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHHHhhc
Q 044858          346 AIVPIAKALK------NK---SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIGY  410 (426)
Q Consensus       346 ai~~~~~~l~------~~---~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s~  410 (426)
                      .+..+.....      +.   +...+..++.....              ...+.-++..||++ .+.++..++.
T Consensus       261 ~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~~--------------~~~~~~~l~~l~~~-~~~~l~aia~  319 (412)
T 1w5s_A          261 RAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEA--------------ASIQTHELEALSIH-ELIILRLIAE  319 (412)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC--------------------CCSSSSSCHH-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc--------------cchHHHHHHcCCHH-HHHHHHHHHH
Confidence            7666554321      11   33444443332110              12344456778876 7777777764

>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=99.55  E-value=2.2e-13  Score=131.37  Aligned_cols=218  Identities=13%  Similarity=0.078  Sum_probs=139.2

Q ss_pred             ccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----c--cceEEEEEecCCc-CHHHH
Q 044858          151 MHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN----L--FEKVISSRVSQTP-QIKEI  219 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~--f~~~~wv~v~~~~-~~~~i  219 (426)
                      ..|+||+++++.+..++.    .+..+.+.|+|++|+|||+||+.+++......    .  ....+|++.+... +...+
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   99 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAV   99 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHH
Confidence            578999999999887765    34467899999999999999999998764321    1  2356788877766 88889


Q ss_pred             HHHHHHHh-CCCcc--ccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC---hhhhcCCCCCCCCCeEEEEeecchhhh-
Q 044858          220 QREIAEKL-GLKID--QESESVRAWRLLEQLKKETKILIILDDIWGSLD---LEAIGIPLADDNGGCKVLLTARSQDVL-  292 (426)
Q Consensus       220 l~~i~~~l-~~~~~--~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~---~~~l~~~l~~~~~~s~iivTtr~~~va-  292 (426)
                      +..++.++ +....  ..+.......+.+.+... +.+|||||++....   .+.+...+.....+..+|+||+..... 
T Consensus       100 ~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~-~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~~~~~  178 (384)
T 2qby_B          100 LSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNI-RAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRD  178 (384)
T ss_dssp             HHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSS-CEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSSTTTTT
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccC-CCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCCchHh
Confidence            99998887 33222  122334456666666543 44999999975421   122011111111678899999875321 


Q ss_pred             ---hc-cCCceeeEEccCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHcC---CchHH-HHHHHHHh--h----cC
Q 044858          293 ---SC-EMDCQQNFVVDVLNDKEAWSLFKKMTGD-CIENGELKSVVTEVVKECA---GLPIA-IVPIAKAL--K----NK  357 (426)
Q Consensus       293 ---~~-~~~~~~~~~l~~L~~~e~~~Lf~~~~~~-~~~~~~~~~~~~~i~~~c~---GlPla-i~~~~~~l--~----~~  357 (426)
                         .. .......+.+++++.++..++|...+.. .....--.+..+.|++.|+   |.|.. +..+-...  .    .-
T Consensus       179 ~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~~~~~i  258 (384)
T 2qby_B          179 YMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASGGGII  258 (384)
T ss_dssp             TSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTTSSSCC
T ss_pred             hhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhcCCCcc
Confidence               10 0111238999999999999999987631 1011111345677888888   98874 33333322  1    12


Q ss_pred             CHHHHHHHHHHH
Q 044858          358 SPYEWRNALRQL  369 (426)
Q Consensus       358 ~~~~w~~~l~~l  369 (426)
                      +.+.+..++...
T Consensus       259 ~~~~v~~~~~~~  270 (384)
T 2qby_B          259 RKEHVDKAIVDY  270 (384)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            777887777664

>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=99.53  E-value=3.1e-13  Score=130.15  Aligned_cols=244  Identities=15%  Similarity=0.119  Sum_probs=150.7

Q ss_pred             cccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc-cceEEEEEecCCcCHHHHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL-FEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~-f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      +..|+||+.+++.+.+++.    ......+.|+|++|+|||||++.+++....... -...+|++.....+...++..++
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~   98 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLL   98 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHT
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHH
Confidence            4679999999999999887    345678999999999999999999987654311 12466777777677888888888


Q ss_pred             HHhCCCcccc--CcHHHHHHHHHHHhc-CCeEEEEEeCCCCcc------ChhhhcCCCCC-CCCCeEEEEeecchhhhhc
Q 044858          225 EKLGLKIDQE--SESVRAWRLLEQLKK-ETKILIILDDIWGSL------DLEAIGIPLAD-DNGGCKVLLTARSQDVLSC  294 (426)
Q Consensus       225 ~~l~~~~~~~--~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~------~~~~l~~~l~~-~~~~s~iivTtr~~~va~~  294 (426)
                      .+++...+..  +.......+.+.+.. +++.+|||||++...      .+..+...+.. ...+..+|+||+.......
T Consensus        99 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~  178 (386)
T 2qby_A           99 ESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDL  178 (386)
T ss_dssp             TTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGG
T ss_pred             HHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhh
Confidence            8876543322  223334555555543 458999999997532      12222111111 2335677888876543210


Q ss_pred             c------CCceeeEEccCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHcC---CchHHHHHHHHHhh------c--
Q 044858          295 E------MDCQQNFVVDVLNDKEAWSLFKKMTGD-CIENGELKSVVTEVVKECA---GLPIAIVPIAKALK------N--  356 (426)
Q Consensus       295 ~------~~~~~~~~l~~L~~~e~~~Lf~~~~~~-~~~~~~~~~~~~~i~~~c~---GlPlai~~~~~~l~------~--  356 (426)
                      .      .-....+.+++++.++..+++.+.+.. .....-..+..+.+++.++   |.|..+..+.....      +  
T Consensus       179 ~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~~~~  258 (386)
T 2qby_A          179 LDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDT  258 (386)
T ss_dssp             CTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCS
T ss_pred             hCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCC
Confidence            0      011258999999999999999986531 1011222456777888887   99985444332221      1  


Q ss_pred             C-CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCChhHHHHHHhh
Q 044858          357 K-SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLIG  409 (426)
Q Consensus       357 ~-~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~s  409 (426)
                      . +.+.+..++....               ...+.-++..||.+ .+..+..++
T Consensus       259 ~i~~~~v~~a~~~~~---------------~~~~~~~~~~l~~~-~~~il~ai~  296 (386)
T 2qby_A          259 KVKEEYVYMAKEEIE---------------RDRVRDIILTLPFH-SKLVLMAVV  296 (386)
T ss_dssp             SCCHHHHHHHHHHHH---------------HHHHHHHHHTSCHH-HHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHh---------------hchHHHHHHcCCHH-HHHHHHHHH
Confidence            1 6666666665432               12344455666654 454444444

>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=99.50  E-value=5.2e-13  Score=119.84  Aligned_cols=199  Identities=12%  Similarity=0.151  Sum_probs=119.7

Q ss_pred             CcccccchHHHHHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      ....++||+.+++.+..++..+. .+.+.|+|++|+||||||+.+++.......+..      ........ ...+....
T Consensus        21 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~------~~~~~~~~-~~~~~~~~   93 (250)
T 1njg_A           21 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA------TPCGVCDN-CREIEQGR   93 (250)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCS------SCCSCSHH-HHHHHTTC
T ss_pred             cHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC------CCCcccHH-HHHHhccC
Confidence            45679999999999999887544 457899999999999999999987653211100      00000000 00010000


Q ss_pred             CC-----CccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchhhh-hcc
Q 044858          228 GL-----KIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQDVL-SCE  295 (426)
Q Consensus       228 ~~-----~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~va-~~~  295 (426)
                      ..     .............+.+.+.    .+++.+|||||++..  ..+..+...+.....++.+|+||+..... ...
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l  173 (250)
T 1njg_A           94 FVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTI  173 (250)
T ss_dssp             CSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHH
T ss_pred             CcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHH
Confidence            00     0000011122223333221    246799999999753  34444444333334578888888765422 111


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhh
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALK  355 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~  355 (426)
                      ......+++++++.++..+++...+...... --.+..+.|++.|+|+|..+..+...+.
T Consensus       174 ~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~G~~~~~~~~~~~~~  232 (250)
T 1njg_A          174 LSRCLQFHLKALDVEQIRHQLEHILNEEHIA-HEPRALQLLARAAEGSLRDALSLTDQAI  232 (250)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHTTCC-BCHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhhhccCCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            1234689999999999999999887422211 1245678899999999999888765543

>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=99.48  E-value=9.2e-13  Score=116.56  Aligned_cols=191  Identities=11%  Similarity=0.080  Sum_probs=119.9

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .....++||+..++.+..++.....+.+.|+|++|+|||+||+.+++.......-...+.+..+...+...+...+....
T Consensus        14 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (226)
T 2chg_A           14 RTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKIKEFA   93 (226)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHHHHHHH
T ss_pred             CCHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHHHHHHh
Confidence            34567899999999999998876666699999999999999999998764322112233444444333333222221111


Q ss_pred             CCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecchhhh-hccCCceeeEEc
Q 044858          228 GLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQDVL-SCEMDCQQNFVV  304 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~~va-~~~~~~~~~~~l  304 (426)
                      ...               ....+++.+|||||++...  ..+.+...+.....++++|+||+..... .........+.+
T Consensus        94 ~~~---------------~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~  158 (226)
T 2chg_A           94 RTA---------------PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRF  158 (226)
T ss_dssp             TSC---------------CSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             ccc---------------CCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeec
Confidence            100               0112568999999997652  2333333332334577888888765321 111122348999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      .+++.++..+++.+.+...... --.+..+.|++.++|.|..+..+...+
T Consensus       159 ~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~g~~r~l~~~l~~~  207 (226)
T 2chg_A          159 KPVPKEAMKKRLLEICEKEGVK-ITEDGLEALIYISGGDFRKAINALQGA  207 (226)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            9999999999999877421111 124567789999999999765554433

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.48  E-value=8.4e-14  Score=109.23  Aligned_cols=79  Identities=13%  Similarity=0.090  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHHHHHHHHHH
Q 044858            8 TAKVAEYLVAPIIRQFTYCCSYNTNLEKLKNELEKLKIARASVQYKVDDSRIKG-DGIQQPVEEWLITVDEAINEVETLI   86 (426)
Q Consensus         8 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~i~~~l~~a~~~~-~~~~~~~~~Wl~~l~~~~yd~ed~l   86 (426)
                      ++.+++++.+.+.+++       ..+.++++++++|+++|..|+++|.+++.+. ...++.++.|+.+||+++||+||+|
T Consensus         3 v~~ll~KL~~ll~~E~-------~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~i   75 (115)
T 3qfl_A            3 ISNLIPKLGELLTEEF-------KLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVV   75 (115)
T ss_dssp             TCSHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH-------HHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555666665554       4578899999999999999999999998763 2468999999999999999999999


Q ss_pred             hhhhhhh
Q 044858           87 ADKEKSN   93 (426)
Q Consensus        87 d~~~~~~   93 (426)
                      |+|.+..
T Consensus        76 D~f~~~~   82 (115)
T 3qfl_A           76 DKFLVQV   82 (115)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9986543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.47  E-value=1.6e-12  Score=125.18  Aligned_cols=217  Identities=15%  Similarity=0.124  Sum_probs=139.7

Q ss_pred             cccccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhc----CccceEEEEEecCCcCHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN----NLFEKVISSRVSQTPQIKEIQR  221 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~il~  221 (426)
                      +..|+||+.+++.+..++.    ....+.+.|+|++|+||||||+.+++.....    +.-...+|++.....+...++.
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            3679999999999999884    3456789999999999999999999876432    1112466788888888999999


Q ss_pred             HHHHHhCCCcccc--CcHHHHHHHHHHHh-cCCeEEEEEeCCCCccC---h-hhhc---CCCCCC--CCCeEEEEeecch
Q 044858          222 EIAEKLGLKIDQE--SESVRAWRLLEQLK-KETKILIILDDIWGSLD---L-EAIG---IPLADD--NGGCKVLLTARSQ  289 (426)
Q Consensus       222 ~i~~~l~~~~~~~--~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~~---~-~~l~---~~l~~~--~~~s~iivTtr~~  289 (426)
                      .++.+++...+..  +.......+.+.+. .+++++|+|||++....   . +.+.   ......  ..+..+|.||+..
T Consensus        98 ~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~  177 (387)
T 2v1u_A           98 AIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSL  177 (387)
T ss_dssp             HHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCS
T ss_pred             HHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCC
Confidence            9999997654332  23334556666664 35689999999986432   1 2221   111111  3456778887765


Q ss_pred             hhh----hc-cCC-ceeeEEccCCCHHHHHHHHHHhhCC----CCCCCchHHHHHHHHHHcC---CchHHHH-HHHHHhh
Q 044858          290 DVL----SC-EMD-CQQNFVVDVLNDKEAWSLFKKMTGD----CIENGELKSVVTEVVKECA---GLPIAIV-PIAKALK  355 (426)
Q Consensus       290 ~va----~~-~~~-~~~~~~l~~L~~~e~~~Lf~~~~~~----~~~~~~~~~~~~~i~~~c~---GlPlai~-~~~~~l~  355 (426)
                      ...    .. ... ....+.+++++.++..+++...+..    ...++   +..+.+++.++   |.|..+. .+.....
T Consensus       178 ~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~G~~r~~~~~l~~a~~  254 (387)
T 2v1u_A          178 GFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDP---DVVPLCAALAAREHGDARRALDLLRVAGE  254 (387)
T ss_dssp             TTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCS---SHHHHHHHHHHSSSCCHHHHHHHHHHHHH
T ss_pred             chHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCH---HHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            321    00 011 1257999999999999999987631    12222   35667888887   9995433 3322221


Q ss_pred             -----c--C-CHHHHHHHHHHH
Q 044858          356 -----N--K-SPYEWRNALRQL  369 (426)
Q Consensus       356 -----~--~-~~~~w~~~l~~l  369 (426)
                           +  . +.+.+..++...
T Consensus       255 ~a~~~~~~~i~~~~v~~a~~~~  276 (387)
T 2v1u_A          255 IAERRREERVRREHVYSARAEI  276 (387)
T ss_dssp             HHHHTTCSCBCHHHHHHHHHHH
T ss_pred             HHHHcCCCCcCHHHHHHHHHHH
Confidence                 1  1 677777776654

>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=99.39  E-value=1.2e-11  Score=119.25  Aligned_cols=201  Identities=14%  Similarity=0.144  Sum_probs=133.0

Q ss_pred             ccccchHHHHHHHHHHhcc----CCcc--EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          151 MHFESRKSTLKGILDALSN----RNFN--MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~~----~~~~--vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ..++||+.+++.+..++..    ....  .+.|+|++|+|||||++.+++....... ...++++.+...+...++..++
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHHHH
Confidence            5699999999999888863    3334  8999999999999999999988754311 2466777777778889999999


Q ss_pred             HHhCCCcccc--CcHHHHHHHHHHHh-cCCeEEEEEeCCCCc--cChhhhcCCCCC-CC---CCeEEEEeecchhhhhcc
Q 044858          225 EKLGLKIDQE--SESVRAWRLLEQLK-KETKILIILDDIWGS--LDLEAIGIPLAD-DN---GGCKVLLTARSQDVLSCE  295 (426)
Q Consensus       225 ~~l~~~~~~~--~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~--~~~~~l~~~l~~-~~---~~s~iivTtr~~~va~~~  295 (426)
                      ..++...+..  +.......+...+. .+++.+|+|||++..  .....+...+.. ..   .+..+|++|+........
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l  175 (389)
T 1fnn_A           96 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNL  175 (389)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTS
T ss_pred             HHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHh
Confidence            9887654322  23333444444443 256899999999764  222333222211 11   367788888765332110


Q ss_pred             C----C--ceeeEEccCCCHHHHHHHHHHhhCCC-CCCCchHHHHHHHHHHc---------CCchHHHHHHHH
Q 044858          296 M----D--CQQNFVVDVLNDKEAWSLFKKMTGDC-IENGELKSVVTEVVKEC---------AGLPIAIVPIAK  352 (426)
Q Consensus       296 ~----~--~~~~~~l~~L~~~e~~~Lf~~~~~~~-~~~~~~~~~~~~i~~~c---------~GlPlai~~~~~  352 (426)
                      .    .  ....+.+.+++.++..+++...+... ....--.+..+.|++.+         +|.|..+..+..
T Consensus       176 ~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~  248 (389)
T 1fnn_A          176 DPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILY  248 (389)
T ss_dssp             CHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHH
T ss_pred             CHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHH
Confidence            0    0  11369999999999999998876420 01122245778899999         788766555443

>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=99.29  E-value=2.1e-11  Score=114.39  Aligned_cols=190  Identities=14%  Similarity=0.118  Sum_probs=116.8

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .....++|++..++.+..++..+..+.+.|+|++|+|||++|+.+++...........++++.+...+...+ ++++..+
T Consensus        18 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~~   96 (323)
T 1sxj_B           18 QVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVV-RNQIKHF   96 (323)
T ss_dssp             SSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHH-HTHHHHH
T ss_pred             CCHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHH-HHHHHHH
Confidence            345678999999999999988776656999999999999999999987643211112344444433332222 2222211


Q ss_pred             CCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchhhh-hccCCceeeEEc
Q 044858          228 GLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQDVL-SCEMDCQQNFVV  304 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~va-~~~~~~~~~~~l  304 (426)
                      .....             .+..+++.++||||++..  ..++.+...+.....++.+|+||....-. .........+++
T Consensus        97 ~~~~~-------------~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~  163 (323)
T 1sxj_B           97 AQKKL-------------HLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRY  163 (323)
T ss_dssp             HHBCC-------------CCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             Hhccc-------------cCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEee
Confidence            10000             000345899999999764  22333333332233567888888664321 111223458999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH-HHHHHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIA-IVPIAK  352 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla-i~~~~~  352 (426)
                      .+++.++..+++...+...... --.+....|++.|+|.|.. +..+..
T Consensus       164 ~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~G~~r~a~~~l~~  211 (323)
T 1sxj_B          164 SKLSDEDVLKRLLQIIKLEDVK-YTNDGLEAIIFTAEGDMRQAINNLQS  211 (323)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            9999999999999876421111 1135678899999999954 444433

>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=99.19  E-value=1e-10  Score=109.89  Aligned_cols=188  Identities=13%  Similarity=0.093  Sum_probs=115.7

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG  228 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~  228 (426)
                      .+..++|++..++.+..++..+..+.+.++|++|+||||+|+.+++.......-...+.+..+....... ....+..  
T Consensus        23 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~--   99 (327)
T 1iqp_A           23 RLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINV-IREKVKE--   99 (327)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHT-THHHHHH--
T ss_pred             CHHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCchHH-HHHHHHH--
Confidence            4567899999999999988877666699999999999999999998754321111223333322111111 1111110  


Q ss_pred             CCccccCcHHHHHHHHHH--HhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchhhh-hccCCceeeEE
Q 044858          229 LKIDQESESVRAWRLLEQ--LKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQDVL-SCEMDCQQNFV  303 (426)
Q Consensus       229 ~~~~~~~~~~~~~~l~~~--l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~va-~~~~~~~~~~~  303 (426)
                                    ....  +..+++.++|+||++..  ...+.+...+.....++++|+||...... .........+.
T Consensus       100 --------------~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~  165 (327)
T 1iqp_A          100 --------------FARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFR  165 (327)
T ss_dssp             --------------HHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEE
T ss_pred             --------------HHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEE
Confidence                          0000  11246789999999754  23333433332234577888888765321 11112245889


Q ss_pred             ccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          304 VDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       304 l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      +.+++.++...++...+..... .--.+....|++.++|.|..+..+...+
T Consensus       166 ~~~l~~~~~~~~l~~~~~~~~~-~~~~~~~~~l~~~~~g~~r~~~~~l~~~  215 (327)
T 1iqp_A          166 FRPLRDEDIAKRLRYIAENEGL-ELTEEGLQAILYIAEGDMRRAINILQAA  215 (327)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTC-EECHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            9999999999999887643221 1124567889999999999765554433

>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=99.09  E-value=1.6e-09  Score=101.22  Aligned_cols=186  Identities=10%  Similarity=0.069  Sum_probs=114.6

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhC
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLG  228 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~  228 (426)
                      ....++|++..++.+..++..+..+.+.++|++|+|||++|+.+.+.......-...+.++.+.......+.        
T Consensus        15 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~--------   86 (319)
T 2chq_A           15 TLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVR--------   86 (319)
T ss_dssp             SGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTSTTCTTTSS--------
T ss_pred             CHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccccChHHHH--------
Confidence            456789999999999998887666569999999999999999999875321111112334433321111100        


Q ss_pred             CCccccCcHHHHHHHHHH--HhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchhh-hhccCCceeeEE
Q 044858          229 LKIDQESESVRAWRLLEQ--LKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQDV-LSCEMDCQQNFV  303 (426)
Q Consensus       229 ~~~~~~~~~~~~~~l~~~--l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~v-a~~~~~~~~~~~  303 (426)
                               .........  +..+++.++|+||++..  ...+.+...+.....++++|+||....- ..........+.
T Consensus        87 ---------~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~  157 (319)
T 2chq_A           87 ---------HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFR  157 (319)
T ss_dssp             ---------HHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEE
T ss_pred             ---------HHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEE
Confidence                     011111100  11246789999999754  2234444444333457788888765432 111122345899


Q ss_pred             ccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHH
Q 044858          304 VDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       304 l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      +.+++.++..+++...+...... --.+....|++.++|.|..+.....
T Consensus       158 ~~~~~~~~~~~~l~~~~~~~~~~-i~~~~l~~l~~~~~G~~r~~~~~l~  205 (319)
T 2chq_A          158 FKPVPKEAMKKRLLEICEKEGVK-ITEDGLEALIYISGGDFRKAINALQ  205 (319)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTCCC-BCHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            99999999999998877432211 1245677888999999986655443

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.07  E-value=4.1e-09  Score=97.59  Aligned_cols=170  Identities=9%  Similarity=0.021  Sum_probs=107.5

Q ss_pred             cccchHHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC---cc--ceEEEEEecCCcCHHHHHHH
Q 044858          152 HFESRKSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN---LF--EKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~---~f--~~~~wv~v~~~~~~~~il~~  222 (426)
                      .+.+|++++++|...|.    .+.++.+.|+|++|+|||++++.+.+......   ..  -..++++.....+...++..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~  100 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEK  100 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHH
Confidence            36799999999887775    56778899999999999999999999875421   11  13556676677788899999


Q ss_pred             HHHHhCCCc-cccCcHHHHHHHHHHH--hcCCeEEEEEeCCCCccChhhhcCCC--C-CCCCCeEEEEeecchhh-----
Q 044858          223 IAEKLGLKI-DQESESVRAWRLLEQL--KKETKILIILDDIWGSLDLEAIGIPL--A-DDNGGCKVLLTARSQDV-----  291 (426)
Q Consensus       223 i~~~l~~~~-~~~~~~~~~~~l~~~l--~~~k~~LlVlDdv~~~~~~~~l~~~l--~-~~~~~s~iivTtr~~~v-----  291 (426)
                      |++++.... ........+..++..+  ..+++++++||+++....-+.+...+  + .......||.++.....     
T Consensus       101 I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~L  180 (318)
T 3te6_A          101 IWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQI  180 (318)
T ss_dssp             HHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHHH
T ss_pred             HHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccchhhc
Confidence            999985432 1122234455555554  24578999999998654222221111  1 11112233434433211     


Q ss_pred             hhcc--CCceeeEEccCCCHHHHHHHHHHhhC
Q 044858          292 LSCE--MDCQQNFVVDVLNDKEAWSLFKKMTG  321 (426)
Q Consensus       292 a~~~--~~~~~~~~l~~L~~~e~~~Lf~~~~~  321 (426)
                      ....  .-....+.+.|++.+|-.+++.+++.
T Consensus       181 ~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~  212 (318)
T 3te6_A          181 NIMPSLKAHFTEIKLNKVDKNELQQMIITRLK  212 (318)
T ss_dssp             HTCHHHHTTEEEEECCCCCHHHHHHHHHHHHH
T ss_pred             chhhhccCCceEEEeCCCCHHHHHHHHHHHHH
Confidence            0000  11135799999999999999998874

>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=99.01  E-value=3.3e-09  Score=101.50  Aligned_cols=196  Identities=12%  Similarity=0.146  Sum_probs=113.0

Q ss_pred             CcccccchHHHHHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      ....++||+..++.+...+..++ .+.+.|+|++|+||||+|+.+.+.......+..       ..+........+....
T Consensus        14 ~~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~-------~~~~~~~~~~~~~~~~   86 (373)
T 1jr3_A           14 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA-------TPCGVCDNCREIEQGR   86 (373)
T ss_dssp             STTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCS-------SCCSSSHHHHHHHTSC
T ss_pred             chhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC-------CCCcccHHHHHHhccC
Confidence            45568999999999999887654 457889999999999999999887643211100       0000000011111000


Q ss_pred             CCC-----ccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchhh-hhcc
Q 044858          228 GLK-----IDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQDV-LSCE  295 (426)
Q Consensus       228 ~~~-----~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~v-a~~~  295 (426)
                      ...     ............+.+.+.    .+++.++|+||++..  ...+.+...+.....++.+|++|....- ....
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l  166 (373)
T 1jr3_A           87 FVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTI  166 (373)
T ss_dssp             CSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHH
T ss_pred             CCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHH
Confidence            000     000000111223333332    246789999999754  2333343333223346677777764432 1111


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHH
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      ......+++.+++.++..+++.+.+...... --.+....|++.++|.|..+..+..
T Consensus       167 ~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~-~~~~a~~~l~~~~~G~~r~~~~~l~  222 (373)
T 1jr3_A          167 LSRCLQFHLKALDVEQIRHQLEHILNEEHIA-HEPRALQLLARAAEGSLRDALSLTD  222 (373)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             HhheeEeeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            2234789999999999999998776321111 1135677899999999998876653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.95  E-value=3.1e-09  Score=91.26  Aligned_cols=153  Identities=14%  Similarity=0.188  Sum_probs=88.9

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-----ccceEEEEEecCCcCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN-----LFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~-----~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ....++||+++++.+.+.+.....+.+.|+|++|+|||+||+.+++......     .....+++..+.      +.   
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~---   90 (195)
T 1jbk_A           20 KLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA------LV---   90 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHH------HH---
T ss_pred             cccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHH------Hh---
Confidence            4567899999999999998876677889999999999999999998764311     012233443321      11   


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHH-hcCCeEEEEEeCCCCcc---------C-hhhhcCCCCCCCCCeEEEEeecchhhh
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQL-KKETKILIILDDIWGSL---------D-LEAIGIPLADDNGGCKVLLTARSQDVL  292 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l-~~~k~~LlVlDdv~~~~---------~-~~~l~~~l~~~~~~s~iivTtr~~~va  292 (426)
                          ...............+.+.+ ..+++.+|+|||++...         . ...+...+ . ..+..+|+||......
T Consensus        91 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~-~-~~~~~~i~~~~~~~~~  164 (195)
T 1jbk_A           91 ----AGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL-A-RGELHCVGATTLDEYR  164 (195)
T ss_dssp             ----TTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHH-H-TTSCCEEEEECHHHHH
T ss_pred             ----ccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhh-c-cCCeEEEEeCCHHHHH
Confidence                00000000111223333333 23568899999997541         1 11121111 1 2345577777655321


Q ss_pred             ------hccCCceeeEEccCCCHHHHHHHH
Q 044858          293 ------SCEMDCQQNFVVDVLNDKEAWSLF  316 (426)
Q Consensus       293 ------~~~~~~~~~~~l~~L~~~e~~~Lf  316 (426)
                            .........+.+.+++.++..+++
T Consensus       165 ~~~~~~~~l~~r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          165 QYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             HHHhcCHHHHHHhceeecCCCCHHHHHHHh
Confidence                  111223446889999988877654

>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=98.93  E-value=8.6e-09  Score=96.66  Aligned_cols=191  Identities=10%  Similarity=0.066  Sum_probs=115.6

Q ss_pred             CcccccchHHHHHHHHHHhc-----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALS-----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~-----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      .+..|+|++..+..+...+.     ......+.|+|++|+|||+||+.+++....     ..++++.+......++.   
T Consensus        10 ~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~-----~~~~~~~~~~~~~~~l~---   81 (324)
T 1hqc_A           10 TLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGV-----NLRVTSGPAIEKPGDLA---   81 (324)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTC-----CEEEECTTTCCSHHHHH---
T ss_pred             cHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCC-----CEEEEeccccCChHHHH---
Confidence            45678999988888877765     233467889999999999999999987642     12344433322222221   


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhc--CCeEEEEEeCCCCcc--ChhhhcCCCC--------C----------CCCCeE
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKK--ETKILIILDDIWGSL--DLEAIGIPLA--------D----------DNGGCK  281 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~--~k~~LlVlDdv~~~~--~~~~l~~~l~--------~----------~~~~s~  281 (426)
                                           ..+..  .++.+|+|||+....  ....+...+.        .          ..++..
T Consensus        82 ---------------------~~l~~~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~  140 (324)
T 1hqc_A           82 ---------------------AILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFT  140 (324)
T ss_dssp             ---------------------HHHTTTCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCE
T ss_pred             ---------------------HHHHHhccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEE
Confidence                                 11211  346788999997652  1111111000        0          012356


Q ss_pred             EEEeecchhhh-hccCCc-eeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhc---
Q 044858          282 VLLTARSQDVL-SCEMDC-QQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKN---  356 (426)
Q Consensus       282 iivTtr~~~va-~~~~~~-~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~---  356 (426)
                      +|.||...... ...... ...+.+.+++.++..+++.+.+...... --.+....|++.|+|.|..+..+...+..   
T Consensus       141 ~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~G~~r~l~~~l~~~~~~a~  219 (324)
T 1hqc_A          141 LIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVR-ITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQ  219 (324)
T ss_dssp             EEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCC-CCHHHHHHHHHHSCSCHHHHHHHHHHHTTTST
T ss_pred             EEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHccCCHHHHHHHHHHHHHHHH
Confidence            77766654321 111122 2589999999999999998877432211 22456788999999999988777655431   


Q ss_pred             ------CCHHHHHHHHHHH
Q 044858          357 ------KSPYEWRNALRQL  369 (426)
Q Consensus       357 ------~~~~~w~~~l~~l  369 (426)
                            .+.+....++..+
T Consensus       220 ~~~~~~i~~~~~~~~~~~~  238 (324)
T 1hqc_A          220 VAGEEVITRERALEALAAL  238 (324)
T ss_dssp             TTSCSCCCHHHHHHHHHHH
T ss_pred             HhcCCCCCHHHHHHHHHHh
Confidence                  1555666655544

>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=98.86  E-value=1.4e-08  Score=96.37  Aligned_cols=197  Identities=15%  Similarity=0.192  Sum_probs=113.6

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .....++|+++.++.+..++..+..+.+.|+|++|+||||+|+.+.+.......+. ....+..+.......+ .+....
T Consensus        34 ~~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~  112 (353)
T 1sxj_D           34 KNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIV-REKVKN  112 (353)
T ss_dssp             SSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHH-TTHHHH
T ss_pred             CCHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHH-HHHHHH
Confidence            34567899999999999998876555589999999999999999998754211121 2233443332333322 222211


Q ss_pred             hC-CCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecchh-hhhccCCceeeE
Q 044858          227 LG-LKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQD-VLSCEMDCQQNF  302 (426)
Q Consensus       227 l~-~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~~-va~~~~~~~~~~  302 (426)
                      +. .........     .......+++-+|++|+++...  ....+...+......+++|++|.... +..........+
T Consensus       113 ~~~~~~~~~~~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i  187 (353)
T 1sxj_D          113 FARLTVSKPSKH-----DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKF  187 (353)
T ss_dssp             HHHSCCCCCCTT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEE
T ss_pred             Hhhhcccccchh-----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceE
Confidence            11 000000000     0011112356799999986542  22333222222234567777775442 211111223578


Q ss_pred             EccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          303 VVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       303 ~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      .+.+++.++....+...+...... --.+..+.|++.++|.|..+..+.
T Consensus       188 ~~~~~~~~~~~~~l~~~~~~~~~~-i~~~~l~~l~~~~~G~~r~~~~~l  235 (353)
T 1sxj_D          188 RFKALDASNAIDRLRFISEQENVK-CDDGVLERILDISAGDLRRGITLL  235 (353)
T ss_dssp             ECCCCCHHHHHHHHHHHHHTTTCC-CCHHHHHHHHHHTSSCHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999999999999998876422211 124567889999999998755543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.84  E-value=7.6e-08  Score=88.45  Aligned_cols=203  Identities=17%  Similarity=0.203  Sum_probs=118.3

Q ss_pred             cCCcccccchHHHHHHHHHHhcc-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC
Q 044858          147 TQDFMHFESRKSTLKGILDALSN-------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT  213 (426)
Q Consensus       147 ~~~~~~~~gR~~~~~~l~~~l~~-------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  213 (426)
                      ...+..++|.+..++.|.+.+..             .....+.|+|++|+|||+||+.+++.....     .+.+..+.-
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~-----~~~v~~~~~   87 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNAT-----FIRVVGSEL   87 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCE-----EEEEEGGGG
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehHHH
Confidence            34567789999998888877642             345679999999999999999999876432     222332211


Q ss_pred             cCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------C----hhhhcCCCC--C
Q 044858          214 PQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------D----LEAIGIPLA--D  275 (426)
Q Consensus       214 ~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~----~~~l~~~l~--~  275 (426)
                      .+              ... .........++......++.+|+|||++...            .    +..+...+.  .
T Consensus        88 ~~--------------~~~-~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~  152 (285)
T 3h4m_A           88 VK--------------KFI-GEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFD  152 (285)
T ss_dssp             CC--------------CST-THHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTC
T ss_pred             HH--------------hcc-chHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCC
Confidence            10              000 0111233344455555667999999996431            0    111111110  1


Q ss_pred             CCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-chHHHHHH
Q 044858          276 DNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAG-LPIAIVPI  350 (426)
Q Consensus       276 ~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G-lPlai~~~  350 (426)
                      ...+..||.||.......    ........+.+.+.+.++..++|...+.......+  .....+++.+.| .|-.|..+
T Consensus       153 ~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~--~~~~~l~~~~~g~~~~~i~~l  230 (285)
T 3h4m_A          153 ARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAED--VNLEEIAKMTEGCVGAELKAI  230 (285)
T ss_dssp             SSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTT--CCHHHHHHHCTTCCHHHHHHH
T ss_pred             CCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCc--CCHHHHHHHcCCCCHHHHHHH
Confidence            234567777776543221    11123458999999999999999988763322111  114567778877 45455544


Q ss_pred             HHHh------hc---CCHHHHHHHHHHHhh
Q 044858          351 AKAL------KN---KSPYEWRNALRQLKR  371 (426)
Q Consensus       351 ~~~l------~~---~~~~~w~~~l~~l~~  371 (426)
                      ....      ..   -+.+....++.....
T Consensus       231 ~~~a~~~a~~~~~~~I~~~d~~~al~~~~~  260 (285)
T 3h4m_A          231 CTEAGMNAIRELRDYVTMDDFRKAVEKIME  260 (285)
T ss_dssp             HHHHHHHHHHTTCSSBCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCcCCHHHHHHHHHHHHh
Confidence            3221      12   167777777776553

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.83  E-value=9.7e-08  Score=93.19  Aligned_cols=181  Identities=17%  Similarity=0.246  Sum_probs=109.6

Q ss_pred             CCcccccchHHHH---HHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHH
Q 044858          148 QDFMHFESRKSTL---KGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREI  223 (426)
Q Consensus       148 ~~~~~~~gR~~~~---~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i  223 (426)
                      .....++|.+..+   ..+...+..+..+.+.|+|++|+||||||+.+.+.....       ++.++.. ....++ +.+
T Consensus        23 ~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~~~-------f~~l~a~~~~~~~i-r~~   94 (447)
T 3pvs_A           23 ENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYANAD-------VERISAVTSGVKEI-REA   94 (447)
T ss_dssp             CSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTTCE-------EEEEETTTCCHHHH-HHH
T ss_pred             CCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhCCC-------eEEEEeccCCHHHH-HHH
Confidence            4567789999888   677777777777889999999999999999999876432       2222222 222222 222


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEE-eecchh--hhhccCCc
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLL-TARSQD--VLSCEMDC  298 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iiv-Ttr~~~--va~~~~~~  298 (426)
                      +.                ........+++.+|+||+++...  ..+.+...+..  ....+|. ||.+..  +.......
T Consensus        95 ~~----------------~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~sR  156 (447)
T 3pvs_A           95 IE----------------RARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALLSR  156 (447)
T ss_dssp             HH----------------HHHHHHHTTCCEEEEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHHTT
T ss_pred             HH----------------HHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHhCc
Confidence            11                11111223578999999997652  22223222221  2334444 444432  11112234


Q ss_pred             eeeEEccCCCHHHHHHHHHHhhCCC------CCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          299 QQNFVVDVLNDKEAWSLFKKMTGDC------IENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       299 ~~~~~l~~L~~~e~~~Lf~~~~~~~------~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      ...+.+.+++.++...++.+.+...      ....--.+..+.|++.++|.+-.+..+...+
T Consensus       157 ~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~Le~a  218 (447)
T 3pvs_A          157 ARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMM  218 (447)
T ss_dssp             EEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             eeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            5688999999999999999887421      1111234577888999999988766554443

>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=98.78  E-value=3.7e-07  Score=82.56  Aligned_cols=183  Identities=15%  Similarity=0.179  Sum_probs=100.7

Q ss_pred             CcccccchHHHHHHHHHHh---cc---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          149 DFMHFESRKSTLKGILDAL---SN---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l---~~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .+..++|.+..++.+.+.+   ..         ...+.+.|+|++|+|||++|+.+++.....     .+.+..+.-.+ 
T Consensus         4 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~-----~~~~~~~~~~~-   77 (262)
T 2qz4_A            4 SFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVP-----FLAMAGAEFVE-   77 (262)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCC-----EEEEETTTTSS-
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCC-----EEEechHHHHh-
Confidence            4556778777666655443   21         234568899999999999999999876421     23333332111 


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-------------C----hhhhcCCCC--CCC
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-------------D----LEAIGIPLA--DDN  277 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-------------~----~~~l~~~l~--~~~  277 (426)
                                   .... ........++.......+.+|+|||++...             .    +..+...+.  ...
T Consensus        78 -------------~~~~-~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~  143 (262)
T 2qz4_A           78 -------------VIGG-LGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTT  143 (262)
T ss_dssp             -------------SSTT-HHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTT
T ss_pred             -------------hccC-hhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCC
Confidence                         0000 011223344444444568999999997541             1    111111111  112


Q ss_pred             CCeEEEEeecchhhhh-ccC---CceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHHH
Q 044858          278 GGCKVLLTARSQDVLS-CEM---DCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPIA  351 (426)
Q Consensus       278 ~~s~iivTtr~~~va~-~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~~  351 (426)
                      .+..||.||....... ...   .....+.+.+.+.++-.+++...+...............+++.+.|.+- .|..+.
T Consensus       144 ~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~  222 (262)
T 2qz4_A          144 DHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANIC  222 (262)
T ss_dssp             CCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHH
Confidence            3556666765543211 011   2236788999999999999988774322222223335778888888754 554443

>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=98.78  E-value=1.7e-08  Score=90.14  Aligned_cols=176  Identities=16%  Similarity=0.119  Sum_probs=103.6

Q ss_pred             Ccccccch---HHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          149 DFMHFESR---KSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       149 ~~~~~~gR---~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .+..|+++   +..++.+..+...+..+.+.|+|++|+||||||+.+++.....  ...+.|+..+...+.      +. 
T Consensus        26 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~--~~~~~~~~~~~~~~~------~~-   96 (242)
T 3bos_A           26 TFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL--ERRSFYIPLGIHASI------ST-   96 (242)
T ss_dssp             STTTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEEGGGGGGS------CG-
T ss_pred             ChhhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEHHHHHHH------HH-
Confidence            44556653   3556666666555566789999999999999999999887643  234556665432110      00 


Q ss_pred             HhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC----hhhhcCCCC--CCCCCeEEEEeecchhhh-----hc
Q 044858          226 KLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD----LEAIGIPLA--DDNGGCKVLLTARSQDVL-----SC  294 (426)
Q Consensus       226 ~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~----~~~l~~~l~--~~~~~s~iivTtr~~~va-----~~  294 (426)
                                      ...+.+  .++.+|||||++....    ...+...+.  ......++|+||+...-.     ..
T Consensus        97 ----------------~~~~~~--~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~  158 (242)
T 3bos_A           97 ----------------ALLEGL--EQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPD  158 (242)
T ss_dssp             ----------------GGGTTG--GGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHH
T ss_pred             ----------------HHHHhc--cCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhh
Confidence                            001111  2467999999975422    122221110  011122578887754310     00


Q ss_pred             cC---CceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHH
Q 044858          295 EM---DCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       295 ~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      ..   .....+++.+++.++..+++...+..... .--.+....|++.++|.+-.+..+..
T Consensus       159 l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~-~~~~~~~~~l~~~~~g~~r~l~~~l~  218 (242)
T 3bos_A          159 LVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGL-QLPEDVGRFLLNRMARDLRTLFDVLD  218 (242)
T ss_dssp             HHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTC-CCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             hhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHccCCHHHHHHHHH
Confidence            01   11268999999999999999987742111 11245677899999998877665543

>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=98.77  E-value=2.9e-07  Score=84.00  Aligned_cols=180  Identities=15%  Similarity=0.185  Sum_probs=96.2

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK  248 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~  248 (426)
                      ....+.+.|+|++|+|||+||+.+++....    . .+.+..+...            .+.  ...........++....
T Consensus        61 ~~~~~~vLl~G~~GtGKT~la~~ia~~~~~----~-~~~i~~~~~~------------~g~--~~~~~~~~~~~~~~~~~  121 (272)
T 1d2n_A           61 RTPLVSVLLEGPPHSGKTALAAKIAEESNF----P-FIKICSPDKM------------IGF--SETAKCQAMKKIFDDAY  121 (272)
T ss_dssp             SCSEEEEEEECSTTSSHHHHHHHHHHHHTC----S-EEEEECGGGC------------TTC--CHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCcHHHHHHHHHHHhCC----C-EEEEeCHHHh------------cCC--chHHHHHHHHHHHHHHH
Confidence            345678899999999999999999987432    1 1222222110            000  00001112233444444


Q ss_pred             cCCeEEEEEeCCCCc-----------cC-hhhhcCCCC---CCCCCeEEEEeecchhhhhc--cCCc-eeeEEccCCCH-
Q 044858          249 KETKILIILDDIWGS-----------LD-LEAIGIPLA---DDNGGCKVLLTARSQDVLSC--EMDC-QQNFVVDVLND-  309 (426)
Q Consensus       249 ~~k~~LlVlDdv~~~-----------~~-~~~l~~~l~---~~~~~s~iivTtr~~~va~~--~~~~-~~~~~l~~L~~-  309 (426)
                      ..++.+|+|||++..           .. .+.+...+.   .......||.||........  ..+. ...+.+++++. 
T Consensus       122 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r  201 (272)
T 1d2n_A          122 KSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATG  201 (272)
T ss_dssp             TSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEH
T ss_pred             hcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHH
Confidence            456899999998542           00 111211111   12233456667766533211  1122 46789999988 


Q ss_pred             HHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC------chHHHHHHHHHhhcCCHHHHHHHHHHHhhcc
Q 044858          310 KEAWSLFKKMTGDCIENGELKSVVTEVVKECAG------LPIAIVPIAKALKNKSPYEWRNALRQLKRNF  373 (426)
Q Consensus       310 ~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G------lPlai~~~~~~l~~~~~~~w~~~l~~l~~~~  373 (426)
                      ++...++.+...  .    ..+....|++.+.|      ++-++..+-......+...+..++..+....
T Consensus       202 ~~i~~i~~~~~~--~----~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~~~~~~~~~~~~~l~~~~  265 (272)
T 1d2n_A          202 EQLLEALELLGN--F----KDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEG  265 (272)
T ss_dssp             HHHHHHHHHHTC--S----CHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTSCGGGHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhcCC--C----CHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhhchHHHHHHHHHHHHHcC
Confidence            677776665321  1    13457788888888      3444433333333335567777777665443

>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=98.70  E-value=6.8e-08  Score=91.71  Aligned_cols=199  Identities=9%  Similarity=0.080  Sum_probs=108.3

Q ss_pred             CcccccchHHHHHHHHHHh-ccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cc--------------------
Q 044858          149 DFMHFESRKSTLKGILDAL-SNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FE--------------------  203 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l-~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~--------------------  203 (426)
                      ....++|++..++.+..++ ..++.+.+.|+|+.|+||||+++.+.........    ++                    
T Consensus        12 ~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~~~   91 (354)
T 1sxj_E           12 SLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSP   91 (354)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECS
T ss_pred             CHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceeeeeccc
Confidence            4567889999999998888 6555445999999999999999999885321110    00                    


Q ss_pred             eEEEEEecCCc-CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCe
Q 044858          204 KVISSRVSQTP-QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGC  280 (426)
Q Consensus       204 ~~~wv~v~~~~-~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s  280 (426)
                      ..+.+..+... ......++++..+.....-...   .  ....+ .+++-+++||++...+  ..+.+...+.....++
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~---~--~ls~l-~~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~  165 (354)
T 1sxj_E           92 YHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQ---D--SKDGL-AHRYKCVIINEANSLTKDAQAALRRTMEKYSKNI  165 (354)
T ss_dssp             SEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTE
T ss_pred             ceEEecHhhcCCcchHHHHHHHHHHHHhcccccc---c--ccccc-CCCCeEEEEeCccccCHHHHHHHHHHHHhhcCCC
Confidence            01111111100 0000122222222111000000   0  00001 1356799999998642  1222322221122467


Q ss_pred             EEEEeecchh-hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCch-HHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          281 KVLLTARSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGEL-KSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       281 ~iivTtr~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~-~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      .+|++|.... +..........+++.+++.++..+++.+.+...... -- .+....|++.++|.+..+..+...+
T Consensus       166 ~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~l~~i~~~~~G~~r~a~~~l~~~  240 (354)
T 1sxj_E          166 RLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQ-LETKDILKRIAQASNGNLRVSLLMLESM  240 (354)
T ss_dssp             EEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCE-ECCSHHHHHHHHHHTTCHHHHHHHHTHH
T ss_pred             EEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCC-CCcHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            7888876643 211112234789999999999999998876421110 01 2456789999999988776655433

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.70  E-value=1.7e-06  Score=80.81  Aligned_cols=185  Identities=17%  Similarity=0.183  Sum_probs=107.0

Q ss_pred             CCcccccchHHHHHHHHHHhc------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDALS------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ....++.|.+..++.|.+.+.            ....+.+.++|++|+|||+||+.+++.....    ..+.++.+.-.+
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~----~~~~i~~~~l~~   84 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNS----TFFSISSSDLVS   84 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTTSC----EEEEEECCSSCC
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcCCC----cEEEEEhHHHHh
Confidence            456677888877777766542            1234678999999999999999999876211    122333332110


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-------------hhhhcCC---CCCCCCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-------------LEAIGIP---LADDNGG  279 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-------------~~~l~~~---l~~~~~~  279 (426)
                                    ... .........++......++.+|+||+++....             ...+...   +.....+
T Consensus        85 --------------~~~-g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~  149 (322)
T 1xwi_A           85 --------------KWL-GESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDG  149 (322)
T ss_dssp             --------------SSC-CSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTT
T ss_pred             --------------hhh-hHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCC
Confidence                          111 11223344555555556789999999975410             0111111   1112345


Q ss_pred             eEEEEeecchhhh-h-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc-hHHHHHHHH
Q 044858          280 CKVLLTARSQDVL-S-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL-PIAIVPIAK  352 (426)
Q Consensus       280 s~iivTtr~~~va-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl-Plai~~~~~  352 (426)
                      ..||.||...... . ........+.+...+.++-.+++...+....... -......|++.+.|. +-.|..+..
T Consensus       150 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-~~~~l~~la~~t~G~sgadl~~l~~  224 (322)
T 1xwi_A          150 ILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSL-TEADFRELGRKTDGYSGADISIIVR  224 (322)
T ss_dssp             EEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCC-CHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            5566666544221 1 0112336788899999999999988875432211 134577899999987 444555544

>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=98.68  E-value=7.5e-07  Score=84.59  Aligned_cols=184  Identities=11%  Similarity=0.086  Sum_probs=106.2

Q ss_pred             CCcccccchHHHHHHHHHHhc------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDALS------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      .....++|.+..++.|.+.+.            ....+.+.|+|++|+|||+||+.+++....     ..+.++.+.-.+
T Consensus        81 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~-----~~~~i~~~~l~~  155 (357)
T 3d8b_A           81 VNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGA-----TFFSISASSLTS  155 (357)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTC-----EEEEEEGGGGCC
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCC-----eEEEEehHHhhc
Confidence            345678899988888877663            234567899999999999999999887532     123444432111


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-------------ChhhhcCCCC----CCCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-------------DLEAIGIPLA----DDNG  278 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-------------~~~~l~~~l~----~~~~  278 (426)
                                    ... .........++......++.+|+||+++...             ....+...+.    ....
T Consensus       156 --------------~~~-g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~  220 (357)
T 3d8b_A          156 --------------KWV-GEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSED  220 (357)
T ss_dssp             --------------SST-THHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCC
T ss_pred             --------------ccc-chHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCC
Confidence                          000 0011223334444444568999999995321             0112211111    1123


Q ss_pred             CeEEEEeecchhhh-h-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-chHHHHHHHH
Q 044858          279 GCKVLLTARSQDVL-S-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAG-LPIAIVPIAK  352 (426)
Q Consensus       279 ~s~iivTtr~~~va-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G-lPlai~~~~~  352 (426)
                      +..||.||...... . ........+.+...+.++..+++...+...... -.......|++.+.| .|-.|..+..
T Consensus       221 ~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-l~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          221 RILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCC-LSEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             CEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBC-CCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCC-ccHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            45566666543221 1 111233578889999999999998776422111 113467789999998 5556666544

>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=98.68  E-value=1.2e-07  Score=88.85  Aligned_cols=185  Identities=13%  Similarity=0.055  Sum_probs=105.5

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .....++|++..+..+..++..+.. .++.+.|++|+|||++|+.+.+....     ..+.++.+. .... .++.++..
T Consensus        23 ~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l~~-----~~~~i~~~~-~~~~-~i~~~~~~   95 (324)
T 3u61_B           23 STIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNA-----DMMFVNGSD-CKID-FVRGPLTN   95 (324)
T ss_dssp             CSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHTTE-----EEEEEETTT-CCHH-HHHTHHHH
T ss_pred             CCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCC-----CEEEEcccc-cCHH-HHHHHHHH
Confidence            4567789999999999998886553 57788888999999999999887632     234444433 2222 22222111


Q ss_pred             hCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc---ChhhhcCCCCCCCCCeEEEEeecchhhh-hccCCceeeE
Q 044858          227 LGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL---DLEAIGIPLADDNGGCKVLLTARSQDVL-SCEMDCQQNF  302 (426)
Q Consensus       227 l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~---~~~~l~~~l~~~~~~s~iivTtr~~~va-~~~~~~~~~~  302 (426)
                      ......               ..+++.+|+|||++...   ..+.+...+.....++++|+||....-. .........+
T Consensus        96 ~~~~~~---------------~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i  160 (324)
T 3u61_B           96 FASAAS---------------FDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVI  160 (324)
T ss_dssp             HHHBCC---------------CSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEE
T ss_pred             HHhhcc---------------cCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEE
Confidence            100000               01368899999998653   2222322221112356788887664321 1111223579


Q ss_pred             EccCCCHHHHHHHHHH-------hhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          303 VVDVLNDKEAWSLFKK-------MTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       303 ~l~~L~~~e~~~Lf~~-------~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      ++++++.++-.+++..       .+......-...+....|++.++|.+..+......+
T Consensus       161 ~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd~R~a~~~L~~~  219 (324)
T 3u61_B          161 TFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSY  219 (324)
T ss_dssp             ECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSCTTHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            9999998885443322       222111111112567789999999877554443333

>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=98.66  E-value=9.6e-07  Score=82.59  Aligned_cols=185  Identities=15%  Similarity=0.152  Sum_probs=109.3

Q ss_pred             ccCCcccccchHHHHHHHHHHhc------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC
Q 044858          146 STQDFMHFESRKSTLKGILDALS------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT  213 (426)
Q Consensus       146 ~~~~~~~~~gR~~~~~~l~~~l~------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  213 (426)
                      |......++|.+..++.|.+.+.            ....+-+.++|++|+|||+||+.+++.....     .+.++.+  
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~-----~~~v~~~--   85 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSSS--   85 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCE-----EEEEEHH--
T ss_pred             CCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCC-----EEEEchH--
Confidence            33456778999998888887762            1124578999999999999999999875422     2223221  


Q ss_pred             cCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-------------hhhhcCC---CCCCC
Q 044858          214 PQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-------------LEAIGIP---LADDN  277 (426)
Q Consensus       214 ~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-------------~~~l~~~---l~~~~  277 (426)
                          ++..        ... ......+..++......++.+|+||+++....             ...+...   +....
T Consensus        86 ----~l~~--------~~~-g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~  152 (322)
T 3eie_A           86 ----DLVS--------KWM-GESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDS  152 (322)
T ss_dssp             ----HHHT--------TTG-GGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSC
T ss_pred             ----HHhh--------ccc-chHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccC
Confidence                1111        000 11123344555555556789999999974411             1112111   11233


Q ss_pred             CCeEEEEeecchhhhh--ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc-hHHHHHHH
Q 044858          278 GGCKVLLTARSQDVLS--CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL-PIAIVPIA  351 (426)
Q Consensus       278 ~~s~iivTtr~~~va~--~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl-Plai~~~~  351 (426)
                      .+..||.||.......  ........+.+...+.++-.++|...+....... -......|++.+.|. +-.|..+.
T Consensus       153 ~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~-~~~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          153 QGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVL-TKEDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             CCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCC-CHHHHHHHHHTTTTCCHHHHHHHH
T ss_pred             CceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCC-CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            4566666776543211  0112235788889999999999998886433211 134567888999884 54554443

>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=98.66  E-value=1.1e-07  Score=94.86  Aligned_cols=189  Identities=13%  Similarity=0.116  Sum_probs=108.1

Q ss_pred             CCcccccchHHHHHHHHHHhcc-----------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe
Q 044858          148 QDFMHFESRKSTLKGILDALSN-----------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV  210 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~-----------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v  210 (426)
                      .....++|++..++.+..++..                 +..+.+.|+|++|+||||+|+.+++...    + ..+.++.
T Consensus        36 ~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~----~-~~i~in~  110 (516)
T 1sxj_A           36 TNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG----Y-DILEQNA  110 (516)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT----C-EEEEECT
T ss_pred             CCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC----C-CEEEEeC
Confidence            3567799999999999998864                 1346899999999999999999998763    2 2344555


Q ss_pred             cCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHH-HhcCCeEEEEEeCCCCccC-----hhhhcCCCCCCCCCeEEEE
Q 044858          211 SQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQ-LKKETKILIILDDIWGSLD-----LEAIGIPLADDNGGCKVLL  284 (426)
Q Consensus       211 ~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~-l~~~k~~LlVlDdv~~~~~-----~~~l~~~l~~~~~~s~iiv  284 (426)
                      +...+.. ++...+............   ....... ...+++.+|+||+++....     +..+...+..  .+..||+
T Consensus       111 s~~~~~~-~~~~~i~~~~~~~~~~~~---~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~--~~~~iIl  184 (516)
T 1sxj_A          111 SDVRSKT-LLNAGVKNALDNMSVVGY---FKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLIL  184 (516)
T ss_dssp             TSCCCHH-HHHHTGGGGTTBCCSTTT---TTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEE
T ss_pred             CCcchHH-HHHHHHHHHhccccHHHH---HhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHh--cCCCEEE
Confidence            4444432 333322221111000000   0000000 1235689999999975421     1222221111  2334666


Q ss_pred             eecchhh--hhccCCceeeEEccCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCchH-HHHHH
Q 044858          285 TARSQDV--LSCEMDCQQNFVVDVLNDKEAWSLFKKMTG--DCIENGELKSVVTEVVKECAGLPI-AIVPI  350 (426)
Q Consensus       285 Ttr~~~v--a~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~--~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~  350 (426)
                      ++.....  ..........+.+.+++.++..+++...+.  +...++   +....|++.++|.+- ++..+
T Consensus       185 i~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~---~~l~~la~~s~GdiR~~i~~L  252 (516)
T 1sxj_A          185 ICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NVIDRLIQTTRGDIRQVINLL  252 (516)
T ss_dssp             EESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHTTTCHHHHHHHH
T ss_pred             EEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHcCCcHHHHHHHH
Confidence            6554321  111223346899999999999999887763  111222   346788999999554 45544

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.65  E-value=8.5e-07  Score=83.53  Aligned_cols=176  Identities=15%  Similarity=0.147  Sum_probs=104.7

Q ss_pred             CcccccchHHHHHHHHHHhcc-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSN-----RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~-----~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      .+..++|++..++.+..++..     .....+.|+|++|+|||+||+.+.+.....  |   +.++.+.......     
T Consensus        27 ~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~--~---~~~~~~~~~~~~~-----   96 (338)
T 3pfi_A           27 NFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSAN--I---KTTAAPMIEKSGD-----   96 (338)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCC--E---EEEEGGGCCSHHH-----
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCC--e---EEecchhccchhH-----
Confidence            567799999998888887762     344578999999999999999998775422  2   2233322211111     


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCC------------------CCCCCeEEE
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLA------------------DDNGGCKVL  283 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~------------------~~~~~s~ii  283 (426)
                                      ....+..  ..+..+|+||++....  ....+...+.                  ...++..+|
T Consensus        97 ----------------~~~~~~~--~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i  158 (338)
T 3pfi_A           97 ----------------LAAILTN--LSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLI  158 (338)
T ss_dssp             ----------------HHHHHHT--CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEE
T ss_pred             ----------------HHHHHHh--ccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEE
Confidence                            1111111  1356788999987541  1111111110                  011235666


Q ss_pred             Eeecchhhh-h-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHH
Q 044858          284 LTARSQDVL-S-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKA  353 (426)
Q Consensus       284 vTtr~~~va-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~  353 (426)
                      .+|...... . ........+.+.+++.++...++.+.+..... .--.+....|++.+.|.|-.+..+...
T Consensus       159 ~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~-~~~~~~~~~l~~~~~G~~r~l~~~l~~  229 (338)
T 3pfi_A          159 GATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNK-TCEEKAALEIAKRSRSTPRIALRLLKR  229 (338)
T ss_dssp             EEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-EECHHHHHHHHHTTTTCHHHHHHHHHH
T ss_pred             EeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            666654321 1 11122368999999999999999887742211 122456788899999999766555443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.63  E-value=4.6e-07  Score=86.40  Aligned_cols=214  Identities=9%  Similarity=0.069  Sum_probs=112.5

Q ss_pred             cccccchHHHHHH---HHHHhccCCc--cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe----cCCcCHHHHH
Q 044858          150 FMHFESRKSTLKG---ILDALSNRNF--NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV----SQTPQIKEIQ  220 (426)
Q Consensus       150 ~~~~~gR~~~~~~---l~~~l~~~~~--~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v----~~~~~~~~il  220 (426)
                      +..|+|++..++.   +...+..+..  +.+.|+|++|+|||++|+.+.+.......|   +.+..    +......+.+
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~---~~~~~~~~~~~~~~~~~~~  119 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPF---TAIAGSEIFSLEMSKTEAL  119 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCE---EEEEGGGGSCSSSCHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCc---ccccchhhhhcccchhHHH
Confidence            6679999888665   4444444433  589999999999999999999887532222   12221    1223344444


Q ss_pred             HHHHHHh-CCC----------------------------cc--ccCcHH---HHHHHHHH-HhcCC----eEEEEEeCCC
Q 044858          221 REIAEKL-GLK----------------------------ID--QESESV---RAWRLLEQ-LKKET----KILIILDDIW  261 (426)
Q Consensus       221 ~~i~~~l-~~~----------------------------~~--~~~~~~---~~~~l~~~-l~~~k----~~LlVlDdv~  261 (426)
                      .+..... +..                            ..  ......   ........ ...++    +.+|+||+++
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~  199 (368)
T 3uk6_A          120 TQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVH  199 (368)
T ss_dssp             HHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGG
T ss_pred             HHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhcc
Confidence            4443321 000                            00  000111   11111111 11233    4599999997


Q ss_pred             Ccc--ChhhhcCCCCCCCCCeEEEEeecc-------------hhhhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCC
Q 044858          262 GSL--DLEAIGIPLADDNGGCKVLLTARS-------------QDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIEN  326 (426)
Q Consensus       262 ~~~--~~~~l~~~l~~~~~~s~iivTtr~-------------~~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~  326 (426)
                      ...  ....+...+.... ...++++|..             ..+..........+.+.+++.++..+++...+..... 
T Consensus       200 ~l~~~~~~~L~~~le~~~-~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~~~~-  277 (368)
T 3uk6_A          200 MLDIESFSFLNRALESDM-APVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDV-  277 (368)
T ss_dssp             GSBHHHHHHHHHHTTCTT-CCEEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHHHHHHTTC-
T ss_pred             ccChHHHHHHHHHhhCcC-CCeeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHHHHHHcCC-
Confidence            542  2222322222222 2234444431             1111111223456899999999999999987742211 


Q ss_pred             CchHHHHHHHHHHcC-CchHHHHHHHHHh------hcC---CHHHHHHHHHH
Q 044858          327 GELKSVVTEVVKECA-GLPIAIVPIAKAL------KNK---SPYEWRNALRQ  368 (426)
Q Consensus       327 ~~~~~~~~~i~~~c~-GlPlai~~~~~~l------~~~---~~~~w~~~l~~  368 (426)
                      .--.+....|++.+. |.|-.+..+....      .+.   +.+..+.++..
T Consensus       278 ~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~  329 (368)
T 3uk6_A          278 EMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSL  329 (368)
T ss_dssp             CBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence            122456788999997 7777655443321      111   56666666654

>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=98.62  E-value=4.9e-07  Score=85.28  Aligned_cols=185  Identities=11%  Similarity=0.108  Sum_probs=106.0

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .....++|.+..++.+...+..++.+.+.++|+.|+||||+|+.+.+...... +. ....++.+.......+. +++..
T Consensus        22 ~~~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~-~~~~~~~~~~~~~~~~~~ir-~~i~~   99 (340)
T 1sxj_C           22 ETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKN-YSNMVLELNASDDRGIDVVR-NQIKD   99 (340)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTS-HHHHEEEECTTSCCSHHHHH-THHHH
T ss_pred             CcHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-ccceEEEEcCcccccHHHHH-HHHHH
Confidence            34566788888888888888877665589999999999999999998764321 21 12233333322222221 11111


Q ss_pred             hCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchh-hhhccCCceeeEE
Q 044858          227 LGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQD-VLSCEMDCQQNFV  303 (426)
Q Consensus       227 l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~-va~~~~~~~~~~~  303 (426)
                      +.....              ...+.+-++|+|+++..  ...+.+...+......+++|++|.... +..........+.
T Consensus       100 ~~~~~~--------------~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~  165 (340)
T 1sxj_C          100 FASTRQ--------------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFR  165 (340)
T ss_dssp             HHHBCC--------------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEE
T ss_pred             HHhhcc--------------cCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEe
Confidence            100000              00124678999998643  222223222211223566777765432 1111122335789


Q ss_pred             ccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHH
Q 044858          304 VDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVP  349 (426)
Q Consensus       304 l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~  349 (426)
                      +.+++.++..+.+.+.+...... --....+.|++.++|.+--+..
T Consensus       166 ~~~l~~~~~~~~l~~~~~~~~~~-i~~~~~~~i~~~s~G~~r~~~~  210 (340)
T 1sxj_C          166 FQPLPQEAIERRIANVLVHEKLK-LSPNAEKALIELSNGDMRRVLN  210 (340)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCC-BCHHHHHHHHHHHTTCHHHHHH
T ss_pred             ccCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHH
Confidence            99999999999888776321111 1134577888899998875433

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.60  E-value=2.6e-06  Score=81.81  Aligned_cols=183  Identities=13%  Similarity=0.136  Sum_probs=105.0

Q ss_pred             CCcccccchHHHHHHHHHHhc------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDALS------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+..++|.+..++.+...+.            ....+.+.|+|++|+|||+||+.+++....     ..+.++.+.-.+
T Consensus       112 ~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~-----~~~~v~~~~l~~  186 (389)
T 3vfd_A          112 VKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNA-----TFFNISAASLTS  186 (389)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTC-----EEEEECSCCC--
T ss_pred             CChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcC-----cEEEeeHHHhhc
Confidence            456788999999998888773            123467899999999999999999877532     123333322111


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------C-h----hhhcCCC---C-CCCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--------D-L----EAIGIPL---A-DDNG  278 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--------~-~----~~l~~~l---~-~~~~  278 (426)
                        ..            . .........++.......+.+|+||+++...        . .    ..+...+   . ....
T Consensus       187 --~~------------~-g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  251 (389)
T 3vfd_A          187 --KY------------V-GEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDD  251 (389)
T ss_dssp             --------------------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----
T ss_pred             --cc------------c-chHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCC
Confidence              00            0 0111233444444444567899999996431        0 0    1111111   0 1122


Q ss_pred             CeEEEEeecchhhh-h-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHHH
Q 044858          279 GCKVLLTARSQDVL-S-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPIA  351 (426)
Q Consensus       279 ~s~iivTtr~~~va-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~~  351 (426)
                      ...||.||...... . ........+.+...+.++-.+++...+...... -.......|++.+.|..- +|..+.
T Consensus       252 ~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~-l~~~~~~~la~~~~g~~~~~l~~L~  326 (389)
T 3vfd_A          252 RVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSP-LTQKELAQLARMTDGYSGSDLTALA  326 (389)
T ss_dssp             CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCC-SCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             CEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            45566666543221 1 111223578899999999999998887532221 123467789999988654 555554

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.57  E-value=1.8e-07  Score=86.88  Aligned_cols=154  Identities=12%  Similarity=0.111  Sum_probs=85.1

Q ss_pred             cccchHHHHHHHHHHhc---------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          152 HFESRKSTLKGILDALS---------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~---------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .++|.+..++.+.+.+.               ......+.|+|++|+|||++|+.+.+...........-++.++..   
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~---  108 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRD---  108 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGG---
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHH---
Confidence            36677766666654432               233457899999999999999998887654322221112333211   


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc-----------cChhhhcCCCCCCCCCeEEEEe
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS-----------LDLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~-----------~~~~~l~~~l~~~~~~s~iivT  285 (426)
                               .+....... .......++...   ++.+|+||+++..           .....+...+.....+..+|+|
T Consensus       109 ---------~l~~~~~g~-~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~  175 (309)
T 3syl_A          109 ---------DLVGQYIGH-TAPKTKEVLKRA---MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILA  175 (309)
T ss_dssp             ---------GTCCSSTTC-HHHHHHHHHHHH---TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEE
T ss_pred             ---------Hhhhhcccc-cHHHHHHHHHhc---CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEe
Confidence                     011111111 111122223222   3469999999733           1122333333233446678888


Q ss_pred             ecchhhh-------hccCCceeeEEccCCCHHHHHHHHHHhhC
Q 044858          286 ARSQDVL-------SCEMDCQQNFVVDVLNDKEAWSLFKKMTG  321 (426)
Q Consensus       286 tr~~~va-------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  321 (426)
                      |......       .........+.+++++.++..+++...+.
T Consensus       176 ~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~  218 (309)
T 3syl_A          176 GYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLD  218 (309)
T ss_dssp             ECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHH
Confidence            7643210       00112237899999999999999988774

>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=98.55  E-value=3.5e-06  Score=82.33  Aligned_cols=185  Identities=17%  Similarity=0.212  Sum_probs=105.7

Q ss_pred             CCcccccchHHHHHHHHHHhc------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDALS------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+..++|.+..++.|.+.+.            ....+.+.|+|++|+|||+||+.+++....      .-++.++... 
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~~------~~~~~v~~~~-  203 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANN------STFFSISSSD-  203 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCCS------SEEEEECCC--
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcCC------CCEEEEeHHH-
Confidence            456678898888888877652            123467899999999999999999987621      1123333221 


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-------------hhhhcCCCCC---CCCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-------------LEAIGIPLAD---DNGG  279 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-------------~~~l~~~l~~---~~~~  279 (426)
                         +....   .+..   .   ..+..++......++.+|+||+++....             ...+...+..   ...+
T Consensus       204 ---l~~~~---~g~~---~---~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~  271 (444)
T 2zan_A          204 ---LVSKW---LGES---E---KLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDG  271 (444)
T ss_dssp             --------------C---C---CTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSS
T ss_pred             ---HHhhh---cchH---H---HHHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCC
Confidence               11110   1100   0   1233444444445789999999975410             1122222211   2345


Q ss_pred             eEEEEeecchhhh-h-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc-hHHHHHHHH
Q 044858          280 CKVLLTARSQDVL-S-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL-PIAIVPIAK  352 (426)
Q Consensus       280 s~iivTtr~~~va-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl-Plai~~~~~  352 (426)
                      ..||.||...... . ........+.+...+.++-..+|...+....... -......|++.+.|. +-.|..+..
T Consensus       272 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-~~~~l~~la~~t~G~sgadl~~l~~  346 (444)
T 2zan_A          272 ILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSL-TEADFQELGRKTDGYSGADISIIVR  346 (444)
T ss_dssp             CEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEEC-CHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             EEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            6666677554321 1 1112335788888889999999988875432111 134567889999984 445554443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.55  E-value=4.3e-06  Score=77.13  Aligned_cols=184  Identities=12%  Similarity=0.125  Sum_probs=104.1

Q ss_pred             CCcccccchHHHHHHHHHHhcc------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDALSN------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      .....++|.+..++.+.+.+..            ...+.+.|+|++|+|||++|+.+++.....     .+.++.+.-.+
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~~-----~~~i~~~~l~~   92 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSAT-----FLNISAASLTS   92 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTCE-----EEEEESTTTSS
T ss_pred             CCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCCC-----eEEeeHHHHhh
Confidence            3566789999988888877631            235678999999999999999999876421     22333322110


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-------------hhhhc---CCCCCC--C
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-------------LEAIG---IPLADD--N  277 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-------------~~~l~---~~l~~~--~  277 (426)
                                    ... .........++......++.+|+||+++....             ...+.   ..++..  .
T Consensus        93 --------------~~~-~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  157 (297)
T 3b9p_A           93 --------------KYV-GDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDG  157 (297)
T ss_dssp             --------------SSC-SCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC-----
T ss_pred             --------------ccc-chHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCC
Confidence                          000 11122333344444445689999999964311             00111   111111  1


Q ss_pred             CCeEEEEeecchhhh-hc-cCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHHHH
Q 044858          278 GGCKVLLTARSQDVL-SC-EMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPIAK  352 (426)
Q Consensus       278 ~~s~iivTtr~~~va-~~-~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~~~  352 (426)
                      .+..||.||...... .. .......+.+...+.++-..++...+...... -.......|++.+.|.+- ++..+..
T Consensus       158 ~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~-~~~~~~~~la~~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          158 DRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSP-LDTEALRRLAKITDGYSGSDLTALAK  234 (297)
T ss_dssp             -CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCC-SCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            345566677654321 10 01223567788888888888888776422111 113456788999999875 5544443

>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=98.54  E-value=1.7e-06  Score=81.95  Aligned_cols=183  Identities=15%  Similarity=0.159  Sum_probs=105.1

Q ss_pred             CCcccccchHHHHHHHHHHhc------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDALS------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+..++|.+..++.|.+.+.            ....+-|.|+|++|+|||+||+.+++.....     .+.++.+    
T Consensus        48 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~-----~~~v~~~----  118 (355)
T 2qp9_X           48 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSSS----  118 (355)
T ss_dssp             CCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTCE-----EEEEEHH----
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC-----EEEeeHH----
Confidence            345678888888888777652            1123458899999999999999999876422     2223221    


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-------------hhhhcCCC---CCCCCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-------------LEAIGIPL---ADDNGG  279 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-------------~~~l~~~l---~~~~~~  279 (426)
                        ++...        .. .........++......++.+|+||+++....             ...+...+   .....+
T Consensus       119 --~l~~~--------~~-g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~  187 (355)
T 2qp9_X          119 --DLVSK--------WM-GESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQG  187 (355)
T ss_dssp             --HHHSC--------C----CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CC
T ss_pred             --HHhhh--------hc-chHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCC
Confidence              21110        00 11122344455555456789999999975421             11121111   112335


Q ss_pred             eEEEEeecchhhh-h-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc-hHHHHHHH
Q 044858          280 CKVLLTARSQDVL-S-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL-PIAIVPIA  351 (426)
Q Consensus       280 s~iivTtr~~~va-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl-Plai~~~~  351 (426)
                      ..||.||...... . ........+.+...+.++-.+++...+....... -......|++.+.|. |-.|..+.
T Consensus       188 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~-~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          188 VLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVL-TKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             EEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCC-CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             eEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCC-CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            5666666554221 0 0112346788999999999999998876432111 134567889999984 54555544

>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=98.54  E-value=1.6e-06  Score=81.50  Aligned_cols=166  Identities=11%  Similarity=0.115  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------ccceEEEEEec---C
Q 044858          157 KSTLKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENN--------------------LFEKVISSRVS---Q  212 (426)
Q Consensus       157 ~~~~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~v~---~  212 (426)
                      ++..+.+...+..++ .+.+.++|+.|+|||++|+.+.+......                    |++ ..++...   .
T Consensus         8 ~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~~~   86 (334)
T 1a5t_A            8 RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLAPEKGKN   86 (334)
T ss_dssp             HHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEECCCTTCS
T ss_pred             HHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccccCC
Confidence            445566667666655 45799999999999999999988754321                    122 2223221   1


Q ss_pred             CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEee
Q 044858          213 TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTA  286 (426)
Q Consensus       213 ~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTt  286 (426)
                      ...+                     +.+..+.+.+.    .+++-++|+|+++...  ..+.+...+.....++.+|++|
T Consensus        87 ~~~i---------------------~~ir~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t  145 (334)
T 1a5t_A           87 TLGV---------------------DAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLAT  145 (334)
T ss_dssp             SBCH---------------------HHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEE
T ss_pred             CCCH---------------------HHHHHHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEe
Confidence            1122                     22223333332    2467899999997542  2333333332233467777776


Q ss_pred             cchh-hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          287 RSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       287 r~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      .+.. +.....+....+++.++++++..+.+.+...  .    ..+....+++.++|.|..+..+
T Consensus       146 ~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~~--~----~~~~~~~l~~~s~G~~r~a~~~  204 (334)
T 1a5t_A          146 REPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT--M----SQDALLAALRLSAGSPGAALAL  204 (334)
T ss_dssp             SCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC--C----CHHHHHHHHHHTTTCHHHHHHT
T ss_pred             CChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhcC--C----CHHHHHHHHHHcCCCHHHHHHH
Confidence            6543 3222223346899999999999999988751  1    1345678999999999866544

>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=98.52  E-value=1.1e-06  Score=85.67  Aligned_cols=203  Identities=13%  Similarity=0.169  Sum_probs=113.6

Q ss_pred             Cccccc-chHH--HHHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFE-SRKS--TLKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~-gR~~--~~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .+..|+ |...  ....+......+. ...+.|+|++|+||||||+.+++.......-..+++++.+      ++..++.
T Consensus       103 tfd~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~------~~~~~~~  176 (440)
T 2z4s_A          103 TFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSE------KFLNDLV  176 (440)
T ss_dssp             SGGGCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHH------HHHHHHH
T ss_pred             ChhhcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH------HHHHHHH
Confidence            345565 5332  3333444433333 5678999999999999999999877543111124455433      2334444


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC---h-hhhcCCCCC-CCCCeEEEEeecchhhh-----h-
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD---L-EAIGIPLAD-DNGGCKVLLTARSQDVL-----S-  293 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~---~-~~l~~~l~~-~~~~s~iivTtr~~~va-----~-  293 (426)
                      ..+....        ...+...+. .++.+|+|||++....   . +.+...+.. ...|..||+||....-.     . 
T Consensus       177 ~~~~~~~--------~~~~~~~~~-~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~  247 (440)
T 2z4s_A          177 DSMKEGK--------LNEFREKYR-KKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDR  247 (440)
T ss_dssp             HHHHTTC--------HHHHHHHHT-TTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHH
T ss_pred             HHHHccc--------HHHHHHHhc-CCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHH
Confidence            3332110        112223332 2567999999975432   1 222222110 13467888888763211     0 


Q ss_pred             --ccCCceeeEEccCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhh------cC--CHHH
Q 044858          294 --CEMDCQQNFVVDVLNDKEAWSLFKKMTG--DCIENGELKSVVTEVVKECAGLPIAIVPIAKALK------NK--SPYE  361 (426)
Q Consensus       294 --~~~~~~~~~~l~~L~~~e~~~Lf~~~~~--~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~------~~--~~~~  361 (426)
                        ........+.+++++.++..+++.+.+.  +...++   ++...|++.++|.+-.+..+...+.      +.  +.+.
T Consensus       248 L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~---e~l~~la~~~~gn~R~l~~~L~~~~~~a~~~~~~It~~~  324 (440)
T 2z4s_A          248 LVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPE---EVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKE  324 (440)
T ss_dssp             HHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHCCSCHHHHHHHHHHHHHHHHHSSSCCCHHH
T ss_pred             HHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCH---HHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence              0011125789999999999999988774  211222   3467788999999876654433221      22  6666


Q ss_pred             HHHHHHHH
Q 044858          362 WRNALRQL  369 (426)
Q Consensus       362 w~~~l~~l  369 (426)
                      ++.++..+
T Consensus       325 ~~~~l~~~  332 (440)
T 2z4s_A          325 AILLLKDF  332 (440)
T ss_dssp             HHHHTSTT
T ss_pred             HHHHHHHH
Confidence            76666543

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.48  E-value=7.2e-06  Score=77.87  Aligned_cols=203  Identities=14%  Similarity=0.154  Sum_probs=116.1

Q ss_pred             ccCCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          146 STQDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       146 ~~~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      |...+.++.|-++.+++|.+.+.             -..++-|.++|++|+|||.||+.+++.....     .+.+..+.
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~-----f~~v~~s~  217 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK-----FIRVSGAE  217 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCE-----EEEEEGGG
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCC-----ceEEEhHH
Confidence            33456677787777776665543             1235668899999999999999999987643     23333332


Q ss_pred             CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC----------------hhhhcCCCC--
Q 044858          213 TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD----------------LEAIGIPLA--  274 (426)
Q Consensus       213 ~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~----------------~~~l~~~l~--  274 (426)
                      -.+              .... .....+..++.......+++|+||+++....                ...+...+.  
T Consensus       218 l~s--------------k~vG-ese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~  282 (405)
T 4b4t_J          218 LVQ--------------KYIG-EGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGF  282 (405)
T ss_dssp             GSC--------------SSTT-HHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTT
T ss_pred             hhc--------------cccc-hHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhcc
Confidence            111              1111 1123344555555556799999999975310                111111111  


Q ss_pred             CCCCCeEEEEeecchhhh----hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH-HHH
Q 044858          275 DDNGGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIA-IVP  349 (426)
Q Consensus       275 ~~~~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla-i~~  349 (426)
                      ....+..||.||......    .+...-...+.++.-+.++-.++|+.++......++..  ...|++.|.|.--| |..
T Consensus       283 ~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvd--l~~lA~~t~G~SGADi~~  360 (405)
T 4b4t_J          283 ETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGIN--LRKVAEKMNGCSGADVKG  360 (405)
T ss_dssp             TCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCC--HHHHHHHCCSCCHHHHHH
T ss_pred             CCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCC--HHHHHHHCCCCCHHHHHH
Confidence            223455566677655432    11223456888988889999999988776433222211  35677888875332 222


Q ss_pred             H---HHH--hh-cC---CHHHHHHHHHHHh
Q 044858          350 I---AKA--LK-NK---SPYEWRNALRQLK  370 (426)
Q Consensus       350 ~---~~~--l~-~~---~~~~w~~~l~~l~  370 (426)
                      +   |.+  ++ ++   +.+++..+++...
T Consensus       361 l~~eA~~~Air~~~~~vt~~Df~~Al~~v~  390 (405)
T 4b4t_J          361 VCTEAGMYALRERRIHVTQEDFELAVGKVM  390 (405)
T ss_dssp             HHHHHHHHHHHTTCSBCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence            2   222  22 22   6677777776654

>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=98.47  E-value=1.1e-05  Score=74.69  Aligned_cols=177  Identities=11%  Similarity=0.168  Sum_probs=101.6

Q ss_pred             CCcccccchHHHHHHHHHHhcc-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALSN-------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~-------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ....++.|.+..++.|.+.+..             ...+.+.|+|++|+|||+||+.+++.....       ++.+    
T Consensus        12 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~-------~i~v----   80 (301)
T 3cf0_A           12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN-------FISI----   80 (301)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCE-------EEEE----
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCC-------EEEE----
Confidence            3456688888777776665531             345678999999999999999999876421       2222    


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------C----hhhhcCCCC--CC
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------D----LEAIGIPLA--DD  276 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~----~~~l~~~l~--~~  276 (426)
                      +..++.....   +..      ......++.......+.+|+||+++...            .    ...+...+.  ..
T Consensus        81 ~~~~l~~~~~---g~~------~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~  151 (301)
T 3cf0_A           81 KGPELLTMWF---GES------EANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST  151 (301)
T ss_dssp             CHHHHHHHHH---TTC------TTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCT
T ss_pred             EhHHHHhhhc---Cch------HHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccC
Confidence            2233332221   111      1123344555544568999999997421            0    111211111  12


Q ss_pred             CCCeEEEEeecchhhh-hccC---CceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH
Q 044858          277 NGGCKVLLTARSQDVL-SCEM---DCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIA  346 (426)
Q Consensus       277 ~~~s~iivTtr~~~va-~~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla  346 (426)
                      ..+..||.||...... ....   .-...+.+...+.++-.+++...+.......+.  ....+++.+.|.|-+
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 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV--DLEFLAKMTNGFSGA  223 (301)
T ss_dssp             TSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSC--CHHHHHHTCSSCCHH
T ss_pred             CCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccc--hHHHHHHHcCCCCHH
Confidence            3456777777655322 1111   233578999999999999998887532211111  123566678877654

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.43  E-value=1.5e-06  Score=85.50  Aligned_cols=151  Identities=17%  Similarity=0.234  Sum_probs=87.5

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCcc----ce-EEEEEecCCcCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLF----EK-VISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----~~-~~wv~v~~~~~~~~il~~i  223 (426)
                      ...+++||+.+++.++..+.......+.|+|++|+|||++|+.+++........    .. .+.++.+.           
T Consensus       178 ~ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~-----------  246 (468)
T 3pxg_A          178 SLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGT-----------  246 (468)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC---------------
T ss_pred             CCCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCc-----------
Confidence            456799999999999999876656677899999999999999999886432100    11 12222220           


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchh------hhhccCC
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQD------VLSCEMD  297 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~------va~~~~~  297 (426)
                        ..    ... .......++..+...++.+|++|  ...+..+.+...+.  ....++|.+|....      .......
T Consensus       247 --~~----~g~-~e~~~~~~~~~~~~~~~~iLfiD--~~~~a~~~L~~~L~--~g~v~vI~at~~~e~~~~~~~~~al~~  315 (468)
T 3pxg_A          247 --KY----RGE-FEDRLKKVMDEIRQAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALER  315 (468)
T ss_dssp             -------------CTTHHHHHHHHHTCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHH
T ss_pred             --cc----cch-HHHHHHHHHHHHHhcCCeEEEEe--CchhHHHHHHHhhc--CCCEEEEecCCHHHHHHHhhcCHHHHH
Confidence              00    000 00123345555555567899999  22222222333332  22456666655443      1111122


Q ss_pred             ceeeEEccCCCHHHHHHHHHHhhC
Q 044858          298 CQQNFVVDVLNDKEAWSLFKKMTG  321 (426)
Q Consensus       298 ~~~~~~l~~L~~~e~~~Lf~~~~~  321 (426)
                      ....+.+++.+.++..+++.....
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            345799999999999999997764

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.42  E-value=6e-06  Score=79.63  Aligned_cols=201  Identities=19%  Similarity=0.247  Sum_probs=111.6

Q ss_pred             CCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..+.++.|-++.+++|.+.+.             -..++-|.++|++|+|||+||+.+++.....     .+.+..+.-.
T Consensus       178 v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~-----~~~v~~s~l~  252 (437)
T 4b4t_L          178 ITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGAN-----FIFSPASGIV  252 (437)
T ss_dssp             SCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGTC
T ss_pred             CChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehhhhc
Confidence            345667787777766655543             1245678999999999999999999987643     2334333211


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------C--------hhhhcCCC--CCC
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--------D--------LEAIGIPL--ADD  276 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--------~--------~~~l~~~l--~~~  276 (426)
                      +              .... .....+..++.......+++|+||+++...        .        +..+...+  ...
T Consensus       253 s--------------k~~G-ese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  317 (437)
T 4b4t_L          253 D--------------KYIG-ESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDN  317 (437)
T ss_dssp             C--------------SSSS-HHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSC
T ss_pred             c--------------ccch-HHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccC
Confidence            1              1111 112234455555555679999999997431        0        11111111  122


Q ss_pred             CCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH-HHHH-
Q 044858          277 NGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIA-IVPI-  350 (426)
Q Consensus       277 ~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla-i~~~-  350 (426)
                      ..+..||.||.......    ....-...+.++.-+.++-.++|+.++......++..  ...|++.+.|+--| |..+ 
T Consensus       318 ~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~d--l~~lA~~t~G~sGADi~~l~  395 (437)
T 4b4t_L          318 LGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFD--FEAAVKMSDGFNGADIRNCA  395 (437)
T ss_dssp             TTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCC--HHHHHHTCCSCCHHHHHHHH
T ss_pred             CCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccC--HHHHHHhCCCCCHHHHHHHH
Confidence            34556777776554321    1112346788887788888888887764322222211  35677888875432 2222 


Q ss_pred             --HHHh--h-cC---CHHHHHHHHHHHh
Q 044858          351 --AKAL--K-NK---SPYEWRNALRQLK  370 (426)
Q Consensus       351 --~~~l--~-~~---~~~~w~~~l~~l~  370 (426)
                        |.+.  + ++   +.+++..+++...
T Consensus       396 ~eA~~~air~~~~~i~~~d~~~Al~~v~  423 (437)
T 4b4t_L          396 TEAGFFAIRDDRDHINPDDLMKAVRKVA  423 (437)
T ss_dssp             HHHHHHHHHTTCSSBCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence              2222  2 22   5666666666544

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.40  E-value=7.6e-07  Score=75.73  Aligned_cols=49  Identities=22%  Similarity=0.302  Sum_probs=43.1

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ....++||+.+++.+.+.+.....+.+.|+|++|+|||+||+.+++...
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~   68 (187)
T 2p65_A           20 KLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIV   68 (187)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHH
T ss_pred             ccchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHH
Confidence            4567899999999999998876677789999999999999999998764

>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=98.38  E-value=1.9e-06  Score=80.69  Aligned_cols=167  Identities=19%  Similarity=0.195  Sum_probs=92.6

Q ss_pred             HHHHHHHhccC--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcH
Q 044858          160 LKGILDALSNR--NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESES  237 (426)
Q Consensus       160 ~~~l~~~l~~~--~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~  237 (426)
                      ...+......+  ....+.|+|++|+||||||+.+++..... .+ ..++++.      .++...+...+...       
T Consensus        23 ~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~-~~-~~~~i~~------~~~~~~~~~~~~~~-------   87 (324)
T 1l8q_A           23 YEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-GY-RVIYSSA------DDFAQAMVEHLKKG-------   87 (324)
T ss_dssp             HHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-TC-CEEEEEH------HHHHHHHHHHHHHT-------
T ss_pred             HHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC-CC-EEEEEEH------HHHHHHHHHHHHcC-------
Confidence            33444444433  34578999999999999999999877543 11 2344443      23333333332110       


Q ss_pred             HHHHHHHHHHhcCCeEEEEEeCCCCccC---h-hhhcCCCCC-CCCCeEEEEeecchhhh-----hc---cCCceeeEEc
Q 044858          238 VRAWRLLEQLKKETKILIILDDIWGSLD---L-EAIGIPLAD-DNGGCKVLLTARSQDVL-----SC---EMDCQQNFVV  304 (426)
Q Consensus       238 ~~~~~l~~~l~~~k~~LlVlDdv~~~~~---~-~~l~~~l~~-~~~~s~iivTtr~~~va-----~~---~~~~~~~~~l  304 (426)
                       ........+.  ++.+|+|||++....   + +.+...+.. ...+.+||+||....-.     ..   .......+.+
T Consensus        88 -~~~~~~~~~~--~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l  164 (324)
T 1l8q_A           88 -TINEFRNMYK--SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEI  164 (324)
T ss_dssp             -CHHHHHHHHH--TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEEC
T ss_pred             -cHHHHHHHhc--CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEe
Confidence             0112222332  367999999975432   1 222222110 12356788888654221     00   1111257899


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      ++ +.++..+++...+..... .--.+....|++.+ |.+-.+
T Consensus       165 ~~-~~~e~~~il~~~~~~~~~-~l~~~~l~~l~~~~-g~~r~l  204 (324)
T 1l8q_A          165 EL-DNKTRFKIIKEKLKEFNL-ELRKEVIDYLLENT-KNVREI  204 (324)
T ss_dssp             CC-CHHHHHHHHHHHHHHTTC-CCCHHHHHHHHHHC-SSHHHH
T ss_pred             CC-CHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHhC-CCHHHH
Confidence            99 999999999988742111 11145677888888 776543

>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=98.36  E-value=2.4e-06  Score=90.51  Aligned_cols=158  Identities=14%  Similarity=0.252  Sum_probs=89.6

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc---c-c-eEEEEEecCCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL---F-E-KVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~---f-~-~~~wv~v~~~~~~~~il~~  222 (426)
                      ....+++||+.++..++..+.....+.+.++|++|+|||+||+.+.+.......   . . .+++++.+.-..       
T Consensus       167 ~~ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~-------  239 (854)
T 1qvr_A          167 GKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA-------  239 (854)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC------------
T ss_pred             CCCcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhc-------
Confidence            346678999999999999988666666889999999999999999987643111   1 1 233343321100       


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhc-CCeEEEEEeCCCCccC-------hh---hhcCCCCCCCCCeEEEEeecchhh
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKK-ETKILIILDDIWGSLD-------LE---AIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~-~k~~LlVlDdv~~~~~-------~~---~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                           +... .......+..++..+.. +++.+|+||+++....       ++   .+...+ . ..+..+|.+|.....
T Consensus       240 -----g~~~-~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l-~-~~~i~~I~at~~~~~  311 (854)
T 1qvr_A          240 -----GAKY-RGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL-A-RGELRLIGATTLDEY  311 (854)
T ss_dssp             ------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH-H-TTCCCEEEEECHHHH
T ss_pred             -----cCcc-chHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHH-h-CCCeEEEEecCchHH
Confidence                 0000 01112234445555543 3689999999975420       11   111111 1 123456655544321


Q ss_pred             -----hhccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          292 -----LSCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       292 -----a~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                           ..........+.+++++.++..+++....
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                 11122334569999999999999997554

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.36  E-value=1.7e-05  Score=76.33  Aligned_cols=175  Identities=14%  Similarity=0.160  Sum_probs=101.7

Q ss_pred             CCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..+.++.|-++.+++|.+.+.             -..++-|.++|++|+|||+||+.+++.....     .+.+..+.-.
T Consensus       206 vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~-----fi~vs~s~L~  280 (467)
T 4b4t_H          206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDAT-----FIRVIGSELV  280 (467)
T ss_dssp             CCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGGC
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCC-----eEEEEhHHhh
Confidence            345567787777777766542             1346778999999999999999999987643     2333332211


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC----------------hhhhcCCC--CCC
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD----------------LEAIGIPL--ADD  276 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~----------------~~~l~~~l--~~~  276 (426)
                                    ..... .....+..++.......+++|+||+++....                ...+...+  ...
T Consensus       281 --------------sk~vG-esek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  345 (467)
T 4b4t_H          281 --------------QKYVG-EGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDP  345 (467)
T ss_dssp             --------------CCSSS-HHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCC
T ss_pred             --------------cccCC-HHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCC
Confidence                          11111 1122344555555556799999999974310                00111111  122


Q ss_pred             CCCeEEEEeecchhhh----hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          277 NGGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       277 ~~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      ..+..||.||......    .+...-...+.+..-+.++-.++|+.++.......+..  ...|++.|.|.-
T Consensus       346 ~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvd--l~~LA~~T~GfS  415 (467)
T 4b4t_H          346 RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIR--WELISRLCPNST  415 (467)
T ss_dssp             TTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCC--HHHHHHHCCSCC
T ss_pred             CCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCC--HHHHHHHCCCCC
Confidence            3345566676554332    11223456888888888888999988775432222211  355778888853

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.32  E-value=2e-05  Score=75.11  Aligned_cols=203  Identities=16%  Similarity=0.196  Sum_probs=112.1

Q ss_pred             ccCCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          146 STQDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       146 ~~~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      |...+.++.|-++.+++|.+.+.             -..++-|.++|++|+|||.||+.+++.....  |   +.++.+.
T Consensus       177 p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~--f---i~v~~s~  251 (437)
T 4b4t_I          177 PTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSAT--F---LRIVGSE  251 (437)
T ss_dssp             CCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCE--E---EEEESGG
T ss_pred             CCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCC--E---EEEEHHH
Confidence            33456667787777776665442             1235679999999999999999999987643  2   2333221


Q ss_pred             CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC----------------hhhhcCCC--C
Q 044858          213 TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD----------------LEAIGIPL--A  274 (426)
Q Consensus       213 ~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~----------------~~~l~~~l--~  274 (426)
                      -              ...... .....+..++.......+++|+||+++....                ...+...+  .
T Consensus       252 l--------------~sk~vG-esek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~  316 (437)
T 4b4t_I          252 L--------------IQKYLG-DGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGF  316 (437)
T ss_dssp             G--------------CCSSSS-HHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHC
T ss_pred             h--------------hhccCc-hHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCc
Confidence            1              111111 1123344555555556799999999874310                01111111  1


Q ss_pred             CCCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHH
Q 044858          275 DDNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVP  349 (426)
Q Consensus       275 ~~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~  349 (426)
                      ....+..||.||.......    +...-...+.+..-+.++-.++|+.++......++.  -...|++.+.|+-- -|..
T Consensus       317 ~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dv--dl~~LA~~T~GfSGADI~~  394 (437)
T 4b4t_I          317 DDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDV--NLETLVTTKDDLSGADIQA  394 (437)
T ss_dssp             CCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCC--CHHHHHHHCCSCCHHHHHH
T ss_pred             CCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcC--CHHHHHHhCCCCCHHHHHH
Confidence            2234556666776554321    111234567888778888888998877543222221  13457777877532 1222


Q ss_pred             H---HHHh--h-cC---CHHHHHHHHHHHh
Q 044858          350 I---AKAL--K-NK---SPYEWRNALRQLK  370 (426)
Q Consensus       350 ~---~~~l--~-~~---~~~~w~~~l~~l~  370 (426)
                      +   |.+.  + ++   +.+++..+++.+.
T Consensus       395 l~~eA~~~Air~~~~~It~eDf~~Al~rv~  424 (437)
T 4b4t_I          395 MCTEAGLLALRERRMQVTAEDFKQAKERVM  424 (437)
T ss_dssp             HHHHHHHHHHHTTCSCBCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCccCHHHHHHHHHHHh
Confidence            2   2222  2 22   5667776666554

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.31  E-value=8.3e-06  Score=78.56  Aligned_cols=176  Identities=13%  Similarity=0.168  Sum_probs=99.8

Q ss_pred             ccCCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          146 STQDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       146 ~~~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      |...+.++.|-++.+++|.+.+.             -..++-|.++||+|+|||.||+.+++.....     .+.++.+.
T Consensus       176 p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~-----f~~v~~s~  250 (434)
T 4b4t_M          176 PTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNAT-----FLKLAAPQ  250 (434)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGG
T ss_pred             CCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCC-----EEEEehhh
Confidence            33456778888888877766543             1245678999999999999999999987643     22333322


Q ss_pred             CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc-------cC---------hhhhcCCCC--
Q 044858          213 TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS-------LD---------LEAIGIPLA--  274 (426)
Q Consensus       213 ~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~-------~~---------~~~l~~~l~--  274 (426)
                      -.              ..... .....+..++.......+++|+||+++..       ..         ...+...+.  
T Consensus       251 l~--------------~~~vG-ese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~  315 (434)
T 4b4t_M          251 LV--------------QMYIG-EGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGF  315 (434)
T ss_dssp             GC--------------SSCSS-HHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTS
T ss_pred             hh--------------hcccc-hHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhcc
Confidence            11              11111 11223444555444457899999998532       00         011111111  


Q ss_pred             CCCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          275 DDNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       275 ~~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                      ....+..||.||.......    ....-...+.++.-+.++-.++|+.++......++..  ...|++.+.|+
T Consensus       316 ~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvd--l~~lA~~t~G~  386 (434)
T 4b4t_M          316 SSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDIN--WQELARSTDEF  386 (434)
T ss_dssp             CSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCC--HHHHHHHCSSC
T ss_pred             CCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCC--HHHHHHhCCCC
Confidence            1223445666776554321    1123346788888888888888877664222122111  35577788775

>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=98.27  E-value=1.9e-05  Score=82.73  Aligned_cols=157  Identities=18%  Similarity=0.210  Sum_probs=95.1

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEEE-EecCCcCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVISS-RVSQTPQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv-~v~~~~~~~~il~~i  223 (426)
                      ...+++||+.++..+++.+.......+.|+|++|+|||++|+.+.+.......    ..+.++. ..+.-          
T Consensus       184 ~~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l----------  253 (758)
T 1r6b_X          184 GIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL----------  253 (758)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC------------
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHH----------
Confidence            45678999999999999988766677899999999999999999987643211    1233321 11110          


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------C---hhhhcCCCCCCCCCeEEEEeecchhhh
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--------D---LEAIGIPLADDNGGCKVLLTARSQDVL  292 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--------~---~~~l~~~l~~~~~~s~iivTtr~~~va  292 (426)
                         +...............+++.+...++.+|+|||++...        .   ...+...+ . ..+.++|.+|......
T Consensus       254 ---~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l-~-~~~~~~I~at~~~~~~  328 (758)
T 1r6b_X          254 ---LAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLL-S-SGKIRVIGSTTYQEFS  328 (758)
T ss_dssp             ----CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCS-S-SCCCEEEEEECHHHHH
T ss_pred             ---hccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHH-h-CCCeEEEEEeCchHHh
Confidence               00000111222344555566655567999999997541        1   11233332 2 2345666666544321


Q ss_pred             ------hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          293 ------SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       293 ------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                            .........+.+.+.+.++..+++....
T Consensus       329 ~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          329 NIFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             CCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHH
Confidence                  1112234579999999999999887654

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.26  E-value=3e-05  Score=74.60  Aligned_cols=172  Identities=17%  Similarity=0.216  Sum_probs=95.8

Q ss_pred             CCcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          148 QDFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..+.++.|-++.+++|.+.+.             -..++-+.++|++|+|||+||+.+++.....     .+.++.+.-.
T Consensus       169 v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~-----~~~v~~~~l~  243 (428)
T 4b4t_K          169 VTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAA-----FIRVNGSEFV  243 (428)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCE-----EEEEEGGGTC
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCC-----eEEEecchhh
Confidence            456677888877777766543             1245668999999999999999999987643     2334333211


Q ss_pred             CHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------C------hhhhcCCCC--CC
Q 044858          215 QIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL----------D------LEAIGIPLA--DD  276 (426)
Q Consensus       215 ~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~----------~------~~~l~~~l~--~~  276 (426)
                      +              .... .....+..++.......++++++|+++...          .      ...+...+.  ..
T Consensus       244 ~--------------~~~G-e~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~  308 (428)
T 4b4t_K          244 H--------------KYLG-EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQ  308 (428)
T ss_dssp             C--------------SSCS-HHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCS
T ss_pred             c--------------cccc-hhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCC
Confidence            1              1111 112334455555555679999999985220          0      111111110  22


Q ss_pred             CCCeEEEEeecchhhh----hccCCceeeEEccCCCHH-HHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCc
Q 044858          277 NGGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDK-EAWSLFKKMTGDCI--ENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       277 ~~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~-e~~~Lf~~~~~~~~--~~~~~~~~~~~i~~~c~Gl  343 (426)
                      ..+..||.||......    .+...-...+++..+++. +-..+|...+....  ...+    ...|++.+.|+
T Consensus       309 ~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~d----l~~lA~~t~G~  378 (428)
T 4b4t_K          309 STNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEAD----LDSLIIRNDSL  378 (428)
T ss_dssp             SCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCC----HHHHHHHTTTC
T ss_pred             CCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccC----HHHHHHHCCCC
Confidence            3455677777654322    112233457788767554 44556665553222  1223    35577778775

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.24  E-value=2.6e-05  Score=70.15  Aligned_cols=181  Identities=18%  Similarity=0.227  Sum_probs=96.3

Q ss_pred             CCcccccchHHHHHHHHHH---hcc---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDA---LSN---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~---l~~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+.+++|.+..++.+.+.   +..         ...+-+.|+|++|+||||||+.+.+.....  |   +.++.+.-.+
T Consensus         9 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~--~---~~i~~~~~~~   83 (257)
T 1lv7_A            9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP--F---FTISGSDFVE   83 (257)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCC--E---EEECSCSSTT
T ss_pred             CCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCC--E---EEEeHHHHHH
Confidence            3556778887766655443   321         123458899999999999999999876421  2   3333221110


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-----------C-----hhhhcCCCC--CCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-----------D-----LEAIGIPLA--DDN  277 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-----------~-----~~~l~~~l~--~~~  277 (426)
                                    .... ........+++......+.++++|+++...           .     ...+...+.  ...
T Consensus        84 --------------~~~~-~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  148 (257)
T 1lv7_A           84 --------------MFVG-VGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGN  148 (257)
T ss_dssp             --------------SCCC-CCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSS
T ss_pred             --------------Hhhh-hhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccC
Confidence                          0001 112233444555544567899999984220           0     011111110  123


Q ss_pred             CCeEEEEeecchhhh-hccC---CceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-chHHHHHH
Q 044858          278 GGCKVLLTARSQDVL-SCEM---DCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAG-LPIAIVPI  350 (426)
Q Consensus       278 ~~s~iivTtr~~~va-~~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~G-lPlai~~~  350 (426)
                      .+..||.||...... ....   .-...+.+...+.++-.+++...+......++.  ....++..+.| .+--|..+
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 EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI--DAAIIARGTPGFSGADLANL  224 (257)
T ss_dssp             SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCCHHHHHHH
T ss_pred             CCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccc--cHHHHHHHcCCCCHHHHHHH
Confidence            355666677654321 1111   223577888888888888888776432211211  13456777888 66555443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.19  E-value=8.3e-06  Score=85.31  Aligned_cols=152  Identities=17%  Similarity=0.229  Sum_probs=88.1

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEEEEecCCcCHHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ...+++||+.+++.+...+......-+.++|++|+|||++|+.+.+.......    ..+. ++.++.            
T Consensus       178 ~ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~-~~~~~~------------  244 (758)
T 3pxi_A          178 SLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKR-VMTLDM------------  244 (758)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCC-EECC--------------
T ss_pred             CCCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCe-EEEecc------------
Confidence            45679999999999999988666667889999999999999999988632110    0111 111111            


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchh------hhhccCCc
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQD------VLSCEMDC  298 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~------va~~~~~~  298 (426)
                         +...... ....+..++..+...++.+|++|.  ..+....+...+.  ....++|.||....      ........
T Consensus       245 ---g~~~~G~-~e~~l~~~~~~~~~~~~~iLfiD~--~~~~~~~L~~~l~--~~~v~~I~at~~~~~~~~~~~d~al~rR  316 (758)
T 3pxi_A          245 ---GTKYRGE-FEDRLKKVMDEIRQAGNIILFIDA--AIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERR  316 (758)
T ss_dssp             ------------CTTHHHHHHHHHTCCCCEEEECC----------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHS
T ss_pred             ---cccccch-HHHHHHHHHHHHHhcCCEEEEEcC--chhHHHHHHHHHh--cCCEEEEeCCChHHHHHHhhccHHHHhh
Confidence               0000000 011233455555556788999992  2222222333332  23456666665543      11111123


Q ss_pred             eeeEEccCCCHHHHHHHHHHhhC
Q 044858          299 QQNFVVDVLNDKEAWSLFKKMTG  321 (426)
Q Consensus       299 ~~~~~l~~L~~~e~~~Lf~~~~~  321 (426)
                      ...+.+++.+.++..+++.....
T Consensus       317 f~~i~v~~p~~~~~~~il~~~~~  339 (758)
T 3pxi_A          317 FQPIQVDQPSVDESIQILQGLRD  339 (758)
T ss_dssp             EEEEECCCCCHHHHHHHHHHTTT
T ss_pred             CcEEEeCCCCHHHHHHHHHHHHH
Confidence            46799999999999999987654

>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=98.16  E-value=1.7e-06  Score=73.60  Aligned_cols=117  Identities=17%  Similarity=0.160  Sum_probs=63.8

Q ss_pred             hHHHHHHHHHHhcc---CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCcc
Q 044858          156 RKSTLKGILDALSN---RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKID  232 (426)
Q Consensus       156 R~~~~~~l~~~l~~---~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~  232 (426)
                      +...++.+.++..+   .....+.|+|+.|+|||||++.+++.......+. ++++      +..++...+.........
T Consensus        19 ~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~-~~~~------~~~~~~~~~~~~~~~~~~   91 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIR-GYFF------DTKDLIFRLKHLMDEGKD   91 (180)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCC-CCEE------EHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCe-EEEE------EHHHHHHHHHHHhcCchH
Confidence            34444555444432   2346899999999999999999998875322222 2233      344555554433321111


Q ss_pred             ccCcHHHHHHHHHHHhcCCeEEEEEeCCCC--ccChhh--hcCCCCC-CCCCeEEEEeecch
Q 044858          233 QESESVRAWRLLEQLKKETKILIILDDIWG--SLDLEA--IGIPLAD-DNGGCKVLLTARSQ  289 (426)
Q Consensus       233 ~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~--~~~~~~--l~~~l~~-~~~~s~iivTtr~~  289 (426)
                          .    .+.+.+.  ++-+|||||++.  .+.|..  +...+.. ...|..+|+||...
T Consensus        92 ----~----~~~~~~~--~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~  143 (180)
T 3ec2_A           92 ----T----KFLKTVL--NSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYS  143 (180)
T ss_dssp             ----S----HHHHHHH--TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCC
T ss_pred             ----H----HHHHHhc--CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence                0    2333333  456999999973  333331  2111111 12466788888654

>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=98.14  E-value=8.6e-06  Score=75.23  Aligned_cols=144  Identities=18%  Similarity=0.090  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhc--CccceEEEEEecC-CcCHHHHHHHHHHHhCCCccc
Q 044858          157 KSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN--NLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQ  233 (426)
Q Consensus       157 ~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~--~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~  233 (426)
                      ++.+..|...+..++.+...++|+.|+||||+|+.+.+.....  .+.+ ..++..+. ..++.++ +++...+....- 
T Consensus         3 ~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d-~~~l~~~~~~~~id~i-r~li~~~~~~p~-   79 (305)
T 2gno_A            3 KDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSPE-   79 (305)
T ss_dssp             -CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCCS-
T ss_pred             HHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCC-EEEEcCCcCCCCHHHH-HHHHHHHhhccc-
Confidence            3445666666666667789999999999999999998753211  2233 34454432 2333332 334433321110 


Q ss_pred             cCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecch-hhhhccCCceeeEEccCCCHH
Q 044858          234 ESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMDCQQNFVVDVLNDK  310 (426)
Q Consensus       234 ~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~~~~~~~l~~L~~~  310 (426)
                                     .+++-++|+|+++..  ...+.+...+..-.+.+.+|++|.+. .+.......  .+++.+++++
T Consensus        80 ---------------~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR--~~~f~~l~~~  142 (305)
T 2gno_A           80 ---------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR--VFRVVVNVPK  142 (305)
T ss_dssp             ---------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT--SEEEECCCCH
T ss_pred             ---------------cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce--eEeCCCCCHH
Confidence                           145679999999754  23344433332233467777776543 332211222  8999999999


Q ss_pred             HHHHHHHHhh
Q 044858          311 EAWSLFKKMT  320 (426)
Q Consensus       311 e~~~Lf~~~~  320 (426)
                      +..+.+.+.+
T Consensus       143 ~i~~~L~~~~  152 (305)
T 2gno_A          143 EFRDLVKEKI  152 (305)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998876

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.11  E-value=1.3e-06  Score=71.52  Aligned_cols=46  Identities=15%  Similarity=0.196  Sum_probs=34.0

Q ss_pred             cccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|+...+.++.+.+.  .....-|.|+|++|+|||++|+.+++...
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~   49 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGR   49 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSST
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCC
Confidence            46788888887777664  22334578999999999999999988653

>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=98.10  E-value=7.2e-05  Score=73.16  Aligned_cols=199  Identities=17%  Similarity=0.216  Sum_probs=107.2

Q ss_pred             CcccccchHHHHHHHHHH---hccC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          149 DFMHFESRKSTLKGILDA---LSNR---------NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~---l~~~---------~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .+.++.|.+..++++.+.   +..+         .++-+.|+|++|+|||+||+.+.+.....  |   +.++.+.-...
T Consensus        14 ~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~--f---~~is~~~~~~~   88 (476)
T 2ce7_A           14 TFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVP--F---FHISGSDFVEL   88 (476)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCC--E---EEEEGGGTTTC
T ss_pred             CHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCC--e---eeCCHHHHHHH
Confidence            455677877665555443   3221         23458899999999999999999876432  2   23333321110


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------------ChhhhcCCCC--CCCC
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL----------------DLEAIGIPLA--DDNG  278 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~----------------~~~~l~~~l~--~~~~  278 (426)
                                    ... ........++.......+++|+||+++...                ....+...+.  ....
T Consensus        89 --------------~~g-~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~  153 (476)
T 2ce7_A           89 --------------FVG-VGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKE  153 (476)
T ss_dssp             --------------CTT-HHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGG
T ss_pred             --------------Hhc-ccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCC
Confidence                          000 011223344555545678999999995431                0112211110  1223


Q ss_pred             CeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHHH--
Q 044858          279 GCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPIA--  351 (426)
Q Consensus       279 ~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~~--  351 (426)
                      +..||.||.......    ....-...+.+.+.+.++-.+++...+......++.  ....|++.+.|..- -|..+.  
T Consensus       154 ~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v--~l~~la~~t~G~sgadL~~lv~~  231 (476)
T 2ce7_A          154 GIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDV--NLEIIAKRTPGFVGADLENLVNE  231 (476)
T ss_dssp             TEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             CEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchh--hHHHHHHhcCCCcHHHHHHHHHH
Confidence            566777776654321    111223478888888888888888776532212221  13447888888762 233221  


Q ss_pred             -HHhh---cC---CHHHHHHHHHHH
Q 044858          352 -KALK---NK---SPYEWRNALRQL  369 (426)
Q Consensus       352 -~~l~---~~---~~~~w~~~l~~l  369 (426)
                       .++.   +.   +...+..+++..
T Consensus       232 Aal~A~~~~~~~I~~~dl~~al~~v  256 (476)
T 2ce7_A          232 AALLAAREGRDKITMKDFEEAIDRV  256 (476)
T ss_dssp             HHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCeecHHHHHHHHHHH
Confidence             1121   11   566676666654

>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=98.08  E-value=0.0001  Score=72.52  Aligned_cols=180  Identities=13%  Similarity=0.172  Sum_probs=101.7

Q ss_pred             CcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          149 DFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      .+..++|.+..+++|.+.+.             .....-+.|+|++|+|||++|+.+.+....     ..+.++.+    
T Consensus       202 ~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~-----~fv~vn~~----  272 (489)
T 3hu3_A          202 GYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA-----FFFLINGP----  272 (489)
T ss_dssp             CGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSS-----EEEEEEHH----
T ss_pred             CHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCC-----CEEEEEch----
Confidence            45568899888888877664             134457899999999999999999877532     12333321    


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-------------ChhhhcCCCC--CCCCCe
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-------------DLEAIGIPLA--DDNGGC  280 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-------------~~~~l~~~l~--~~~~~s  280 (426)
                        ++.    ..+    . .........++.....+++.+|+||+++...             ....+...+.  ....+.
T Consensus       273 --~l~----~~~----~-g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v  341 (489)
T 3hu3_A          273 --EIM----SKL----A-GESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  341 (489)
T ss_dssp             --HHH----TSC----T-THHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCE
T ss_pred             --Hhh----hhh----c-chhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCce
Confidence              111    100    0 0111223344555555678999999994221             0111111111  123355


Q ss_pred             EEEEeecchhhh-h--cc-CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc-hHHHHHH
Q 044858          281 KVLLTARSQDVL-S--CE-MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL-PIAIVPI  350 (426)
Q Consensus       281 ~iivTtr~~~va-~--~~-~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl-Plai~~~  350 (426)
                      .||.||...... .  .. ..-...+.+...+.++-.+++...+.......+  .....+++.+.|. +-.|..+
T Consensus       342 ~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~--~~l~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADD--VDLEQVANETHGHVGADLAAL  414 (489)
T ss_dssp             EEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTT--CCHHHHHHTCTTCCHHHHHHH
T ss_pred             EEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcch--hhHHHHHHHccCCcHHHHHHH
Confidence            666676654321 1  11 123357899999999999999988753221111  1134567777775 5445444

>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=98.04  E-value=3e-05  Score=71.64  Aligned_cols=46  Identities=24%  Similarity=0.346  Sum_probs=36.1

Q ss_pred             cccchHHHHHHHHHHhcc--------------CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALSN--------------RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~--------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|++..++.+...+..              .....+.++|++|+|||++|+.+.+...
T Consensus        16 ~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~   75 (310)
T 1ofh_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (310)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            467888888877766543              2345688999999999999999998763

>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=97.98  E-value=0.00055  Score=64.06  Aligned_cols=220  Identities=16%  Similarity=0.120  Sum_probs=115.0

Q ss_pred             CcccccchHHHHHHHHHHhcc-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALSN-----RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~-----~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ....++|.+..++.+...+..     ..+..+.++|++|+||||||+.+.+.....  |.   ....+-.....++    
T Consensus        23 ~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~--~~---~~sg~~~~~~~~l----   93 (334)
T 1in4_A           23 SLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN--IH---VTSGPVLVKQGDM----   93 (334)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC--EE---EEETTTCCSHHHH----
T ss_pred             cHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC--EE---EEechHhcCHHHH----
Confidence            456678887777766555542     234678999999999999999999876432  11   1111111111111    


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCC--------CC----------CCeEEE
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLAD--------DN----------GGCKVL  283 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~--------~~----------~~s~ii  283 (426)
                                       ..+...+  .++.++++|++....  ..+.+...+..        ..          +...++
T Consensus        94 -----------------~~~~~~~--~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li  154 (334)
T 1in4_A           94 -----------------AAILTSL--ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLV  154 (334)
T ss_dssp             -----------------HHHHHHC--CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEE
T ss_pred             -----------------HHHHHHc--cCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeEEE
Confidence                             1111111  134577788875431  11111100000        00          112222


Q ss_pred             -Eeecchhhhh-ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh------h
Q 044858          284 -LTARSQDVLS-CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL------K  355 (426)
Q Consensus       284 -vTtr~~~va~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l------~  355 (426)
                       .|++...+.. ........+.+++.+.++..+++.+.+..... ....+.+..|++.++|.|-.+..+...+      .
T Consensus       155 ~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~-~~~~~~~~~ia~~~~G~~R~a~~ll~~~~~~a~~~  233 (334)
T 1in4_A          155 GATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV-EIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVV  233 (334)
T ss_dssp             EEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-CBCHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHH
T ss_pred             EecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHc
Confidence             2444333221 11122346899999999999999987642111 2224678899999999998665544322      1


Q ss_pred             -c-C-CHHHHHHHHHHHhhccccCCCCcchhhhhhhHHhhhcCCCCC
Q 044858          356 -N-K-SPYEWRNALRQLKRNFLRSFSGTQAVAAYSTIQLSYNQLGGE  399 (426)
Q Consensus       356 -~-~-~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~  399 (426)
                       . . +.+.-+.+++.+.... ......+ ..+...+.-+|..=|..
T Consensus       234 ~~~~It~~~v~~al~~~~~~~-~~l~~~~-~~~l~~~~~~~~~~~~~  278 (334)
T 1in4_A          234 KADRINTDIVLKTMEVLNIDD-EGLDEFD-RKILKTIIEIYRGGPVG  278 (334)
T ss_dssp             TCSSBCHHHHHHHHHHHTCCT-TCCCHHH-HHHHHHHHHHSTTCCBC
T ss_pred             CCCCcCHHHHHHHHHHhCCCc-CCCCHHH-HHHHHHHHHHhCCCcch
Confidence             1 2 6666777777653211 1111111 34555566666544443

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.96  E-value=1.9e-05  Score=73.11  Aligned_cols=104  Identities=16%  Similarity=0.237  Sum_probs=56.6

Q ss_pred             ccchHHHHHHHHHHhccC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          153 FESRKSTLKGILDALSNR---------NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~~---------~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ++|.+..++.+...+...         ....+.++|++|+|||++|+.+++.....  -...+.+..+...... ....+
T Consensus        19 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~--~~~~~~~~~~~~~~~~-~~~~l   95 (311)
T 4fcw_A           19 VVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKH-AVSRL   95 (311)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC--GGGEEEEEGGGCCSTT-HHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC--CcceEEeecccccccc-cHHHh
Confidence            567777777766665421         13478999999999999999999876432  1123445544332211 11111


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                         ++......... ....+...+......+|+||++...
T Consensus        96 ---~g~~~~~~~~~-~~~~~~~~~~~~~~~vl~lDEi~~l  131 (311)
T 4fcw_A           96 ---IGAPPGYVGYE-EGGQLTEAVRRRPYSVILFDAIEKA  131 (311)
T ss_dssp             ---HCCCTTSTTTT-TCCHHHHHHHHCSSEEEEEETGGGS
T ss_pred             ---cCCCCcccccc-ccchHHHHHHhCCCeEEEEeChhhc
Confidence               22211110000 0012333343344579999999754

>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=97.93  E-value=9.3e-05  Score=72.51  Aligned_cols=49  Identities=12%  Similarity=0.112  Sum_probs=36.3

Q ss_pred             CcccccchHHHHHHHHH---HhccC--CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          149 DFMHFESRKSTLKGILD---ALSNR--NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~---~l~~~--~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..++|.++.++.+..   .+..+  ..+-+.++|++|+|||+||+.+.+...
T Consensus        35 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~   88 (456)
T 2c9o_A           35 AASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELG   88 (456)
T ss_dssp             EETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             chhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhC
Confidence            34678898887765444   33333  235788999999999999999998764

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=97.91  E-value=1e-05  Score=73.40  Aligned_cols=175  Identities=21%  Similarity=0.225  Sum_probs=87.6

Q ss_pred             CcccccchHHHHHHHHHHhc---c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          149 DFMHFESRKSTLKGILDALS---N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~---~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .+..++|.+..++.+.+.+.   .         ...+-+.|+|++|+|||+||+.+++.....  |-   .+..+.-.+.
T Consensus         9 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~--~~---~v~~~~~~~~   83 (268)
T 2r62_A            9 RFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVP--FF---SMGGSSFIEM   83 (268)
T ss_dssp             CSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCC--CC---CCCSCTTTTS
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC--EE---EechHHHHHh
Confidence            34556776655554444332   1         123347799999999999999999876432  21   1111110000


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc-----------------ChhhhcCCCCC---C
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL-----------------DLEAIGIPLAD---D  276 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~-----------------~~~~l~~~l~~---~  276 (426)
                               ..+..  ..    ....+++.....++.+|+|||++...                 ....+...+..   .
T Consensus        84 ---------~~~~~--~~----~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  148 (268)
T 2r62_A           84 ---------FVGLG--AS----RVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSE  148 (268)
T ss_dssp             ---------CSSSC--SS----SSSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCS
T ss_pred             ---------hcchH--HH----HHHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccC
Confidence                     00000  00    01122233333457899999995431                 12222222211   1


Q ss_pred             CCCeEEEEeecchhhh----hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH
Q 044858          277 NGGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI  345 (426)
Q Consensus       277 ~~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl  345 (426)
                      .....||.||......    .....-...+.+.+.+.++-.+++...+......++.  ....|++.+.|.|-
T Consensus       149 ~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~--~~~~la~~~~g~~g  219 (268)
T 2r62_A          149 NAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDV--NLQEVAKLTAGLAG  219 (268)
T ss_dssp             CSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSC--CTTTTTSSSCSSCH
T ss_pred             CCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCcc--CHHHHHHHcCCCCH
Confidence            1234566676655321    1111223568888899999999998776432111110  02235666777653

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.80  E-value=7.4e-05  Score=64.45  Aligned_cols=114  Identities=17%  Similarity=0.142  Sum_probs=62.0

Q ss_pred             HHHHHHHHHhccC----CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc
Q 044858          158 STLKGILDALSNR----NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ  233 (426)
Q Consensus       158 ~~~~~l~~~l~~~----~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~  233 (426)
                      ..++.+..++...    ....+.|+|++|+|||+||+.+++.....  ...++++++      .++...+......    
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~--~~~~~~~~~------~~~~~~~~~~~~~----  103 (202)
T 2w58_A           36 KAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKR--NVSSLIVYV------PELFRELKHSLQD----  103 (202)
T ss_dssp             HHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT--TCCEEEEEH------HHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEh------HHHHHHHHHHhcc----
Confidence            3445555555432    22678999999999999999999887643  234556554      3444444433211    


Q ss_pred             cCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhh--hcC-CCCCC-CCCeEEEEeecch
Q 044858          234 ESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEA--IGI-PLADD-NGGCKVLLTARSQ  289 (426)
Q Consensus       234 ~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~--l~~-~l~~~-~~~s~iivTtr~~  289 (426)
                      ...    ..+...+.+  .-+|||||++..  ..|..  +.. .+... ..+.++|+||...
T Consensus       104 ~~~----~~~~~~~~~--~~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~~  159 (202)
T 2w58_A          104 QTM----NEKLDYIKK--VPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFD  159 (202)
T ss_dssp             CCC----HHHHHHHHH--SSEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESSC
T ss_pred             chH----HHHHHHhcC--CCEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC
Confidence            111    123333433  239999999643  33322  211 11111 2355788888754

>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=97.80  E-value=0.00011  Score=76.18  Aligned_cols=152  Identities=13%  Similarity=0.174  Sum_probs=85.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .++-|.++|++|+|||+||+.+++.....     .+.++.+      ++    ..    ... ......+..+++.....
T Consensus       237 ~p~GILL~GPPGTGKT~LAraiA~elg~~-----~~~v~~~------~l----~s----k~~-gese~~lr~lF~~A~~~  296 (806)
T 3cf2_A          237 PPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGP------EI----MS----KLA-GESESNLRKAFEEAEKN  296 (806)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHTTTTCE-----EEEEEHH------HH----HS----SCT-THHHHHHHHHHHHHTTS
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhCCe-----EEEEEhH------Hh----hc----ccc-hHHHHHHHHHHHHHHHc
Confidence            35678999999999999999999876532     2333322      11    10    111 11123344555555566


Q ss_pred             CeEEEEEeCCCCcc--------Ch-----hhhcCCCC--CCCCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHH
Q 044858          251 TKILIILDDIWGSL--------DL-----EAIGIPLA--DDNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKE  311 (426)
Q Consensus       251 k~~LlVlDdv~~~~--------~~-----~~l~~~l~--~~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e  311 (426)
                      .+++|+||+++...        ..     ..+...+.  ....+..||.||.......    ....-...+++..-+.++
T Consensus       297 ~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~  376 (806)
T 3cf2_A          297 APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG  376 (806)
T ss_dssp             CSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHH
T ss_pred             CCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHH
Confidence            79999999996431        10     11111110  1123444555665443221    111234678898888888


Q ss_pred             HHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          312 AWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       312 ~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      -.++|...+......++.  -...|++++.|.-
T Consensus       377 R~~IL~~~l~~~~~~~dv--dl~~lA~~T~Gfs  407 (806)
T 3cf2_A          377 RLEILQIHTKNMKLADDV--DLEQVANETHGHV  407 (806)
T ss_dssp             HHHHHHHTCSSSEECTTC--CHHHHHHHCCSCC
T ss_pred             HHHHHHHHhcCCCCCccc--CHHHHHHhcCCCC
Confidence            899998776533222211  1456778888864

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.74  E-value=6.2e-06  Score=67.21  Aligned_cols=46  Identities=7%  Similarity=0.077  Sum_probs=32.0

Q ss_pred             cccchHHHHHHHHHHhcc--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALSN--RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~--~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|+...+.++.+.+..  ....-|.|+|++|+|||++|+.+++...
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~~   52 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNGT   52 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTTS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC
Confidence            467777777777666541  2234478999999999999999987543

>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=97.72  E-value=0.00019  Score=71.73  Aligned_cols=156  Identities=17%  Similarity=0.159  Sum_probs=74.7

Q ss_pred             ccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          153 FESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ++|-++....+.+.+.      ......+.++|++|+||||||+.+.......  |   ..+.++...+...+.......
T Consensus        83 i~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~~--~---~~i~~~~~~~~~~~~g~~~~~  157 (543)
T 3m6a_A           83 HHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGRK--F---VRISLGGVRDESEIRGHRRTY  157 (543)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTCE--E---EEECCCC--------------
T ss_pred             hccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCCC--e---EEEEecccchhhhhhhHHHHH
Confidence            4565555554433322      2245689999999999999999999877432  2   223333322222221111111


Q ss_pred             hCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC------hhhhcCCCCC--------C-------CCCeEEEEe
Q 044858          227 LGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD------LEAIGIPLAD--------D-------NGGCKVLLT  285 (426)
Q Consensus       227 l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~------~~~l~~~l~~--------~-------~~~s~iivT  285 (426)
                      .+..      .......+..... ..-+++||++.....      ...+...+..        .       .....+|.|
T Consensus       158 ig~~------~~~~~~~~~~a~~-~~~vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~t  230 (543)
T 3m6a_A          158 VGAM------PGRIIQGMKKAGK-LNPVFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIAT  230 (543)
T ss_dssp             ------------CHHHHHHTTCS-SSEEEEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEE
T ss_pred             hccC------chHHHHHHHHhhc-cCCEEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEec
Confidence            1110      0011112222222 234888999975421      1222222210        0       023456666


Q ss_pred             ecchhhh-hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          286 ARSQDVL-SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       286 tr~~~va-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      |...... .........+.+.+++.++-..++...+
T Consensus       231 tN~~~~l~~aL~~R~~vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          231 ANNLATIPGPLRDRMEIINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             CSSTTTSCHHHHHHEEEEECCCCCHHHHHHHHHHTH
T ss_pred             cCccccCCHHHHhhcceeeeCCCCHHHHHHHHHHHH
Confidence            6554321 1111233578999999999999888764

>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=97.67  E-value=0.00046  Score=61.76  Aligned_cols=149  Identities=16%  Similarity=0.232  Sum_probs=76.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeE
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKI  253 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~  253 (426)
                      -+.|+|++|+|||||++.++.....     ..+.+..      .++.    ... .    ......+..+++......+.
T Consensus        51 g~ll~G~~G~GKTtl~~~i~~~~~~-----~~i~~~~------~~~~----~~~-~----~~~~~~i~~~~~~~~~~~~~  110 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARAVAGEARV-----PFITASG------SDFV----EMF-V----GVGAARVRDLFETAKRHAPC  110 (254)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTC-----CEEEEEH------HHHH----HSC-T----THHHHHHHHHHHHHTTSSSE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC-----CEEEeeH------HHHH----HHH-h----hHHHHHHHHHHHHHHhcCCe
Confidence            3899999999999999999987642     1223321      1111    100 0    00111233444444334578


Q ss_pred             EEEEeCCCCcc------------C----hhhhcCCCCCC--CCCeEEEEeecchhhhh----ccCCceeeEEccCCCHHH
Q 044858          254 LIILDDIWGSL------------D----LEAIGIPLADD--NGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKE  311 (426)
Q Consensus       254 LlVlDdv~~~~------------~----~~~l~~~l~~~--~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e  311 (426)
                      ++++|+++...            .    ...+...+...  ....-++.||.......    ....-...+.++..+.++
T Consensus       111 i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~  190 (254)
T 1ixz_A          111 IVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKG  190 (254)
T ss_dssp             EEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHH
T ss_pred             EEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHH
Confidence            99999984221            0    11121112111  12233444555544321    111234578888888888


Q ss_pred             HHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          312 AWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       312 ~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      -.+++...+......++.  ....+++.+.|.-
T Consensus       191 r~~il~~~~~~~~~~~~~--~~~~la~~~~G~~  221 (254)
T 1ixz_A          191 REQILRIHARGKPLAEDV--DLALLAKRTPGFV  221 (254)
T ss_dssp             HHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCC
T ss_pred             HHHHHHHHHcCCCCCccc--CHHHHHHHcCCCC
Confidence            888887766432211111  1335666777653

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.61  E-value=6.2e-05  Score=78.70  Aligned_cols=148  Identities=16%  Similarity=0.189  Sum_probs=81.1

Q ss_pred             cccchHHHHHHHHHHhcc-------C--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          152 HFESRKSTLKGILDALSN-------R--NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~-------~--~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .++|.+..++.+...+..       +  ....+.++|++|+|||++|+.+.+.....  -...+.++.+.-.+...    
T Consensus       492 ~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~--~~~~i~i~~s~~~~~~~----  565 (758)
T 3pxi_A          492 RVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGD--EESMIRIDMSEYMEKHS----  565 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSC--TTCEEEEEGGGGCSSCC----
T ss_pred             cCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC--CcceEEEechhcccccc----
Confidence            477888888777776651       1  12268999999999999999999876321  22344555443221000    


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCC-----CC------CCCCeEEEEeecch
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPL-----AD------DNGGCKVLLTARSQ  289 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l-----~~------~~~~s~iivTtr~~  289 (426)
                                . .    ...+...+......+|+||++....  ....+...+     ..      ...+++||+||...
T Consensus       566 ----------~-~----~~~l~~~~~~~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~  630 (758)
T 3pxi_A          566 ----------T-S----GGQLTEKVRRKPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVG  630 (758)
T ss_dssp             ----------C-C-------CHHHHHHCSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSS
T ss_pred             ----------c-c----cchhhHHHHhCCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCC
Confidence                      0 0    0111222323344699999996542  122221111     10      12356788888731


Q ss_pred             h-------------hhh-ccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          290 D-------------VLS-CEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       290 ~-------------va~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      .             ... ....-...+.+.+|+.++...++...+
T Consensus       631 ~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l  675 (758)
T 3pxi_A          631 ASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMS  675 (758)
T ss_dssp             TTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHH
Confidence            1             000 011223589999999999998887654

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.58  E-value=0.0004  Score=63.71  Aligned_cols=27  Identities=26%  Similarity=0.314  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..+.++|++|+|||+||+.+++...
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~   61 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMG   61 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356788999999999999999999874

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.55  E-value=0.00015  Score=67.03  Aligned_cols=46  Identities=13%  Similarity=0.256  Sum_probs=34.9

Q ss_pred             cccchHHHHHHHHHHhcc--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALSN--RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~--~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|+...+.++.+.+..  .....|.|+|++|+|||++|+.+++...
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~   50 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSA   50 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSS
T ss_pred             CcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCc
Confidence            467777777777766542  3344578999999999999999998653

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=97.53  E-value=0.0023  Score=57.92  Aligned_cols=153  Identities=12%  Similarity=0.151  Sum_probs=81.0

Q ss_pred             CcccccchHHHHHHHHHHhc----c---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          149 DFMHFESRKSTLKGILDALS----N---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~----~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ...++.|-++.++.|.+.+.    .         .-.+-+.|+|++|+|||||++.+......     ..+.+..+.-.+
T Consensus         8 ~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~-----~~i~i~g~~l~~   82 (274)
T 2x8a_A            8 TWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGL-----NFISVKGPELLN   82 (274)
T ss_dssp             ----CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTC-----EEEEEETTTTCS
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCC-----CEEEEEcHHHHh
Confidence            45556676666666555332    0         11223899999999999999999987543     233443322111


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC---------h----hhhcCCCCC--CCCCe
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD---------L----EAIGIPLAD--DNGGC  280 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~---------~----~~l~~~l~~--~~~~s  280 (426)
                      .              .. ......+..+++......++++++|++.....         .    ..+...+..  .....
T Consensus        83 ~--------------~~-~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~  147 (274)
T 2x8a_A           83 M--------------YV-GESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQV  147 (274)
T ss_dssp             S--------------TT-HHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCSTTCE
T ss_pred             h--------------hh-hHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCE
Confidence            0              00 00011233344443334689999999964311         0    111111111  12234


Q ss_pred             EEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhC
Q 044858          281 KVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTG  321 (426)
Q Consensus       281 ~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  321 (426)
                      -++.+|....+..    ....-...+.++.-+.++-.++|+....
T Consensus       148 i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~  192 (274)
T 2x8a_A          148 FIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITK  192 (274)
T ss_dssp             EEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTT
T ss_pred             EEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHh
Confidence            4555666554431    1123356788988899999999987764

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.50  E-value=0.00094  Score=60.65  Aligned_cols=175  Identities=15%  Similarity=0.208  Sum_probs=88.7

Q ss_pred             CCcccccchHHHHHHHHHH---hcc---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILDA---LSN---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~---l~~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+..++|.+..+.++.+.   +..         .-.+-+.|+|++|+|||||++.+......     ..+.+...    
T Consensus        37 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~-----~~i~~~~~----  107 (278)
T 1iy2_A           37 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV-----PFITASGS----  107 (278)
T ss_dssp             CCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTC-----CEEEEEHH----
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCC-----CEEEecHH----
Confidence            3456677776655444333   211         11223899999999999999999987642     12333221    


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------Ch----hhhcCCCCCCC--
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------DL----EAIGIPLADDN--  277 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~~----~~l~~~l~~~~--  277 (426)
                        ++..    .. .    ......+..+++......+.++++|++....            .+    ..+...+....  
T Consensus       108 --~~~~----~~-~----~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~  176 (278)
T 1iy2_A          108 --DFVE----MF-V----GVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKD  176 (278)
T ss_dssp             --HHHH----ST-T----THHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTT
T ss_pred             --HHHH----HH-h----hHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCC
Confidence              1111    00 0    0001123344444433457899999984210            01    11211222111  


Q ss_pred             CCeEEEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          278 GGCKVLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       278 ~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      ....++.||.......    ....-...+.+...+.++-.+++...+......++.  ....++..+.|..
T Consensus       177 ~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~--~~~~la~~~~G~~  245 (278)
T 1iy2_A          177 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV--DLALLAKRTPGFV  245 (278)
T ss_dssp             CCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCC
T ss_pred             CCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCccc--CHHHHHHHcCCCC
Confidence            2233444555543321    111234578888889888888888776432211111  1335667777754

>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=97.49  E-value=0.00023  Score=74.43  Aligned_cols=45  Identities=13%  Similarity=0.260  Sum_probs=34.5

Q ss_pred             cccchHHHHHHHHHHhcc---------CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          152 HFESRKSTLKGILDALSN---------RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .++|.+..++.+...+..         .....+.++|++|+|||++|+.+.+..
T Consensus       459 ~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l  512 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            467888877777666541         122368999999999999999999876

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.45  E-value=0.0017  Score=63.92  Aligned_cols=175  Identities=15%  Similarity=0.194  Sum_probs=90.2

Q ss_pred             CCcccccchHHHHHHHHH---HhccC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILD---ALSNR---------NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~---~l~~~---------~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+.++.|.++.+.++.+   .+.+.         -++-+.|+|++|+|||+||+.++.....     ..+.++.+.-.+
T Consensus        28 ~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~-----~~i~i~g~~~~~  102 (499)
T 2dhr_A           28 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV-----PFITASGSDFVE  102 (499)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTC-----CEEEEEGGGGTS
T ss_pred             CCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCC-----CEEEEehhHHHH
Confidence            345667887766555444   33221         1234899999999999999999987642     123343322110


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------C----hhhhcCCCCC--CC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL------------D----LEAIGIPLAD--DN  277 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~------------~----~~~l~~~l~~--~~  277 (426)
                                    .... .....+..+++......++++++|+++...            .    ...+...+..  ..
T Consensus       103 --------------~~~g-~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~  167 (499)
T 2dhr_A          103 --------------MFVG-VGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKD  167 (499)
T ss_dssp             --------------SCTT-HHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSS
T ss_pred             --------------hhhh-hHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccC
Confidence                          0000 000111122222222245899999995321            0    1122111211  12


Q ss_pred             CCeEEEEeecchhhhhc-c---CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          278 GGCKVLLTARSQDVLSC-E---MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       278 ~~s~iivTtr~~~va~~-~---~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      .+..++.||........ .   ..-...+.++..+.++-.+++...+......++.  ....|++.+.|+.
T Consensus       168 ~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv--~l~~lA~~t~G~~  236 (499)
T 2dhr_A          168 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV--DLALLAKRTPGFV  236 (499)
T ss_dssp             CCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSS--TTHHHHTTSCSCC
T ss_pred             ccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHH--HHHHHHHhcCCCC
Confidence            23445556655543211 1   1223578888888888888888766432212211  1345777787765

>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=97.35  E-value=0.0012  Score=58.41  Aligned_cols=91  Identities=14%  Similarity=0.106  Sum_probs=55.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEEEecCCcCHHHHHHHHHHHhCCCcc----------ccCcH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISSRVSQTPQIKEIQREIAEKLGLKID----------QESES  237 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~----------~~~~~  237 (426)
                      -.++.|+|++|+|||||+..+........    .-..++|++....++...+. ++++.++....          ..+..
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~  102 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNTD  102 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCHH
Confidence            35899999999999999999987532211    12467888877655554443 34455554321          11111


Q ss_pred             ---HHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          238 ---VRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       238 ---~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                         .....+.+.+...+.-+||||++...
T Consensus       103 ~~~~~~~~~~~~~~~~~~~lliiD~~~~~  131 (243)
T 1n0w_A          103 HQTQLLYQASAMMVESRYALLIVDSATAL  131 (243)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETSSGG
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEeCchHH
Confidence               12233444454457889999998643

>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=97.34  E-value=0.0016  Score=59.49  Aligned_cols=85  Identities=8%  Similarity=0.040  Sum_probs=57.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHH-HHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRA-WRLLEQL  247 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~-~~l~~~l  247 (426)
                      ++-|.|++|+|||||+.++.........-..++|++....++..     .+++++.+.+.     ....+.+ ..+.+.+
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l  104 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVNQL  104 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHHHH
Confidence            68999999999999999988765532112367899888777753     36777765432     1222333 3333443


Q ss_pred             ---hcCCeEEEEEeCCCCc
Q 044858          248 ---KKETKILIILDDIWGS  263 (426)
Q Consensus       248 ---~~~k~~LlVlDdv~~~  263 (426)
                         .++++-+||+|-+...
T Consensus       105 ~~i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          105 DAIERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             HTCCTTCCEEEEEECSTTC
T ss_pred             HHhhccCceEEEEeccccc
Confidence               4567899999998644

>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=97.30  E-value=0.0029  Score=59.23  Aligned_cols=159  Identities=7%  Similarity=-0.098  Sum_probs=97.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      .-.++..++|+.|.||++.+..+.+..... .|+....+.+....++.++...+..                   .-+ -
T Consensus        16 ~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~-------------------~pl-f   74 (343)
T 1jr3_D           16 GLRAAYLLLGNDPLLLQESQDAVRQVAAAQ-GFEEHHTFSIDPNTDWNAIFSLCQA-------------------MSL-F   74 (343)
T ss_dssp             CCCSEEEEEESCHHHHHHHHHHHHHHHHHH-TCCEEEEEECCTTCCHHHHHHHHHH-------------------HHH-C
T ss_pred             CCCcEEEEECCcHHHHHHHHHHHHHHHHhC-CCCeeEEEEecCCCCHHHHHHHhcC-------------------cCC-c
Confidence            445789999999999999999998876432 2432222233334455444433211                   011 2


Q ss_pred             CCeEEEEEeCCCC-c--cChhhhcCCCCCCCCCeEEEEeecch-------hhhhccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          250 ETKILIILDDIWG-S--LDLEAIGIPLADDNGGCKVLLTARSQ-------DVLSCEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       250 ~k~~LlVlDdv~~-~--~~~~~l~~~l~~~~~~s~iivTtr~~-------~va~~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      +++-++|+|+++. .  ..++.+...+..-.+++.+|++|...       .+..........++..+++.++....+.+.
T Consensus        75 ~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~  154 (343)
T 1jr3_D           75 ASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAAR  154 (343)
T ss_dssp             CSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHH
Confidence            4567889999865 3  34454544443333477777766431       222222344578999999999999888887


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCchHHHHHH
Q 044858          320 TGDCIENGELKSVVTEVVKECAGLPIAIVPI  350 (426)
Q Consensus       320 ~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~  350 (426)
                      +...... --.+.+..|++.++|.+..+...
T Consensus       155 ~~~~g~~-i~~~a~~~l~~~~~gdl~~~~~e  184 (343)
T 1jr3_D          155 AKQLNLE-LDDAANQVLCYCYEGNLLALAQA  184 (343)
T ss_dssp             HHHTTCE-ECHHHHHHHHHSSTTCHHHHHHH
T ss_pred             HHHcCCC-CCHHHHHHHHHHhchHHHHHHHH
Confidence            6422211 12456788999999988877654

>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=97.27  E-value=0.0022  Score=55.64  Aligned_cols=85  Identities=24%  Similarity=0.174  Sum_probs=50.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCc-----------cc-cCc-HH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKI-----------DQ-ESE-SV  238 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~-----------~~-~~~-~~  238 (426)
                      -.++.|.|++|+|||||+.++..  ..   -..++|++.....+...+.. +.+.++...           .. ... ..
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~--~~---~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL--LS---GKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQRR   93 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH--HH---CSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--Hc---CCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHHH
Confidence            35899999999999999999988  21   23577887766556555443 433333210           00 111 11


Q ss_pred             HHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          239 RAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       239 ~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      .+..+ ..+...++-+||||.+...
T Consensus        94 ~~~~~-~~l~~~~~~lliiD~~~~~  117 (220)
T 2cvh_A           94 VIGSL-KKTVDSNFALVVVDSITAH  117 (220)
T ss_dssp             HHHHH-HHHCCTTEEEEEEECCCCC
T ss_pred             HHHHH-HHHhhcCCCEEEEcCcHHH
Confidence            22222 2333225789999998644

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.26  E-value=0.00068  Score=59.48  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=31.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .++.|.|++|+|||||+..+.......+  ..++|+....  +...+...
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~--~~v~~~~~~~--~~~~~~~~   69 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKGLRDG--DPCIYVTTEE--SRDSIIRQ   69 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHT--CCEEEEESSS--CHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCC--CeEEEEEccc--CHHHHHHH
Confidence            5899999999999999999986654321  2355555433  44444443

>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=97.17  E-value=0.00064  Score=62.40  Aligned_cols=69  Identities=22%  Similarity=0.224  Sum_probs=42.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe--cCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV--SQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v--~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      +++.|+|++|+|||+||.++....     -..++|++.  ....+.               -..+.......+.+.+.+.
T Consensus       124 sviLI~GpPGsGKTtLAlqlA~~~-----G~~VlyIs~~~eE~v~~---------------~~~~le~~l~~i~~~l~~~  183 (331)
T 2vhj_A          124 GMVIVTGKGNSGKTPLVHALGEAL-----GGKDKYATVRFGEPLSG---------------YNTDFNVFVDDIARAMLQH  183 (331)
T ss_dssp             EEEEEECSCSSSHHHHHHHHHHHH-----HTTSCCEEEEBSCSSTT---------------CBCCHHHHHHHHHHHHHHC
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhC-----CCCEEEEEecchhhhhh---------------hhcCHHHHHHHHHHHHhhC
Confidence            567899999999999999998761     112446666  222110               0012233344455556543


Q ss_pred             CeEEEEEeCCCCc
Q 044858          251 TKILIILDDIWGS  263 (426)
Q Consensus       251 k~~LlVlDdv~~~  263 (426)
                       + +||+|++...
T Consensus       184 -~-LLVIDsI~aL  194 (331)
T 2vhj_A          184 -R-VIVIDSLKNV  194 (331)
T ss_dssp             -S-EEEEECCTTT
T ss_pred             -C-EEEEeccccc
Confidence             4 9999999644

>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=97.16  E-value=0.0027  Score=59.55  Aligned_cols=90  Identities=18%  Similarity=0.182  Sum_probs=56.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEEEecCCcCHHHHHHHHHHHhCCCcc----------ccCc-
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISSRVSQTPQIKEIQREIAEKLGLKID----------QESE-  236 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~----------~~~~-  236 (426)
                      -.++.|+|++|+||||||.++........    .-..++|++....++...+. +++..++....          ..+. 
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g~~~~~~l~~l~~~~~~~~e  200 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFNVDHDAVLDNVLYARAYTSE  200 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcCCCHHHHHhceeEeecCCHH
Confidence            36899999999999999999987643211    12468899888877766654 34455554321          0111 


Q ss_pred             --HHHHHHHHHHHhc--CCeEEEEEeCCCC
Q 044858          237 --SVRAWRLLEQLKK--ETKILIILDDIWG  262 (426)
Q Consensus       237 --~~~~~~l~~~l~~--~k~~LlVlDdv~~  262 (426)
                        ...+..+...+.+  .+.-+||+|.+..
T Consensus       201 ~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          201 HQMELLDYVAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             HHHHHHHHHHHHHHHSCSSEEEEEEETSGG
T ss_pred             HHHHHHHHHHHHHHhcCCCccEEEEechHH
Confidence              1222334444444  5677999999853

>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=97.11  E-value=0.002  Score=59.84  Aligned_cols=90  Identities=24%  Similarity=0.284  Sum_probs=57.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEEEEecCCcCHHHHHHHHHHHhCCCcc---------ccCcH-
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVISSRVSQTPQIKEIQREIAEKLGLKID---------QESES-  237 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~---------~~~~~-  237 (426)
                      -.++.|+|++|+|||+|+.++.........    -..++|++....++...+. ++++.++....         ..... 
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~~~~~~~~l~~~~~~~~~  185 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLDIDNVMNNIYYIRAINTD  185 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCCHHHHhccEEEEeCCCHH
Confidence            358999999999999999999876432110    2367899888877766655 34556654321         01111 


Q ss_pred             ---HHHHHHHHHHhc-CCeEEEEEeCCCC
Q 044858          238 ---VRAWRLLEQLKK-ETKILIILDDIWG  262 (426)
Q Consensus       238 ---~~~~~l~~~l~~-~k~~LlVlDdv~~  262 (426)
                         ..+..+...+.+ .+.-+||+|.+..
T Consensus       186 ~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          186 HQIAIVDDLQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHHHHHHHHHHHHHHCTTEEEEEETTTTH
T ss_pred             HHHHHHHHHHHHHHhccCCCEEEEeCcHH
Confidence               123344445544 5678999999853

>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=97.11  E-value=0.0025  Score=59.73  Aligned_cols=85  Identities=16%  Similarity=0.149  Sum_probs=53.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc------cCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ------ESESVRAWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~------~~~~~~~~~l~~  245 (426)
                      -.++.|.|++|+|||||+.++.......  -..++|++....++..     .++.++...+.      .+....+..+..
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~--gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~~  133 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKM--GGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVDE  133 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHHH
Confidence            3689999999999999999999876542  2346788777666643     45556554321      112222223333


Q ss_pred             HHhcCCeEEEEEeCCCCc
Q 044858          246 QLKKETKILIILDDIWGS  263 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~~~  263 (426)
                      .+...+.-++|+|.+...
T Consensus       134 l~~~~~~dlvVIDSi~~l  151 (356)
T 3hr8_A          134 LVRSGVVDLIVVDSVAAL  151 (356)
T ss_dssp             HHHTSCCSEEEEECTTTC
T ss_pred             HhhhcCCCeEEehHhhhh
Confidence            333355669999998543

>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=97.09  E-value=0.00058  Score=72.24  Aligned_cols=46  Identities=20%  Similarity=0.322  Sum_probs=35.6

Q ss_pred             cccchHHHHHHHHHHhcc-------C--CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALSN-------R--NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~-------~--~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|.+..+..+...+..       +  ....+.|+|++|+|||++|+.+.+...
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~  613 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF  613 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc
Confidence            468888877777666541       1  124789999999999999999998764

>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=97.05  E-value=0.0028  Score=58.87  Aligned_cols=89  Identities=17%  Similarity=0.224  Sum_probs=56.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc------------Ccc--ceEEEEEecCCcCHHHHHHHHHHHhCCCcc-----
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN------------NLF--EKVISSRVSQTPQIKEIQREIAEKLGLKID-----  232 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~------------~~f--~~~~wv~v~~~~~~~~il~~i~~~l~~~~~-----  232 (426)
                      -.++.|.|++|+|||+||.++.......            +..  ..++|++....++...+.. +++.++.+..     
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~  176 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLDN  176 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhcC
Confidence            3689999999999999999998753211            101  4678998888777776654 4455654321     


Q ss_pred             ----ccCcH----HHHHHHHHHHhc-CCeEEEEEeCCC
Q 044858          233 ----QESES----VRAWRLLEQLKK-ETKILIILDDIW  261 (426)
Q Consensus       233 ----~~~~~----~~~~~l~~~l~~-~k~~LlVlDdv~  261 (426)
                          .....    ..+..+...+.+ .+.-+||+|.+.
T Consensus       177 l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          177 TFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             EEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             EEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence                11111    123344455554 556799999985

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=97.01  E-value=0.003  Score=60.30  Aligned_cols=89  Identities=16%  Similarity=0.160  Sum_probs=54.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc----CccceEEEEEecCCcCHHHHHHHHHHHhCCCcc---------ccCc---
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN----NLFEKVISSRVSQTPQIKEIQREIAEKLGLKID---------QESE---  236 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~---------~~~~---  236 (426)
                      .++.|+|++|+|||||+.+++-.....    ..-..++|++....++...+ ..+++.++....         ....   
T Consensus       179 ei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl~~~~vleni~~~~~~~~~~  257 (400)
T 3lda_A          179 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGLDPDDALNNVAYARAYNADH  257 (400)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSHHH
T ss_pred             cEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCCChHhHhhcEEEeccCChHH
Confidence            589999999999999999876432211    12345788887766665543 346666664321         0111   


Q ss_pred             -HHHHHHHHHHHhcCCeEEEEEeCCCC
Q 044858          237 -SVRAWRLLEQLKKETKILIILDDIWG  262 (426)
Q Consensus       237 -~~~~~~l~~~l~~~k~~LlVlDdv~~  262 (426)
                       ......+...+...+.-+||+|.+..
T Consensus       258 ~~~~l~~~~~~l~~~~~~llVIDs~t~  284 (400)
T 3lda_A          258 QLRLLDAAAQMMSESRFSLIVVDSVMA  284 (400)
T ss_dssp             HHHHHHHHHHHHHHSCEEEEEEETGGG
T ss_pred             HHHHHHHHHHHHHhcCCceEEecchhh
Confidence             12233444445455788999999743

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.97  E-value=0.0012  Score=53.90  Aligned_cols=39  Identities=26%  Similarity=0.240  Sum_probs=29.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      ....+.|+|+.|+|||||++.++......+ + ..+++...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g-~-~~~~~~~~   73 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEAG-K-NAAYIDAA   73 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTTT-C-CEEEEETT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhcC-C-cEEEEcHH
Confidence            456899999999999999999998775421 2 24555544

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.96  E-value=0.0013  Score=60.77  Aligned_cols=53  Identities=21%  Similarity=0.312  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHhccC---CccEEEEEcCCCCcHHHHHHHHHHHhh-hcCccceEEEEEe
Q 044858          156 RKSTLKGILDALSNR---NFNMIGVYGMGGIGKTTLVKEVGRQAK-ENNLFEKVISSRV  210 (426)
Q Consensus       156 R~~~~~~l~~~l~~~---~~~vi~I~G~~GiGKTtLa~~v~~~~~-~~~~f~~~~wv~v  210 (426)
                      +...+..+.+++...   ....+.|+|++|+|||+||..+++... ..+ + .+.++++
T Consensus       133 ~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g-~-~v~~~~~  189 (308)
T 2qgz_A          133 RMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKG-V-STTLLHF  189 (308)
T ss_dssp             HHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSC-C-CEEEEEH
T ss_pred             HHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhcC-C-cEEEEEH
Confidence            344445555555431   246788999999999999999999876 432 2 3445544

>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=96.93  E-value=0.0039  Score=58.45  Aligned_cols=84  Identities=20%  Similarity=0.244  Sum_probs=53.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~~~l~~~  246 (426)
                      -.++.|.|++|+||||||.++.......  -..++|++....++..     .++.++...+.     ....+....+.+.
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~~~--g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~~  133 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQAA--GGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIADM  133 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            3689999999999999999998765432  2357888887766643     24556544321     1122222233333


Q ss_pred             H-hcCCeEEEEEeCCCC
Q 044858          247 L-KKETKILIILDDIWG  262 (426)
Q Consensus       247 l-~~~k~~LlVlDdv~~  262 (426)
                      + ...+.-+||+|.+..
T Consensus       134 l~~~~~~~lIVIDsl~~  150 (349)
T 2zr9_A          134 LVRSGALDIIVIDSVAA  150 (349)
T ss_dssp             HHTTTCCSEEEEECGGG
T ss_pred             HHhcCCCCEEEEcChHh
Confidence            3 334567999999854

>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=96.93  E-value=0.00097  Score=69.10  Aligned_cols=173  Identities=12%  Similarity=0.160  Sum_probs=81.5

Q ss_pred             CcccccchHHHHHHHHHHhc-------------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          149 DFMHFESRKSTLKGILDALS-------------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~-------------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ....+.|-++.+++|.+.+.             -..++-+.++|++|+|||.||+.+.+.....       ++.++    
T Consensus       475 ~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~-------f~~v~----  543 (806)
T 3cf2_A          475 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN-------FISIK----  543 (806)
T ss_dssp             CSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCE-------EEECC----
T ss_pred             CHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCc-------eEEec----
Confidence            34455666766666655443             1124457899999999999999999887642       23332    


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------C--------hhhhcCCCC--CCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--------D--------LEAIGIPLA--DDN  277 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--------~--------~~~l~~~l~--~~~  277 (426)
                      ..+++    .    .+-.. ....+..+++......+++|+||+++...        .        ...+...+.  ...
T Consensus       544 ~~~l~----s----~~vGe-se~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~  614 (806)
T 3cf2_A          544 GPELL----T----MWFGE-SEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK  614 (806)
T ss_dssp             HHHHH----T----TTCSS-CHHHHHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSS
T ss_pred             cchhh----c----cccch-HHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCC
Confidence            12221    1    11112 23456677777766789999999986431        0        111111111  112


Q ss_pred             CCeEEEEeecchhhh----hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCc
Q 044858          278 GGCKVLLTARSQDVL----SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGL  343 (426)
Q Consensus       278 ~~s~iivTtr~~~va----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~Gl  343 (426)
                      .+.-||-||......    .+...-...+.+..-+.++-.++|+..+......++.  -...|++.+.|+
T Consensus       615 ~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~--dl~~la~~t~g~  682 (806)
T 3cf2_A          615 KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV--DLEFLAKMTNGF  682 (806)
T ss_dssp             SSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC---------------
T ss_pred             CCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCC--CHHHHHHhCCCC
Confidence            233344455443321    1112334567776666666677777666433222221  124455666654

>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=96.90  E-value=0.0045  Score=56.66  Aligned_cols=87  Identities=16%  Similarity=0.100  Sum_probs=47.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKK  249 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  249 (426)
                      +..+++|+|++|+||||++..+.......... .+..+.... .....+.+....+..+.+.........+...+..+ .
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~-~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~~~~~l~~al~~~-~  181 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHK-KIAFITTDTYRIAAVEQLKTYAELLQAPLEVCYTKEEFQQAKELF-S  181 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCC-CEEEEECCCSSTTHHHHHHHHHTTTTCCCCBCSSHHHHHHHHHHG-G
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCC-EEEEEecCcccchHHHHHHHHHHhcCCCeEecCCHHHHHHHHHHh-c
Confidence            45799999999999999999998876642212 344444332 22333444444444444332222222233333333 2


Q ss_pred             CCeEEEEEeCC
Q 044858          250 ETKILIILDDI  260 (426)
Q Consensus       250 ~k~~LlVlDdv  260 (426)
                       +.=++++|-.
T Consensus       182 -~~dlvIiDT~  191 (296)
T 2px0_A          182 -EYDHVFVDTA  191 (296)
T ss_dssp             -GSSEEEEECC
T ss_pred             -CCCEEEEeCC
Confidence             3457888943

>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=96.86  E-value=0.0055  Score=57.75  Aligned_cols=84  Identities=20%  Similarity=0.247  Sum_probs=53.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~~~l~~~  246 (426)
                      -.++.|.|++|+||||||.++.......  -..++|++....++..     .++.++.+.+.     ....+.+....+.
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~--g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~~  146 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKA--GGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMEL  146 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHC--CCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHHH
Confidence            3578999999999999999988776433  2367899888766643     24555544321     1122222233333


Q ss_pred             H-hcCCeEEEEEeCCCC
Q 044858          247 L-KKETKILIILDDIWG  262 (426)
Q Consensus       247 l-~~~k~~LlVlDdv~~  262 (426)
                      + .....-+||+|.+..
T Consensus       147 l~~~~~~~lVVIDsl~~  163 (366)
T 1xp8_A          147 LVRSGAIDVVVVDSVAA  163 (366)
T ss_dssp             HHTTTCCSEEEEECTTT
T ss_pred             HHhcCCCCEEEEeChHH
Confidence            3 334556999999853

>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=96.78  E-value=0.0087  Score=52.19  Aligned_cols=89  Identities=25%  Similarity=0.296  Sum_probs=51.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc---C-ccceEEEEEecCCcCHHHHHHHHHHHhCCCcc---------cc-C---
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN---N-LFEKVISSRVSQTPQIKEIQREIAEKLGLKID---------QE-S---  235 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~---~-~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~---------~~-~---  235 (426)
                      .+++|+|+.|+|||||++.+.......   . .-...+|+.......... +..+.+..+....         .. .   
T Consensus        26 ~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (231)
T 4a74_A           26 AITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRGLDPDEVLKHIYVARAFNSNH  104 (231)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH-HHHHHHHTTSCHHHHHHTEEEEECCSHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH-HHHHHHHcCCCHHHHhhcEEEEecCChHH
Confidence            589999999999999999998743321   1 123467776655444333 3334444433211         00 1   


Q ss_pred             cHHHHHHHHHHHh-----cCCeEEEEEeCCCC
Q 044858          236 ESVRAWRLLEQLK-----KETKILIILDDIWG  262 (426)
Q Consensus       236 ~~~~~~~l~~~l~-----~~k~~LlVlDdv~~  262 (426)
                      .......+...+.     ..++-++|+|....
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~  136 (231)
T 4a74_A          105 QMLLVQQAEDKIKELLNTDRPVKLLIVDSLTS  136 (231)
T ss_dssp             HHHHHHHHHHHHHHHTTSSSCEEEEEEETSSH
T ss_pred             HHHHHHHHHHHHHHhcccCCceeEEEECChHH
Confidence            1111233344443     45788999999854

>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=96.77  E-value=0.006  Score=57.31  Aligned_cols=83  Identities=23%  Similarity=0.286  Sum_probs=52.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~~~l~~~  246 (426)
                      -.++.|.|++|+||||||.++.......  -..++|++....++..     .+..++...+.     .........+.+.
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~~~~~--g~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~~  135 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDA  135 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHHH
Confidence            3689999999999999999998776543  2357888887776643     24555544321     1122223333333


Q ss_pred             H-hcCCeEEEEEeCCC
Q 044858          247 L-KKETKILIILDDIW  261 (426)
Q Consensus       247 l-~~~k~~LlVlDdv~  261 (426)
                      + ...+.-+||+|.+.
T Consensus       136 l~~~~~~~lVVIDsl~  151 (356)
T 1u94_A          136 LARSGAVDVIVVDSVA  151 (356)
T ss_dssp             HHHHTCCSEEEEECGG
T ss_pred             HHhccCCCEEEEcCHH
Confidence            3 23455699999974

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.70  E-value=0.0019  Score=55.52  Aligned_cols=43  Identities=19%  Similarity=0.341  Sum_probs=33.4

Q ss_pred             hHHHHHHHHHHhcc---CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          156 RKSTLKGILDALSN---RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       156 R~~~~~~l~~~l~~---~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      |++.++.+.+.+..   ....+|+|.|+.|+||||+++.+......
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~~   48 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            55666777776653   34578999999999999999999876543

>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=96.67  E-value=0.0051  Score=59.45  Aligned_cols=88  Identities=18%  Similarity=0.328  Sum_probs=52.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCC-------CccccCcHH------
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGL-------KIDQESESV------  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~-------~~~~~~~~~------  238 (426)
                      +.+.|+|.+|+|||||+..+......+. .+..+++.+++.. ...++..++...-..       ..-.++...      
T Consensus       152 q~~~i~G~sGvGKTtL~~~l~~~~~~~~-~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~~  230 (473)
T 1sky_E          152 GKIGLFGGAGVGKTVLIQELIHNIAQEH-GGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVAL  230 (473)
T ss_dssp             CEEEEECCSSSCHHHHHHHHHHHHHHHT-CCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEECCCCCCccHHHHHHHhhhhhcc-CcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHHH
Confidence            3588999999999999999988765432 2344666666554 455565555432100       000111110      


Q ss_pred             HHHHHHHHHh--cCCeEEEEEeCCC
Q 044858          239 RAWRLLEQLK--KETKILIILDDIW  261 (426)
Q Consensus       239 ~~~~l~~~l~--~~k~~LlVlDdv~  261 (426)
                      ....+.+++.  ++++.||++||+.
T Consensus       231 ~~ltiAEyFrd~~G~~VLl~~D~it  255 (473)
T 1sky_E          231 TGLTMAEYFRDEQGQDGLLFIDNIF  255 (473)
T ss_dssp             HHHHHHHHHHHHSCCEEEEEEECTH
T ss_pred             HHHHHHHHHHHhcCCcEEEEeccHH
Confidence            1113344443  4899999999994

>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=96.61  E-value=0.0023  Score=60.04  Aligned_cols=99  Identities=19%  Similarity=0.219  Sum_probs=51.7

Q ss_pred             HHHHHhcc-CCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEEEEecCCcC-HHHHHHHHHHHhCCCccccCcHH
Q 044858          162 GILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQTPQ-IKEIQREIAEKLGLKIDQESESV  238 (426)
Q Consensus       162 ~l~~~l~~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~-~~~il~~i~~~l~~~~~~~~~~~  238 (426)
                      .+++.+.. .+-..++|+|++|+|||||++.+.+....+ ..+. ++++-+++... +.++.+.+-..+-......+...
T Consensus       163 raID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~-~I~~lIGER~~Ev~~~~~~~~~~vV~atadep~~~  241 (422)
T 3ice_A          163 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCV-LMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASR  241 (422)
T ss_dssp             HHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSE-EEEEEESSCHHHHHHHHTTCSSEEEEECTTSCHHH
T ss_pred             eeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCee-EEEEEecCChHHHHHHHHHhCeEEEEeCCCCCHHH
Confidence            34444431 234579999999999999999988765432 1233 34566665542 33332222000000111111111


Q ss_pred             H------HHHHHHHH-hcCCeEEEEEeCCC
Q 044858          239 R------AWRLLEQL-KKETKILIILDDIW  261 (426)
Q Consensus       239 ~------~~~l~~~l-~~~k~~LlVlDdv~  261 (426)
                      .      .-..-+++ .+++.+||++||+.
T Consensus       242 r~~~a~~alt~AEyfrd~G~dVLil~DslT  271 (422)
T 3ice_A          242 HVQVAEMVIEKAKRLVEHKKDVIILLDSIT  271 (422)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEEeCch
Confidence            1      11122233 35899999999984

>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=96.56  E-value=0.0013  Score=61.66  Aligned_cols=51  Identities=18%  Similarity=0.221  Sum_probs=37.2

Q ss_pred             cCCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          147 TQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       147 ~~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+..++|.+..+..+......+...-+.|+|++|+|||+||+.+.+...
T Consensus        20 ~~~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           20 VFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CCCchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhCc
Confidence            345667889888666554444333334488999999999999999998754

>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=96.56  E-value=0.01  Score=55.63  Aligned_cols=91  Identities=24%  Similarity=0.271  Sum_probs=52.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCcc----ceEEEEEecCCcCHHHHHHHHHHHhCCCcc---------cc-C--
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLF----EKVISSRVSQTPQIKEIQREIAEKLGLKID---------QE-S--  235 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f----~~~~wv~v~~~~~~~~il~~i~~~l~~~~~---------~~-~--  235 (426)
                      -.++.|+|+.|+|||||+.++..........    ..++|++....+....+ ..+++..+....         .. .  
T Consensus       131 G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~~  209 (349)
T 1pzn_A          131 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNSN  209 (349)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCChH
Confidence            4689999999999999999998765211001    24578877665544433 334444433211         00 0  


Q ss_pred             -cHHHHHHHHHHHhc-----CCeEEEEEeCCCCc
Q 044858          236 -ESVRAWRLLEQLKK-----ETKILIILDDIWGS  263 (426)
Q Consensus       236 -~~~~~~~l~~~l~~-----~k~~LlVlDdv~~~  263 (426)
                       ....+..+...+..     .++-+||+|.+-..
T Consensus       210 ~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          210 HQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             HHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence             11122233333332     46889999998654

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.55  E-value=0.0028  Score=54.77  Aligned_cols=41  Identities=22%  Similarity=0.400  Sum_probs=31.4

Q ss_pred             HHHHHHHHHhcc--CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          158 STLKGILDALSN--RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       158 ~~~~~l~~~l~~--~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +.+++|.+.+..  ++..+|+|+|+.|+|||||++.+......
T Consensus         6 ~~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~~   48 (208)
T 3c8u_A            6 ALCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALSA   48 (208)
T ss_dssp             HHHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            345566666553  35579999999999999999999887653

>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=96.50  E-value=0.017  Score=55.59  Aligned_cols=28  Identities=29%  Similarity=0.420  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ++.+|.++|++|+||||++..+......
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~  126 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQK  126 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHH
Confidence            4679999999999999999999877664

>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=96.50  E-value=0.002  Score=57.90  Aligned_cols=48  Identities=13%  Similarity=0.141  Sum_probs=32.9

Q ss_pred             cccccchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          150 FMHFESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..++|+...+..+.+.+.  ......+.|+|++|+|||++|+.+++...
T Consensus         5 f~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~   54 (265)
T 2bjv_A            5 KDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSS   54 (265)
T ss_dssp             -----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTST
T ss_pred             cccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcC
Confidence            4457788877777766554  12235678999999999999999998754

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.35  E-value=0.0067  Score=56.41  Aligned_cols=44  Identities=18%  Similarity=0.250  Sum_probs=36.4

Q ss_pred             cccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|++..++.+...+..+.  .+.++|++|+|||+||+.+.+...
T Consensus        28 ~i~g~~~~~~~l~~~l~~~~--~vll~G~pGtGKT~la~~la~~~~   71 (331)
T 2r44_A           28 VVVGQKYMINRLLIGICTGG--HILLEGVPGLAKTLSVNTLAKTMD   71 (331)
T ss_dssp             TCCSCHHHHHHHHHHHHHTC--CEEEESCCCHHHHHHHHHHHHHTT
T ss_pred             ceeCcHHHHHHHHHHHHcCC--eEEEECCCCCcHHHHHHHHHHHhC
Confidence            46788888888887776543  588999999999999999988664

>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=96.35  E-value=0.0023  Score=53.52  Aligned_cols=25  Identities=24%  Similarity=0.282  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|.|+|++|+||||+++.+.+...
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            5799999999999999999988754

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.31  E-value=0.027  Score=51.91  Aligned_cols=50  Identities=16%  Similarity=0.207  Sum_probs=36.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .++.|.|.+|+||||||.++......++  ..++|++..  .+..++...+...
T Consensus        69 ~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~~  118 (315)
T 3bh0_A           69 NFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIVT  118 (315)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHHH
Confidence            5799999999999999999987765433  456777654  4566666666543

>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=96.29  E-value=0.017  Score=55.98  Aligned_cols=88  Identities=22%  Similarity=0.373  Sum_probs=57.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC--------c------cccCcH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK--------I------DQESES  237 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~--------~------~~~~~~  237 (426)
                      .-++|.|.+|+|||+|+.++.+.... .+-+.++++-+.... ...++.+++...-...        .      .+++..
T Consensus       166 qr~gIfgg~GvGKT~L~~~l~~~~a~-~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtvvV~~t~d~p~~  244 (498)
T 1fx0_B          166 GKIGLFGGAGVGKTVLIMELINNIAK-AHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPG  244 (498)
T ss_dssp             CCEEEEECSSSSHHHHHHHHHHHTTT-TCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEEEEEECTTSCHH
T ss_pred             CeEEeecCCCCCchHHHHHHHHHHHh-hCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceEEEEeCCCCCHH
Confidence            45899999999999999999887543 234677788777654 5667777776542221        0      011111


Q ss_pred             ------HHHHHHHHHHhc--CCeEEEEEeCCC
Q 044858          238 ------VRAWRLLEQLKK--ETKILIILDDIW  261 (426)
Q Consensus       238 ------~~~~~l~~~l~~--~k~~LlVlDdv~  261 (426)
                            .....+-+++..  ++.+||++||+-
T Consensus       245 ~R~~~~~~altiAEyfrd~~G~dVLl~~Dsit  276 (498)
T 1fx0_B          245 ARMRVGLTALTMAEYFRDVNEQDVLLFIDNIF  276 (498)
T ss_dssp             HHTTHHHHHHHTHHHHTTTSCCEEEEEEECSH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                  122344455543  899999999984

>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=96.29  E-value=0.027  Score=54.11  Aligned_cols=29  Identities=28%  Similarity=0.231  Sum_probs=25.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ++.+|.++|++|+||||++..+.......
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~  124 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKR  124 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            46799999999999999999998777653

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.28  E-value=0.024  Score=54.68  Aligned_cols=29  Identities=31%  Similarity=0.455  Sum_probs=25.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ++++|.++|.+|+||||++..+......+
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~  127 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREK  127 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            46799999999999999999998877653

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.27  E-value=0.021  Score=52.68  Aligned_cols=27  Identities=22%  Similarity=0.271  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.+|+|.|+.|+|||||++.+.....
T Consensus        91 ~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           91 VPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            456899999999999999999877654

>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=96.26  E-value=0.0026  Score=52.80  Aligned_cols=25  Identities=20%  Similarity=0.220  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|.|.|+.|+||||+++.+.....
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4789999999999999999987754

>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=96.25  E-value=0.025  Score=54.55  Aligned_cols=88  Identities=19%  Similarity=0.341  Sum_probs=56.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------------ccccCcH-
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------------IDQESES-  237 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------------~~~~~~~-  237 (426)
                      .-++|.|.+|+|||+|+.++.+.... .+-+.++++-+.+.. ...++.+++...-...             ...++.. 
T Consensus       154 Qr~~Ifgg~G~GKT~L~~~i~~~~~~-~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~~~~rtvvV~~t~d~p~~~  232 (482)
T 2ck3_D          154 GKIGLFGGAGVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGA  232 (482)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTTT-TCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHH
T ss_pred             CeeeeecCCCCChHHHHHHHHHhhHh-hCCCEEEEEECCCcchHHHHHHHHhhhccccccccCCceEEEEEECCCCCHHH
Confidence            56899999999999999999887543 234566777777654 5667777776653221             0011111 


Q ss_pred             -----HHHHHHHHHHh--cCCeEEEEEeCCC
Q 044858          238 -----VRAWRLLEQLK--KETKILIILDDIW  261 (426)
Q Consensus       238 -----~~~~~l~~~l~--~~k~~LlVlDdv~  261 (426)
                           .....+-+++.  +++.+||++||+-
T Consensus       233 r~~~~~~a~tiAEyfrd~~G~dVLll~Dsit  263 (482)
T 2ck3_D          233 RARVALTGLTVAEYFRDQEGQDVLLFIDNIF  263 (482)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSCEEEEEECTH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                 11223444454  4899999999984

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.22  E-value=0.02  Score=50.42  Aligned_cols=46  Identities=17%  Similarity=0.175  Sum_probs=31.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .++.|.|++|+|||||+.++.......  -..++|++...  +..++...
T Consensus        24 ~~~~i~G~~GsGKTtl~~~~~~~~~~~--~~~v~~~~~e~--~~~~~~~~   69 (247)
T 2dr3_A           24 NVVLLSGGPGTGKTIFSQQFLWNGLKM--GEPGIYVALEE--HPVQVRQN   69 (247)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHHT--TCCEEEEESSS--CHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccC--CHHHHHHH
Confidence            589999999999999999887665432  23466776544  34444433

>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=96.21  E-value=0.0024  Score=53.03  Aligned_cols=20  Identities=35%  Similarity=0.547  Sum_probs=18.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEV  192 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v  192 (426)
                      .+|.|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            47899999999999999999

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.16  E-value=0.003  Score=52.83  Aligned_cols=22  Identities=32%  Similarity=0.389  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+|.|.|++|+||||+|+.+..
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

>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=96.15  E-value=0.026  Score=51.77  Aligned_cols=88  Identities=19%  Similarity=0.210  Sum_probs=47.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH--HHHHHHHHHHhCCCccc---cCcH-HH-HHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI--KEIQREIAEKLGLKIDQ---ESES-VR-AWRL  243 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~--~~il~~i~~~l~~~~~~---~~~~-~~-~~~l  243 (426)
                      ...+|.|+|++|+||||++..+.......+  ..+..+... .+..  .+-+...++..+.+.-.   ..+. .. ...+
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g--~kV~lv~~D-~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~al  179 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEG--KSVVLAAAD-TFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAV  179 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEEC-TTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhcC--CEEEEEccc-cccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHH
Confidence            457999999999999999999998776431  234444432 2222  22233445555543211   1111 11 1223


Q ss_pred             HHHHhcCCeEEEEEeCCCC
Q 044858          244 LEQLKKETKILIILDDIWG  262 (426)
Q Consensus       244 ~~~l~~~k~~LlVlDdv~~  262 (426)
                      ...+.. +.-++++|..-.
T Consensus       180 ~~a~~~-~~dvvIiDtpg~  197 (306)
T 1vma_A          180 AHALAR-NKDVVIIDTAGR  197 (306)
T ss_dssp             HHHHHT-TCSEEEEEECCC
T ss_pred             HHHHhc-CCCEEEEECCCc
Confidence            333433 344888897643

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.15  E-value=0.0035  Score=53.68  Aligned_cols=26  Identities=38%  Similarity=0.388  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|.|+|+.|+||||+++.+.....
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999997763

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=96.13  E-value=0.0058  Score=53.26  Aligned_cols=38  Identities=21%  Similarity=0.211  Sum_probs=29.0

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.+...+.......|+|+|.+|+|||||+..+.....
T Consensus        26 a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           26 ADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             HHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            34444444455678899999999999999999987753

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.10  E-value=0.0033  Score=52.92  Aligned_cols=25  Identities=12%  Similarity=0.315  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|+|+.|+|||||++.+.....
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5899999999999999999987653

>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=96.10  E-value=0.0034  Score=53.18  Aligned_cols=24  Identities=25%  Similarity=0.373  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..+++|+|+.|+|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999875

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.07  E-value=0.0044  Score=60.97  Aligned_cols=44  Identities=16%  Similarity=0.162  Sum_probs=36.1

Q ss_pred             cccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          152 HFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|+++.++.+...+..+  .-+.++|++|+|||+||+.+.+...
T Consensus        23 ~ivGq~~~i~~l~~al~~~--~~VLL~GpPGtGKT~LAraLa~~l~   66 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSG--ESVFLLGPPGIAKSLIARRLKFAFQ   66 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHT--CEEEEECCSSSSHHHHHHHGGGGBS
T ss_pred             hhHHHHHHHHHHHHHHhcC--CeeEeecCchHHHHHHHHHHHHHHh
Confidence            3678888888887776654  3588999999999999999998764

>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=96.06  E-value=0.0042  Score=53.20  Aligned_cols=28  Identities=29%  Similarity=0.329  Sum_probs=24.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..+|+|+|+.|+|||||++.+.....
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4567999999999999999999988765

>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=96.05  E-value=0.0043  Score=52.58  Aligned_cols=26  Identities=31%  Similarity=0.296  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...+|.|.|++|+||||+++.+....
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            34689999999999999999998765

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.04  E-value=0.0041  Score=52.39  Aligned_cols=26  Identities=27%  Similarity=0.442  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.|.|+|+.|+||||+++.+.....
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999987653

>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=96.03  E-value=0.058  Score=49.91  Aligned_cols=58  Identities=24%  Similarity=0.330  Sum_probs=36.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec-CCcCHHHHHHHHHHHhCC
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS-QTPQIKEIQREIAEKLGL  229 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~il~~i~~~l~~  229 (426)
                      ++..+++|+|+.|+||||+++.+........ . .+.+.... ......+-+....+.++.
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l~~~~-g-~V~l~g~D~~r~~a~eql~~~~~~~gv  185 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWLKNHG-F-SVVIAASDTFRAGAIEQLEEHAKRIGV  185 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHHHHTT-C-CEEEEEECCSSTTHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhcC-C-EEEEEeecccccchHHHHHHHHHHcCc
Confidence            4567999999999999999999988766432 2 23333322 122334444555555553

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.03  E-value=0.0034  Score=52.24  Aligned_cols=25  Identities=28%  Similarity=0.373  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|+|+|+.|+|||||++.+.....
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            5799999999999999999987654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.00  E-value=0.0042  Score=53.23  Aligned_cols=25  Identities=24%  Similarity=0.392  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+|.|.|+.|+||||+|+.+....
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            4689999999999999999998775

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.00  E-value=0.0045  Score=53.00  Aligned_cols=27  Identities=30%  Similarity=0.447  Sum_probs=23.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ....+|+|+|+.|+|||||++.+....
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

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.99  E-value=0.073  Score=52.22  Aligned_cols=28  Identities=29%  Similarity=0.354  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ++.+|+|+|.+|+||||++..+......
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~  127 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQR  127 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4568999999999999999999876654

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=95.98  E-value=0.0073  Score=55.02  Aligned_cols=81  Identities=12%  Similarity=0.017  Sum_probs=44.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-ccceEEEEEecCCcCHHHHHHHHHHHh------CC-CccccCcHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENN-LFEKVISSRVSQTPQIKEIQREIAEKL------GL-KIDQESESVRAW  241 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~-~f~~~~wv~v~~~~~~~~il~~i~~~l------~~-~~~~~~~~~~~~  241 (426)
                      +++.+|+|+|+.|+|||||++.+........ .......|+...-.-.......+....      .. ..+...+...+.
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l~~~g~~~~~~~iv~~D~f~~~~~~~~~l~~~~~~~~l~~~~g~p~a~d~~~l~  108 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLLQ  108 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhhhcCCCCceEEEeccccccCChHHHHHHhccccccchhhhccCcchhHHHHHH
Confidence            4567899999999999999999987765421 122333334443333334444443221      00 012233445555


Q ss_pred             HHHHHHhcC
Q 044858          242 RLLEQLKKE  250 (426)
Q Consensus       242 ~l~~~l~~~  250 (426)
                      ..+..+..+
T Consensus       109 ~~l~~l~~g  117 (290)
T 1odf_A          109 EVLNTIFNN  117 (290)
T ss_dssp             HHHHHHTC-
T ss_pred             HHHHHhhcc
Confidence            666666544

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.97  E-value=0.0046  Score=53.37  Aligned_cols=27  Identities=26%  Similarity=0.314  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+|+|+|+.|+|||||++.+.....
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            456899999999999999999987654

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.94  E-value=0.0046  Score=52.28  Aligned_cols=26  Identities=27%  Similarity=0.414  Sum_probs=23.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+|.|.|+.|+||||+++.+.+....
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            46899999999999999999987653

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=95.92  E-value=0.005  Score=52.01  Aligned_cols=25  Identities=24%  Similarity=0.345  Sum_probs=22.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|.|.|++|+||||+++.+.....
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5799999999999999999998765

>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=95.90  E-value=0.0047  Score=51.82  Aligned_cols=26  Identities=38%  Similarity=0.493  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|.|+|++|+||||+++.+.+...
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~   36 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSG   36 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999987653

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.89  E-value=0.015  Score=65.73  Aligned_cols=95  Identities=21%  Similarity=0.142  Sum_probs=59.6

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc------
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ------  233 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~------  233 (426)
                      ++.++.+..=...+++.|+|++|+|||+||.++.......  =..++|+++...++...     ++.++.+.+.      
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~--G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~ 1487 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQP 1487 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTT--TCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECC
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEEcccccCHHH-----HHHcCCCchhceeecC
Confidence            5555441111245789999999999999999998765533  33577888877766555     4455533211      


Q ss_pred             cCcHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          234 ESESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       234 ~~~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                      .+.......+.+...+.+..+||+|.+.
T Consensus      1488 ~~~E~~l~~~~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1488 DTGEQALEICDALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             SSHHHHHHHHHHHHHHTCCSEEEESCGG
T ss_pred             ChHHHHHHHHHHHHhcCCCCEEEEcChh
Confidence            1122333333444455678899999984

>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=95.87  E-value=0.022  Score=52.41  Aligned_cols=29  Identities=24%  Similarity=0.239  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+..+|+|.|+.|+|||||++.+..-...
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~~  116 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLAR  116 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhccc
Confidence            34568999999999999999999887654

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.87  E-value=0.0054  Score=52.52  Aligned_cols=25  Identities=28%  Similarity=0.401  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+++|+|+.|+|||||++.+....
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

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.87  E-value=0.0064  Score=52.77  Aligned_cols=39  Identities=21%  Similarity=0.218  Sum_probs=29.4

Q ss_pred             HHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          159 TLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       159 ~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+.+...+...+.++|+|+|.+|+|||||+..+.....
T Consensus        17 ~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           17 LAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             HHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            344444444445678999999999999999999987753

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=95.86  E-value=0.0048  Score=53.78  Aligned_cols=108  Identities=16%  Similarity=0.082  Sum_probs=58.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHh---
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLK---  248 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~---  248 (426)
                      -.++.|+|+.|+||||++..+..+....+ . .++.+......  . -...++..++...+.... .....+.+.+.   
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g-~-kVli~~~~~d~--r-~~~~i~srlG~~~~~~~~-~~~~~i~~~i~~~~   85 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYAD-V-KYLVFKPKIDT--R-SIRNIQSRTGTSLPSVEV-ESAPEILNYIMSNS   85 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTT-C-CEEEEEECCCG--G-GCSSCCCCCCCSSCCEEE-SSTHHHHHHHHSTT
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcC-C-EEEEEEeccCc--h-HHHHHHHhcCCCcccccc-CCHHHHHHHHHHHh
Confidence            46889999999999999999988876532 2 23333322211  1 112344445543322110 01122333333   


Q ss_pred             -cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecc
Q 044858          249 -KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARS  288 (426)
Q Consensus       249 -~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~  288 (426)
                       .++.-+|++|.+...  +..+.+. .+.+  .|..||+|.+.
T Consensus        86 ~~~~~dvViIDEaQ~l~~~~ve~l~-~L~~--~gi~Vil~Gl~  125 (223)
T 2b8t_A           86 FNDETKVIGIDEVQFFDDRICEVAN-ILAE--NGFVVIISGLD  125 (223)
T ss_dssp             SCTTCCEEEECSGGGSCTHHHHHHH-HHHH--TTCEEEEECCS
T ss_pred             hCCCCCEEEEecCccCcHHHHHHHH-HHHh--CCCeEEEEecc
Confidence             234459999999743  2222221 1111  26789999884

>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=95.86  E-value=0.013  Score=49.73  Aligned_cols=117  Identities=17%  Similarity=0.123  Sum_probs=61.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec---CCcCHHHHHHHHH---HHhCC--CccccC---c----H
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS---QTPQIKEIQREIA---EKLGL--KIDQES---E----S  237 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~---~~~~~~~il~~i~---~~l~~--~~~~~~---~----~  237 (426)
                      ..|.|++..|.||||.|--..-+.-..+ + .+.++...   .......++..+.   .+++.  .+....   +    .
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G-~-rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~  106 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHG-K-NVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACM  106 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTT-C-CEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCC-C-eEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHH
Confidence            4677777778999999998887765432 3 33344332   2333444444431   00000  111111   1    1


Q ss_pred             HHHHHHHHHHhcCCeEEEEEeCCCC-----ccChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          238 VRAWRLLEQLKKETKILIILDDIWG-----SLDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       238 ~~~~~l~~~l~~~k~~LlVlDdv~~-----~~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                      .......+.+..++-=|||||++-.     ....+.+...+........||+|+|...-
T Consensus       107 ~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~  165 (196)
T 1g5t_A          107 AVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHR  165 (196)
T ss_dssp             HHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCH
T ss_pred             HHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcH
Confidence            1223444445445556999999832     22333333333333446789999999643

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.86  E-value=0.0062  Score=51.41  Aligned_cols=28  Identities=21%  Similarity=0.312  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...+|.|.|+.|+||||+++.+......
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            4568999999999999999999987764

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.86  E-value=0.0087  Score=54.50  Aligned_cols=26  Identities=23%  Similarity=0.215  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+.+|.|.|++|+||||+|+.+....
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            45689999999999999999998764

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.85  E-value=0.0048  Score=53.05  Aligned_cols=26  Identities=35%  Similarity=0.457  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...+|.|+|++|+|||||++.+....
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            34679999999999999999998765

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.81  E-value=0.0063  Score=51.65  Aligned_cols=27  Identities=30%  Similarity=0.295  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+|.|.|+.|+||||+++.+.+...
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l~   34 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKYG   34 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346899999999999999999987653

>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=95.79  E-value=0.005  Score=52.08  Aligned_cols=25  Identities=32%  Similarity=0.392  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.|.|+||+|+|||||++.+.....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            3588999999999999999987654

>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=95.78  E-value=0.0071  Score=50.20  Aligned_cols=28  Identities=32%  Similarity=0.305  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..+++.|+|+.|+|||||+..+......
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l~~   30 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAAVR   30 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhhHh
Confidence            4578999999999999999999987664

>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=95.78  E-value=0.0061  Score=52.05  Aligned_cols=26  Identities=27%  Similarity=0.344  Sum_probs=23.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +++.+|+|+|+.|+||||+++.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            45678999999999999999999875

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.78  E-value=0.0058  Score=52.69  Aligned_cols=27  Identities=33%  Similarity=0.406  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+|+|+|+.|+|||||++.+.....
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            446899999999999999999987654

>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=95.77  E-value=0.007  Score=50.43  Aligned_cols=25  Identities=28%  Similarity=0.509  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+|.|+|+.|+||||+++.+....
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            4689999999999999999998764

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.77  E-value=0.0061  Score=51.61  Aligned_cols=25  Identities=24%  Similarity=0.169  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +.+|.|.|+.|+||||+|+.+.+..
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            4579999999999999999998764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.75  E-value=0.0065  Score=52.06  Aligned_cols=25  Identities=28%  Similarity=0.316  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+|+|+|+.|+||||+++.+....
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

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.74  E-value=0.013  Score=54.59  Aligned_cols=42  Identities=21%  Similarity=0.296  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHhc----cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          157 KSTLKGILDALS----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       157 ~~~~~~l~~~l~----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +...+.+++.+.    .+....|.|+|+.|+||||+++.+......
T Consensus         5 ~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~~   50 (359)
T 2ga8_A            5 HKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIINE   50 (359)
T ss_dssp             HHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            444455555543    455667999999999999999999877653

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.73  E-value=0.006  Score=54.47  Aligned_cols=25  Identities=20%  Similarity=0.328  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|.|.|+.|+||||||+.+.....
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcCC
Confidence            4789999999999999999987653

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.73  E-value=0.0072  Score=51.75  Aligned_cols=26  Identities=27%  Similarity=0.318  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +..+|+|.|+.|+||||+++.+.+..
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            45789999999999999999998764

>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=95.73  E-value=0.0072  Score=50.97  Aligned_cols=25  Identities=24%  Similarity=0.300  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +...|.|+|+.|+||||+++.+.+.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999999876

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.72  E-value=0.0056  Score=51.11  Aligned_cols=25  Identities=28%  Similarity=0.454  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.|.|.|++|+||||+|+.+.....
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l~   29 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3689999999999999999987654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.68  E-value=0.0071  Score=50.06  Aligned_cols=27  Identities=30%  Similarity=0.523  Sum_probs=22.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+|.|.|+.|+||||+++.+.....
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHhC
Confidence            457899999999999999999988754

>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=95.68  E-value=0.041  Score=50.19  Aligned_cols=88  Identities=23%  Similarity=0.201  Sum_probs=50.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCCccc----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLKIDQ----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~~~~----~~~~~~~~~l~~~  246 (426)
                      ..++.++|.+|+||||++..+.......+  ..+.++..... +...+.++...+..+.+.-.    .+....+....+.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g--~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~~  175 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKG--FKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEK  175 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTT--CCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHHH
Confidence            56899999999999999999988776432  23445544322 22333344455555543211    1223333445555


Q ss_pred             HhcCCeEEEEEeCCC
Q 044858          247 LKKETKILIILDDIW  261 (426)
Q Consensus       247 l~~~k~~LlVlDdv~  261 (426)
                      +.....=++++|-.-
T Consensus       176 ~~~~~~D~ViIDTpg  190 (297)
T 1j8m_F          176 FLSEKMEIIIVDTAG  190 (297)
T ss_dssp             HHHTTCSEEEEECCC
T ss_pred             HHhCCCCEEEEeCCC
Confidence            542222378888764

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=95.68  E-value=0.012  Score=55.57  Aligned_cols=45  Identities=22%  Similarity=0.177  Sum_probs=34.3

Q ss_pred             ccchHHHHHHHHHHhc-------------c--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          153 FESRKSTLKGILDALS-------------N--RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~-------------~--~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++|.+..++.+...+.             .  .....+.++|++|+|||++|+.+++...
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~   76 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLD   76 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            5677777777766662             0  1345689999999999999999998763

>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=95.66  E-value=0.0075  Score=51.44  Aligned_cols=27  Identities=15%  Similarity=0.315  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.++|+|+|+.|+|||||++.+.....
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            446899999999999999999987653

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.65  E-value=0.007  Score=51.72  Aligned_cols=24  Identities=29%  Similarity=0.612  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|+|.|+.|+||||+++.+.+...
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            689999999999999999988764

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.65  E-value=0.0056  Score=52.39  Aligned_cols=24  Identities=29%  Similarity=0.432  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +.++|+|+.|+|||||++.+....
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            578999999999999999998754

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.65  E-value=0.0079  Score=52.21  Aligned_cols=28  Identities=25%  Similarity=0.247  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.++|.|.|++|+||||.|+.+.+...
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~~g   54 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQKFH   54 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHHHC
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            3568999999999999999999998764

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.64  E-value=0.0055  Score=51.08  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=19.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVG  193 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~  193 (426)
                      ..+++|+|+.|+|||||++.++
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHc
Confidence            4689999999999999999644

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.62  E-value=0.0079  Score=51.70  Aligned_cols=26  Identities=19%  Similarity=0.263  Sum_probs=23.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+|.|.|+.|+||||+++.+.+....
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~   30 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIEL   30 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            57999999999999999999987654

>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=95.61  E-value=0.0081  Score=50.46  Aligned_cols=24  Identities=42%  Similarity=0.529  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|+|+.|+|||||++.+.....
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            578999999999999999987764

>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=95.61  E-value=0.007  Score=51.19  Aligned_cols=22  Identities=27%  Similarity=0.483  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+++|+|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999975

>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=95.61  E-value=0.0062  Score=51.25  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++|.|.|++|+||||+|+.+.....
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcC
Confidence            4689999999999999999988654

>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=95.61  E-value=0.0075  Score=52.58  Aligned_cols=24  Identities=33%  Similarity=0.470  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+|+|+|+.|+||||+++.+....
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            579999999999999999998754

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.60  E-value=0.0077  Score=51.22  Aligned_cols=26  Identities=23%  Similarity=0.247  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|.|.|+.|+||||+|+.+.+...
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            36899999999999999999988654

>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=95.59  E-value=0.0089  Score=51.11  Aligned_cols=27  Identities=19%  Similarity=0.210  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+|.|.|+.|+||||+|+.+.....
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            345899999999999999999987653

>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=95.59  E-value=0.008  Score=53.32  Aligned_cols=27  Identities=19%  Similarity=0.271  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++.+|+|+|+.|+|||||++.+.+...
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~lg   52 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQNFG   52 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            357899999999999999999996653

>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=95.58  E-value=0.048  Score=49.70  Aligned_cols=88  Identities=24%  Similarity=0.300  Sum_probs=48.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCCccc----cCcHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLKIDQ----ESESVRAWRLLE  245 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~~~~----~~~~~~~~~l~~  245 (426)
                      ...+++|+|.+|+||||++..++......+  ..+.++...... ....-+.......+.+.-.    .+........+.
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~--~~v~l~~~d~~~~~~~~ql~~~~~~~~l~~~~~~~~~~p~~l~~~~l~  174 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEE  174 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTT--CCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEecCCcccHhHHHHHHHhcccCCeEEEEcCCCCCHHHHHHHHHH
Confidence            346899999999999999999998776432  234444432211 1112233444555543221    122233333444


Q ss_pred             HHhcCCeEEEEEeCC
Q 044858          246 QLKKETKILIILDDI  260 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv  260 (426)
                      .+...+.=++++|-.
T Consensus       175 ~~~~~~~D~viiDtp  189 (295)
T 1ls1_A          175 KARLEARDLILVDTA  189 (295)
T ss_dssp             HHHHHTCCEEEEECC
T ss_pred             HHHhCCCCEEEEeCC
Confidence            443123457888987

>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=95.56  E-value=0.008  Score=53.86  Aligned_cols=26  Identities=27%  Similarity=0.506  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|.|.|++|+||||+|+.+.....
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999998754

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=95.55  E-value=0.02  Score=54.93  Aligned_cols=88  Identities=17%  Similarity=0.250  Sum_probs=53.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcC-ccc-eEEEEEecCC-cCHHHHHHHHHHHhCC-------CccccCcHH-----
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENN-LFE-KVISSRVSQT-PQIKEIQREIAEKLGL-------KIDQESESV-----  238 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~-~f~-~~~wv~v~~~-~~~~~il~~i~~~l~~-------~~~~~~~~~-----  238 (426)
                      -+.|.|..|+|||+|+.++.+.....+ +-+ .++++-+.+. ....++.+++...-..       .....+...     
T Consensus       153 r~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~~a~  232 (465)
T 3vr4_D          153 KLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATP  232 (465)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHHHHH
T ss_pred             EEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHHHHH
Confidence            478999999999999999988765421 111 4566666654 4566677766543111       111111111     


Q ss_pred             -HHHHHHHHHh--cCCeEEEEEeCCC
Q 044858          239 -RAWRLLEQLK--KETKILIILDDIW  261 (426)
Q Consensus       239 -~~~~l~~~l~--~~k~~LlVlDdv~  261 (426)
                       ....+-+++.  .++++||++||+-
T Consensus       233 ~~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          233 RMALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEcChH
Confidence             1234555665  3899999999984

>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=95.54  E-value=0.0084  Score=53.40  Aligned_cols=28  Identities=21%  Similarity=0.257  Sum_probs=23.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++.+|+|.|+.|+||||+|+.+.....
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3567899999999999999999988644

>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=95.53  E-value=0.015  Score=56.12  Aligned_cols=88  Identities=17%  Similarity=0.259  Sum_probs=54.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCc--cceEEEEEecCC-cCHHHHHHHHHHHhCCC-------ccccCcHH----
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNL--FEKVISSRVSQT-PQIKEIQREIAEKLGLK-------IDQESESV----  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~--f~~~~wv~v~~~-~~~~~il~~i~~~l~~~-------~~~~~~~~----  238 (426)
                      .-++|.|.+|+|||+|+.++.+.....+.  =+.++++-+.+. ....++.+++...-...       ..+.+...    
T Consensus       153 Qr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~r~~~  232 (469)
T 2c61_A          153 QKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVT  232 (469)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHHHHHH
Confidence            34678899999999999999988764221  134566666654 35667777776532111       11111111    


Q ss_pred             --HHHHHHHHHh--cCCeEEEEEeCC
Q 044858          239 --RAWRLLEQLK--KETKILIILDDI  260 (426)
Q Consensus       239 --~~~~l~~~l~--~~k~~LlVlDdv  260 (426)
                        ....+-+++.  +++.+||++||+
T Consensus       233 ~~~a~tiAEyfrdd~G~dVLl~~Dsl  258 (469)
T 2c61_A          233 PRMALTAAEYLAYEHGMHVLVILTDI  258 (469)
T ss_dssp             HHHHHHHHHHHHHHHCCEEEEEEECH
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeCH
Confidence              1223445554  589999999997

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.53  E-value=0.0054  Score=51.46  Aligned_cols=26  Identities=23%  Similarity=0.271  Sum_probs=18.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|.|.|+.|+||||+|+.+.+...
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            46899999999999999999987654

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.53  E-value=0.0086  Score=50.39  Aligned_cols=24  Identities=21%  Similarity=0.302  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..|.|.|+.|+||||+++.+.+..
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            579999999999999999998765

>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=95.53  E-value=0.0081  Score=51.63  Aligned_cols=25  Identities=36%  Similarity=0.550  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+|+|+|+.|+||||+++.+....
T Consensus        21 ~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998753

>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=95.50  E-value=0.0099  Score=51.23  Aligned_cols=28  Identities=18%  Similarity=0.165  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+|+|.|+.|+||||+++.+.+....
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3468999999999999999999987654

>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=95.50  E-value=0.0075  Score=50.05  Aligned_cols=25  Identities=32%  Similarity=0.371  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|.|.|+.|+||||+|+.+.+...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999988654

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=95.50  E-value=0.056  Score=51.85  Aligned_cols=29  Identities=28%  Similarity=0.304  Sum_probs=24.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ...++.|+|++|+||||++..+.......
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~  125 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK  125 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            35689999999999999999998877643

>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=95.50  E-value=0.018  Score=50.94  Aligned_cols=27  Identities=19%  Similarity=0.128  Sum_probs=23.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+..|.|.|++|+||||+|+.+.+..
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            356789999999999999999998765

>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=95.50  E-value=0.01  Score=50.07  Aligned_cols=26  Identities=31%  Similarity=0.275  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|.|.|+.|+||||+++.+.+...
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~   31 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999987653

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.47  E-value=0.0098  Score=51.17  Aligned_cols=32  Identities=28%  Similarity=0.174  Sum_probs=25.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccce
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEK  204 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~  204 (426)
                      ..+|+|.|+.|+||||+++.+.+..... +++.
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~-~~~~   41 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNN-NVEV   41 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHc-CCcE
Confidence            4689999999999999999999876542 3444

>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=95.47  E-value=0.0082  Score=51.41  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+|+|+|+.|+||||+++.+..
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            3689999999999999999987

>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=95.44  E-value=0.0098  Score=51.67  Aligned_cols=26  Identities=19%  Similarity=0.161  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...|.|.|+.|+||||+++.+.+...
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            45799999999999999999987653

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.40  E-value=0.0094  Score=51.87  Aligned_cols=27  Identities=15%  Similarity=0.106  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ....|.|.|+.|+||||+++.+.+...
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346799999999999999999988754

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=95.38  E-value=0.017  Score=54.74  Aligned_cols=26  Identities=23%  Similarity=0.319  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+.++|++|+|||++|+.+.+...
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~~l~   97 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAKHLD   97 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhC
Confidence            34688999999999999999998763

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.38  E-value=0.0096  Score=52.05  Aligned_cols=25  Identities=20%  Similarity=0.247  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...|.|.|+.|+||||+++.+.+..
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            4679999999999999999998765

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=95.38  E-value=0.0068  Score=56.84  Aligned_cols=51  Identities=20%  Similarity=0.126  Sum_probs=33.7

Q ss_pred             HHHHHhcc-CCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEEEEecCC
Q 044858          162 GILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQT  213 (426)
Q Consensus       162 ~l~~~l~~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~  213 (426)
                      .+++.+.. .+-+-+.|+|.+|+|||+|+.++.+....+ ..+. ++++-+++.
T Consensus       164 raID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~-~V~~lIGER  216 (427)
T 3l0o_A          164 RLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTI-RIILLIDER  216 (427)
T ss_dssp             HHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSE-EEEEECSCC
T ss_pred             hhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhhcCCCeE-EEEEEeccC
Confidence            45555542 233568999999999999999998876532 1233 345666654

>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=95.37  E-value=0.012  Score=53.93  Aligned_cols=28  Identities=32%  Similarity=0.546  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+++|+|++|+|||||++.+......
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~  128 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQN  128 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            4579999999999999999999877654

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.36  E-value=0.014  Score=52.07  Aligned_cols=27  Identities=26%  Similarity=0.238  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.+|.|+|++|+||||+|+.+.....
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            456899999999999999999987653

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.34  E-value=0.071  Score=49.44  Aligned_cols=61  Identities=11%  Similarity=0.092  Sum_probs=39.7

Q ss_pred             HHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          159 TLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       159 ~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .++.+..-+..  -.++.|.|.+|+||||||.++.......  -..++|++.  .-+..++...++.
T Consensus        35 ~LD~~~gGl~~--G~LiiIaG~pG~GKTt~al~ia~~~a~~--g~~Vl~fSl--Ems~~ql~~Rlls   95 (338)
T 4a1f_A           35 QLDNYTSGFNK--GSLVIIGARPSMGKTSLMMNMVLSALND--DRGVAVFSL--EMSAEQLALRALS   95 (338)
T ss_dssp             HHHHHHCSBCT--TCEEEEEECTTSCHHHHHHHHHHHHHHT--TCEEEEEES--SSCHHHHHHHHHH
T ss_pred             HHHHHhcCCCC--CcEEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEEeC--CCCHHHHHHHHHH
Confidence            34555432222  2579999999999999999998876542  234566554  4455666666544

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.31  E-value=0.011  Score=52.35  Aligned_cols=26  Identities=27%  Similarity=0.312  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +..+|+|.|+.|+|||||++.+....
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            44689999999999999999998754

>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=95.31  E-value=0.0093  Score=51.17  Aligned_cols=22  Identities=32%  Similarity=0.433  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+|+|.|+.|+||||+++.+..
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            4789999999999999999976

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.30  E-value=0.0095  Score=51.81  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+++|+|+.|+|||||++.+....
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3579999999999999999998755

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.30  E-value=0.011  Score=48.69  Aligned_cols=24  Identities=25%  Similarity=0.232  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|.|+.|+||||+++.+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999988654

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=95.29  E-value=0.021  Score=54.85  Aligned_cols=89  Identities=17%  Similarity=0.246  Sum_probs=53.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc--------Cccc-eEEEEEecCC-cCHHHHHHHHHHHhCC-------CccccC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN--------NLFE-KVISSRVSQT-PQIKEIQREIAEKLGL-------KIDQES  235 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~--------~~f~-~~~wv~v~~~-~~~~~il~~i~~~l~~-------~~~~~~  235 (426)
                      .-+.|.|.+|+|||+|+.++.+.....        ++-+ .++++-+.+. ....++.+++...-..       .....+
T Consensus       148 Qr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~rtvvv~~t~d~p  227 (464)
T 3gqb_B          148 QKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDP  227 (464)
T ss_dssp             CBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGGEEEEEEETTSC
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccceEEEEECCCCC
Confidence            347899999999999999998876541        1122 4566666654 3556666665442100       111111


Q ss_pred             cHH------HHHHHHHHHh--cCCeEEEEEeCCC
Q 044858          236 ESV------RAWRLLEQLK--KETKILIILDDIW  261 (426)
Q Consensus       236 ~~~------~~~~l~~~l~--~~k~~LlVlDdv~  261 (426)
                      ...      ....+-+++.  +++++||++||+-
T Consensus       228 ~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlT  261 (464)
T 3gqb_B          228 TIERILTPRMALTVAEYLAFEHDYHVLVILTDMT  261 (464)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence            111      1234555665  3899999999984

>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=95.29  E-value=0.011  Score=50.93  Aligned_cols=25  Identities=20%  Similarity=0.337  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||++.+..-.
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3589999999999999999998765

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.28  E-value=0.011  Score=49.92  Aligned_cols=24  Identities=38%  Similarity=0.486  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|+|.|+.|+||||+++.+.+...
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~   25 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLK   25 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999998764

>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=95.28  E-value=0.013  Score=54.03  Aligned_cols=40  Identities=25%  Similarity=0.416  Sum_probs=29.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      ++.+||+|.|-||+||||.+..+..-....+  ..+.-+.+.
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~~G--kkVllID~D   85 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSILG--KRVLQIGCD   85 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEEES
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHHCC--CeEEEEecC
Confidence            3568999999999999999999887766532  235555554

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.22  E-value=0.013  Score=52.18  Aligned_cols=27  Identities=33%  Similarity=0.377  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+|+|.|+.|+||||+++.+.....
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~Lg   52 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESLN   52 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhcC
Confidence            346899999999999999999986653

>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=95.20  E-value=0.012  Score=51.12  Aligned_cols=26  Identities=19%  Similarity=0.250  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||.+.+.....
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCC
Confidence            46899999999999999999987654

>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=95.19  E-value=0.0068  Score=52.28  Aligned_cols=25  Identities=32%  Similarity=0.602  Sum_probs=22.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +|+|.|+.|+||||+++.+......
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            6899999999999999999887653

>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=95.18  E-value=0.013  Score=50.05  Aligned_cols=25  Identities=24%  Similarity=0.190  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...|+|.|+.|+||||+++.+.+..
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            4579999999999999999998865

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.16  E-value=0.013  Score=50.71  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|.|+.|+||||+|+.+.....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~   25 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYE   25 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999987653

>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=95.14  E-value=0.013  Score=48.09  Aligned_cols=26  Identities=31%  Similarity=0.285  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-.+++|.|+.|+|||||++.+....
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            34689999999999999999998865

>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=95.10  E-value=0.015  Score=50.08  Aligned_cols=28  Identities=29%  Similarity=0.271  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ....+|.|.|+.|+||||+++.+.....
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3457899999999999999999988765

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.10  E-value=0.039  Score=48.60  Aligned_cols=48  Identities=21%  Similarity=0.276  Sum_probs=31.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      .++.|.|.+|+|||++|.++......+. -..+++++..  .+...+.+.+
T Consensus        31 ~l~~i~G~pG~GKT~l~l~~~~~~~~~~-~~~v~~~s~E--~~~~~~~~~~   78 (251)
T 2zts_A           31 TTVLLTGGTGTGKTTFAAQFIYKGAEEY-GEPGVFVTLE--ERARDLRREM   78 (251)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS--SCHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCceeeccc--CCHHHHHHHH
Confidence            5889999999999999999765432211 2245555544  3455555544

>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=95.09  E-value=0.014  Score=49.65  Aligned_cols=25  Identities=32%  Similarity=0.480  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ...+|+|+|+.|+||||+++.+.+.
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHh
Confidence            4568999999999999999999876

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.05  E-value=0.15  Score=49.41  Aligned_cols=50  Identities=10%  Similarity=0.026  Sum_probs=35.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .++.|.|.+|+||||||.++........ -..++|++..  .+..++...++.
T Consensus       201 ~l~ii~G~pg~GKT~lal~ia~~~a~~~-g~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          201 SLNIIAARPAMGKTAFALTIAQNAALKE-GVGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTT-CCCEEEEESS--SCHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHhC-CCeEEEEECC--CCHHHHHHHHHH
Confidence            5789999999999999999988765421 1246666554  455666666654

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.02  E-value=0.11  Score=50.41  Aligned_cols=61  Identities=13%  Similarity=0.192  Sum_probs=39.1

Q ss_pred             HHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          159 TLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       159 ~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .++.+..-+..  -.++.|.|.+|+|||||+.++........ -..++|++..  .+...+...++
T Consensus       192 ~LD~~~gGl~~--G~liiI~G~pG~GKTtl~l~ia~~~~~~~-g~~Vl~~s~E--~s~~~l~~r~~  252 (454)
T 2r6a_A          192 ELDRMTSGFQR--SDLIIVAARPSVGKTAFALNIAQNVATKT-NENVAIFSLE--MSAQQLVMRML  252 (454)
T ss_dssp             HHHHHHSSBCT--TCEEEEECCTTSCHHHHHHHHHHHHHHHS-SCCEEEEESS--SCHHHHHHHHH
T ss_pred             HHHhhcCCCCC--CCEEEEECCCCCCHHHHHHHHHHHHHHhC-CCcEEEEECC--CCHHHHHHHHH
Confidence            35555432222  35799999999999999999988765421 1246666654  34455555553

>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=95.01  E-value=0.016  Score=50.25  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      ..+|+|.|+.|+||||+++.+..
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            46899999999999999999975

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.01  E-value=0.013  Score=48.70  Aligned_cols=27  Identities=26%  Similarity=0.402  Sum_probs=23.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ++++|+|+.|+|||||++.+.......
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~~   29 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRER   29 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            579999999999999999998876653

>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=95.00  E-value=0.014  Score=50.40  Aligned_cols=23  Identities=22%  Similarity=0.290  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .|.|.|+.|+||||+|+.+.+..
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            47899999999999999998765

>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=94.97  E-value=0.03  Score=46.71  Aligned_cols=27  Identities=26%  Similarity=0.337  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+++.|+|+.|+|||||+..+......
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~~   32 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALCA   32 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhccc
Confidence            578999999999999999999887553

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=94.97  E-value=0.016  Score=48.41  Aligned_cols=27  Identities=22%  Similarity=0.187  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..+|.|.|+.|+||||+++.+......
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~   31 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVC   31 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            457899999999999999999887643

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.94  E-value=0.1  Score=44.34  Aligned_cols=51  Identities=25%  Similarity=0.309  Sum_probs=33.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      .|+|-|.-|+||||.++.+.+.....+ . .++...-+......+..+.++..
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~~g-~-~v~~treP~~t~~~~~ir~~l~~   52 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEKRG-K-KVILKREPGGTETGEKIRKILLE   52 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTT-C-CEEEEESSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC-C-cEEEEECCCCCcHHHHHHHHhhc
Confidence            478899999999999999999887643 2 23333333334445555555543

>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=94.93  E-value=0.051  Score=47.71  Aligned_cols=52  Identities=21%  Similarity=0.325  Sum_probs=34.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      ..+|.|.|+.|+||||+++.+.+..... .+..+....-+......+.+++++
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~~-~~~~~~~~rep~~t~~g~~ir~~l   78 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQN-GIDHITRTREPGGTLLAEKLRALV   78 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc-CCCeeeeecCCCCCHHHHHHHHHH
Confidence            4689999999999999999999887653 355333333332223334444444

>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=94.91  E-value=0.017  Score=50.61  Aligned_cols=26  Identities=23%  Similarity=0.395  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.+|+|.|++|+||||+++.+.....
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999987653

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=94.89  E-value=0.13  Score=49.82  Aligned_cols=60  Identities=15%  Similarity=0.150  Sum_probs=38.2

Q ss_pred             HHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          159 TLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       159 ~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      .++.++.-+.  .-.++.|.|.+|+||||+|.++......+  -..++|++...  +..++...++
T Consensus       186 ~LD~~lgGl~--~G~liiIaG~pG~GKTtlal~ia~~~a~~--g~~vl~fSlEm--s~~ql~~R~~  245 (444)
T 3bgw_A          186 ELDRMTYGYK--RRNFVLIAARPSMGKTAFALKQAKNMSDN--DDVVNLHSLEM--GKKENIKRLI  245 (444)
T ss_dssp             HHHHHHSSBC--SSCEEEEEECSSSSHHHHHHHHHHHHHHT--TCEEEEECSSS--CTTHHHHHHH
T ss_pred             HHHhhcCCCC--CCcEEEEEeCCCCChHHHHHHHHHHHHHc--CCEEEEEECCC--CHHHHHHHHH
Confidence            3455543222  23579999999999999999998877654  23466665543  3344444443

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.89  E-value=0.017  Score=58.44  Aligned_cols=47  Identities=15%  Similarity=0.165  Sum_probs=38.6

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ....++|.+..++.+...+..+  ..+.|+|++|+||||||+.+.....
T Consensus        39 ~l~~i~G~~~~l~~l~~~i~~g--~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           39 LIDQVIGQEHAVEVIKTAANQK--RHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             HHHHCCSCHHHHHHHHHHHHTT--CCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             ccceEECchhhHhhccccccCC--CEEEEEeCCCCCHHHHHHHHhccCC
Confidence            4566889988888777776655  4689999999999999999998764

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=94.88  E-value=0.015  Score=49.21  Aligned_cols=24  Identities=33%  Similarity=0.472  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +++|+|+.|+|||||++.+.....
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhcc
Confidence            689999999999999999987664

>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=94.87  E-value=0.017  Score=52.39  Aligned_cols=24  Identities=21%  Similarity=0.609  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+.+|+|.|+.|+||||+|+.+..
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999999983

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.83  E-value=0.02  Score=52.41  Aligned_cols=28  Identities=29%  Similarity=0.399  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+++|+|+.|+||||+++.+......
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  126 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  126 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3468999999999999999999887654

>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=94.82  E-value=0.017  Score=52.71  Aligned_cols=25  Identities=16%  Similarity=0.317  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .++|.|.|+.|+||||||..+....
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            3689999999999999999998764

>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=94.82  E-value=0.038  Score=48.35  Aligned_cols=28  Identities=32%  Similarity=0.343  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...+|+|.|+.|+||||+++.+.+....
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            3468999999999999999999988764

>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=94.82  E-value=0.018  Score=49.25  Aligned_cols=25  Identities=16%  Similarity=0.363  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++|+|.|+.|+||||+++.+.....
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A            3 GIVTIDGPSASGKSSVARRVAAALG   27 (208)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            3899999999999999999987654

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.81  E-value=0.041  Score=51.66  Aligned_cols=39  Identities=28%  Similarity=0.485  Sum_probs=29.3

Q ss_pred             HHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          160 LKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       160 ~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...++..+.  .++..+|+|+|.+|+|||||+..+......
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l~~  105 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIE  105 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            334444443  456779999999999999999999876543

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.80  E-value=0.017  Score=50.94  Aligned_cols=24  Identities=17%  Similarity=0.315  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||.+.+..-.
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            789999999999999999998654

>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=94.78  E-value=0.054  Score=52.79  Aligned_cols=43  Identities=21%  Similarity=0.355  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          156 RKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       156 R~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ....+..+...+.+++ +.+.|.|.+|+|||+++..+.......
T Consensus        30 Q~~av~~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~~l~~~   72 (459)
T 3upu_A           30 QKNAFNIVMKAIKEKK-HHVTINGPAGTGATTLTKFIIEALIST   72 (459)
T ss_dssp             HHHHHHHHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            3444555555655543 489999999999999999998877654

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=94.78  E-value=0.028  Score=47.96  Aligned_cols=25  Identities=16%  Similarity=0.105  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+.|+|++|+||||+|..+++...
T Consensus        59 n~ili~GPPGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           59 NCLVFCGPANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             SEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4699999999999999999988764

>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=94.78  E-value=0.021  Score=52.11  Aligned_cols=26  Identities=27%  Similarity=0.186  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..++|.|+|+.|+||||||..+....
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhC
Confidence            45689999999999999999998764

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=94.77  E-value=0.052  Score=47.20  Aligned_cols=56  Identities=21%  Similarity=0.227  Sum_probs=35.7

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhh-cCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE-NNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~-~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      ......|.|.|+.|+||||+++.+.+.... .+ +.......-+......+.+++++.
T Consensus        18 ~~~~~~i~~~G~~g~GKst~~~~l~~~l~~~~g-~~v~~~treP~~t~~g~~ir~~l~   74 (223)
T 3ld9_A           18 GPGSMFITFEGIDGSGKTTQSHLLAEYLSEIYG-VNNVVLTREPGGTLLNESVRNLLF   74 (223)
T ss_dssp             -CCCEEEEEECSTTSSHHHHHHHHHHHHHHHHC-GGGEEEEESSCSSHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhhccC-ceeeEeeeCCCCChHHHHHHHHHh
Confidence            345678999999999999999999988765 32 443331222223334455555554

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=94.75  E-value=0.017  Score=50.00  Aligned_cols=25  Identities=20%  Similarity=0.235  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..|.|.|+.|+||||+++.+.+...
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l~   30 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEYG   30 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999988753

>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=94.73  E-value=0.015  Score=51.13  Aligned_cols=25  Identities=24%  Similarity=0.470  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCC
Confidence            3589999999999999999987543

>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=94.71  E-value=0.02  Score=52.71  Aligned_cols=28  Identities=21%  Similarity=0.251  Sum_probs=23.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..+|+|+|+.|+|||||++.+.....
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3456899999999999999999987654

>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=94.71  E-value=0.084  Score=59.04  Aligned_cols=85  Identities=20%  Similarity=0.173  Sum_probs=53.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc------cCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ------ESESVRAWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~------~~~~~~~~~l~~  245 (426)
                      -.++.|.|++|+||||||.++.......  -..++|++.....+..  .   ++.++.+.+.      .+.......+.+
T Consensus       732 G~lVlI~G~PG~GKTtLal~lA~~aa~~--g~~VlyiS~Ees~~ql--~---A~~lGvd~~~L~i~~~~~leei~~~l~~  804 (1706)
T 3cmw_A          732 GRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPI--Y---ARKLGVDIDNLLCSQPDTGEQALEICDA  804 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEECTTSCCCHH--H---HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CceEEEECCCCCCcHHHHHHHHHHHHHc--CCCeEEEeccchHHHH--H---HHHcCCChhheEEecCCcHHHHHHHHHH
Confidence            3589999999999999999998876543  2256777776665532  1   5556643221      122222233333


Q ss_pred             HHhcCCeEEEEEeCCCCc
Q 044858          246 QLKKETKILIILDDIWGS  263 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~~~  263 (426)
                      .....+.-+||+|.+...
T Consensus       805 lv~~~~~~lVVIDsLq~l  822 (1706)
T 3cmw_A          805 LARSGAVDVIVVDSVAAL  822 (1706)
T ss_dssp             HHHHTCCSEEEESCSTTC
T ss_pred             HHHccCCCEEEEechhhh
Confidence            333456779999998643

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.70  E-value=0.018  Score=53.22  Aligned_cols=27  Identities=19%  Similarity=0.336  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.++|.|+|+.|+|||||+..+.....
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHCC
Confidence            346899999999999999999987653

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.69  E-value=0.019  Score=53.20  Aligned_cols=25  Identities=32%  Similarity=0.368  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|+|.|+.|+||||||..+.....
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            5899999999999999999988654

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=94.69  E-value=0.025  Score=54.54  Aligned_cols=47  Identities=23%  Similarity=0.338  Sum_probs=34.0

Q ss_pred             cccchHHHHHHHHHHhcc--------------CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          152 HFESRKSTLKGILDALSN--------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       152 ~~~gR~~~~~~l~~~l~~--------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .++|.++.++.+...+..              ..++-|.++|++|+||||+|+.+......
T Consensus        16 ~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~   76 (444)
T 1g41_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA   76 (444)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             HhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            356777666666554421              13456899999999999999999987643

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=94.68  E-value=0.071  Score=46.02  Aligned_cols=52  Identities=23%  Similarity=0.267  Sum_probs=34.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      ..|.+.|+.|+||||+++.+.+.....+ +..+....-+....+.+.+++++.
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~~~-~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQLG-IRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTT-CCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcC-CCcceeeeCCCCCHHHHHHHHHHh
Confidence            5799999999999999999998877543 423333333333334555566654

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.68  E-value=0.013  Score=51.44  Aligned_cols=25  Identities=24%  Similarity=0.262  Sum_probs=16.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH-HHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVG-RQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~-~~~  196 (426)
                      ..+++|+|+.|+|||||++.+. ...
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            3689999999999999999998 553

>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=94.66  E-value=0.023  Score=49.77  Aligned_cols=26  Identities=19%  Similarity=0.103  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...|.|.|+.|+||||+|+.+.+...
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45799999999999999999988754

>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=94.65  E-value=0.11  Score=60.84  Aligned_cols=138  Identities=11%  Similarity=0.096  Sum_probs=74.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      +-+.++|++|+|||++|+.+.....   .+ ..+.++.+...+...+...+-..+.........      ...-...+++
T Consensus      1268 ~~vLL~GPpGtGKT~la~~~l~~~~---~~-~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~------~~~P~~~gk~ 1337 (2695)
T 4akg_A         1268 RGIILCGPPGSGKTMIMNNALRNSS---LY-DVVGINFSKDTTTEHILSALHRHTNYVTTSKGL------TLLPKSDIKN 1337 (2695)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSCS---SC-EEEEEECCTTCCHHHHHHHHHHHBCCEEETTTE------EEEEBSSSSC
T ss_pred             CeEEEECCCCCCHHHHHHHHHhcCC---CC-ceEEEEeecCCCHHHHHHHHHHHhhhccccCCc------cccCCCCCce
Confidence            4578999999999999987765432   12 345677777777777666665544321100000      0000003678


Q ss_pred             EEEEEeCCCCc--cC------hhhhcCCCCC-----CC-------CCeEEEEeecchh------hhhccCCceeeEEccC
Q 044858          253 ILIILDDIWGS--LD------LEAIGIPLAD-----DN-------GGCKVLLTARSQD------VLSCEMDCQQNFVVDV  306 (426)
Q Consensus       253 ~LlVlDdv~~~--~~------~~~l~~~l~~-----~~-------~~s~iivTtr~~~------va~~~~~~~~~~~l~~  306 (426)
                      +++.+||+.-.  +.      .+.+...+..     ..       .+..+|.++-...      +..........+.+..
T Consensus      1338 ~VlFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~vi~i~~ 1417 (2695)
T 4akg_A         1338 LVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGY 1417 (2695)
T ss_dssp             EEEEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEEEECCC
T ss_pred             EEEEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeEEEeCC
Confidence            99999997422  21      1111111110     01       1233444443221      1111223457889999


Q ss_pred             CCHHHHHHHHHHhh
Q 044858          307 LNDKEAWSLFKKMT  320 (426)
Q Consensus       307 L~~~e~~~Lf~~~~  320 (426)
                      .+.++-..+|...+
T Consensus      1418 P~~~~l~~I~~~il 1431 (2695)
T 4akg_A         1418 PSGKSLSQIYEIYY 1431 (2695)
T ss_dssp             CTTTHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999888888765

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.65  E-value=0.052  Score=52.68  Aligned_cols=85  Identities=18%  Similarity=0.201  Sum_probs=50.9

Q ss_pred             cEEEEEcCCCCcHHHHH-HHHHHHhhhcCccc-eEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHHH---
Q 044858          173 NMIGVYGMGGIGKTTLV-KEVGRQAKENNLFE-KVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESVR---  239 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~~---  239 (426)
                      .-+.|.|..|+|||+|| ..+.+...    -+ .++++-+++.. ...++.+.+...-...       ...++....   
T Consensus       163 QR~~Ifg~~g~GKT~Lal~~I~~~~~----~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~a  238 (502)
T 2qe7_A          163 QRELIIGDRQTGKTTIAIDTIINQKG----QDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLYLA  238 (502)
T ss_dssp             CBCEEEECSSSCHHHHHHHHHHGGGS----CSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHHHH
T ss_pred             CEEEEECCCCCCchHHHHHHHHHhhc----CCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHHHH
Confidence            45789999999999995 56666542    34 34667776654 5566677666532211       111111111   


Q ss_pred             ---HHHHHHHHh-cCCeEEEEEeCCC
Q 044858          240 ---AWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       240 ---~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                         ...+-+++. +++.+||++||+.
T Consensus       239 ~~~a~tiAEyfrd~G~dVLl~~Dslt  264 (502)
T 2qe7_A          239 PYAGCAMGEYFMYKGKHALVVYDDLS  264 (502)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEEecHH
Confidence               123334443 4799999999974

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.64  E-value=0.016  Score=50.52  Aligned_cols=24  Identities=29%  Similarity=0.537  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||.+.+..-.
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            589999999999999999987543

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.64  E-value=0.012  Score=53.69  Aligned_cols=27  Identities=22%  Similarity=0.385  Sum_probs=20.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+|+|.|+.|+||||+|+.+.+...
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999987654

>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=94.62  E-value=0.053  Score=52.68  Aligned_cols=85  Identities=16%  Similarity=0.184  Sum_probs=50.6

Q ss_pred             cEEEEEcCCCCcHHHHH-HHHHHHhhhcCccc-eEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHHH---
Q 044858          173 NMIGVYGMGGIGKTTLV-KEVGRQAKENNLFE-KVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESVR---  239 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~~---  239 (426)
                      .-+.|.|..|+|||+|| ..+.+...    -+ .++++-+++.. .+.++.+.+...-...       ...++....   
T Consensus       176 QR~~I~g~~g~GKT~Lal~~I~~~~~----~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a  251 (515)
T 2r9v_A          176 QRELIIGDRQTGKTAIAIDTIINQKG----QGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIA  251 (515)
T ss_dssp             CBEEEEEETTSSHHHHHHHHHHTTTT----TTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHH
T ss_pred             CEEEEEcCCCCCccHHHHHHHHHhhc----CCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHH
Confidence            45899999999999995 56766542    34 34667776654 5566666665432111       111111111   


Q ss_pred             ---HHHHHHHHh-cCCeEEEEEeCCC
Q 044858          240 ---AWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       240 ---~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                         ...+-+++. +++.+||++||+.
T Consensus       252 ~~~a~tiAEyfrd~G~dVLli~DslT  277 (515)
T 2r9v_A          252 PYAGCAMGEYFAYSGRDALVVYDDLS  277 (515)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEeccHH
Confidence               123334443 4799999999984

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.58  E-value=0.019  Score=50.98  Aligned_cols=25  Identities=36%  Similarity=0.385  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|+|+|+.|+||||+++.+.....
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcC
Confidence            5799999999999999999988654

>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=94.58  E-value=0.022  Score=49.15  Aligned_cols=23  Identities=22%  Similarity=0.095  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .|.|.|+.|+||||+++.+.+..
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            47899999999999999998765

>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=94.57  E-value=0.023  Score=48.87  Aligned_cols=24  Identities=25%  Similarity=0.404  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +|.|.|++|+||+|.|+.+.+...
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g   25 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKG   25 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            578999999999999999998764

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.57  E-value=0.022  Score=49.57  Aligned_cols=23  Identities=30%  Similarity=0.300  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .|.|.|+.|+||||+++.+....
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            58899999999999999998765

>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=94.55  E-value=0.077  Score=48.25  Aligned_cols=37  Identities=27%  Similarity=0.217  Sum_probs=27.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRV  210 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v  210 (426)
                      .++.|.|++|+|||||+..+........ -..++|+..
T Consensus        36 ~~~~i~G~~G~GKTTl~~~ia~~~~~~~-G~~v~~~~~   72 (296)
T 1cr0_A           36 EVIMVTSGSGMGKSTFVRQQALQWGTAM-GKKVGLAML   72 (296)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTS-CCCEEEEES
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHHc-CCeEEEEeC
Confidence            5899999999999999999988765431 113555554

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.50  E-value=0.022  Score=52.45  Aligned_cols=25  Identities=24%  Similarity=0.223  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++|.|+|+.|+||||||..+.....
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~   30 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALP   30 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            5899999999999999999987653

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.46  E-value=0.028  Score=52.74  Aligned_cols=28  Identities=29%  Similarity=0.399  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...+++|+|+.|+||||+++.+......
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  183 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  183 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccc
Confidence            3568999999999999999999887654

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.45  E-value=0.016  Score=49.87  Aligned_cols=23  Identities=30%  Similarity=0.287  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+++|+|+.|+|||||++.+..-
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            57999999999999999999876

>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=94.40  E-value=0.023  Score=50.04  Aligned_cols=26  Identities=23%  Similarity=0.360  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||++.+..-..
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   56 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAEMD   56 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTCSE
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            35899999999999999999986543

>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=94.38  E-value=0.024  Score=54.54  Aligned_cols=28  Identities=29%  Similarity=0.381  Sum_probs=24.1

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+.+.+|.|+|++|+||||+|+.+....
T Consensus       255 ~~~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          255 SPNPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             CSSCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            3456799999999999999999998764

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.37  E-value=0.02  Score=51.24  Aligned_cols=25  Identities=24%  Similarity=0.425  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3589999999999999999987543

>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=94.36  E-value=0.02  Score=51.59  Aligned_cols=25  Identities=24%  Similarity=0.404  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||++.+..-.
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCC
Confidence            3589999999999999999987543

>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=94.36  E-value=0.073  Score=51.76  Aligned_cols=89  Identities=16%  Similarity=0.241  Sum_probs=52.0

Q ss_pred             cEEEEEcCCCCcHHHHH-HHHHHHhhh----cCccc-eEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHH
Q 044858          173 NMIGVYGMGGIGKTTLV-KEVGRQAKE----NNLFE-KVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESV  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa-~~v~~~~~~----~~~f~-~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~  238 (426)
                      .-+.|.|..|+|||+|| ..+.+....    .++-+ .++++-+++.. .+.++.+.+...-...       ...++...
T Consensus       163 QR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~  242 (510)
T 2ck3_A          163 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPL  242 (510)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHH
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceEEEECCCCCHHH
Confidence            45789999999999995 566666542    12233 46677777654 5566666665532111       11111111


Q ss_pred             H------HHHHHHHHh-cCCeEEEEEeCCC
Q 044858          239 R------AWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       239 ~------~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                      .      ...+-+++. +++.+||++||+.
T Consensus       243 r~~a~~~a~tiAEyfrd~G~dVLli~Dslt  272 (510)
T 2ck3_A          243 QYLAPYSGCSMGEYFRDNGKHALIIYDDLS  272 (510)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCcEEEEEcCHH
Confidence            1      112333443 4799999999984

>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=94.32  E-value=0.12  Score=57.78  Aligned_cols=83  Identities=20%  Similarity=0.180  Sum_probs=58.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc------cCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ------ESESVRAWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~------~~~~~~~~~l~~  245 (426)
                      -++|-|+|+.|+||||||.++.......  -...+|+...+..++.-     ++.+|.+.+.      ......+.....
T Consensus      1431 g~~iei~g~~~sGkttl~~~~~a~~~~~--g~~~~~i~~e~~~~~~~-----~~~~Gv~~~~l~~~~p~~~e~~l~~~~~ 1503 (1706)
T 3cmw_A         1431 GRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDA 1503 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhc--CCeEEEEecCCCCCHHH-----HHHcCCCHHHeEEeCCCcHHHHHHHHHH
Confidence            4789999999999999999998765433  45678998888777663     7778876543      112223333444


Q ss_pred             HHhcCCeEEEEEeCCC
Q 044858          246 QLKKETKILIILDDIW  261 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~  261 (426)
                      .+..+..-+||+|-|-
T Consensus      1504 ~~~s~~~~~vvvDsv~ 1519 (1706)
T 3cmw_A         1504 LARSGAVDVIVVDSVA 1519 (1706)
T ss_dssp             HHHHTCCSEEEESCST
T ss_pred             HHHcCCCCEEEEccHH
Confidence            4455677899999884

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.31  E-value=0.11  Score=58.86  Aligned_cols=84  Identities=20%  Similarity=0.173  Sum_probs=53.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHH-HHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVR-AWRLLE  245 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~-~~~l~~  245 (426)
                      ..++.|.|++|+||||||.++.......  -..++|++.....+...     ++.++.+.+.     ....+. ...+..
T Consensus       383 G~lilI~G~pGsGKTtLaLqia~~~a~~--G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~I~~~~~~e~il~~~~~  455 (2050)
T 3cmu_A          383 GRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDA  455 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHHHTT--TCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEEcCCCHHHHH-----HHHcCCCHHHeEEeCCCCHHHHHHHHHH
Confidence            4689999999999999999998876543  23578888877766432     5566654321     112222 222222


Q ss_pred             HHhcCCeEEEEEeCCCC
Q 044858          246 QLKKETKILIILDDIWG  262 (426)
Q Consensus       246 ~l~~~k~~LlVlDdv~~  262 (426)
                      ...+.+.-+||+|.+..
T Consensus       456 lv~~~~~~lIVIDSL~a  472 (2050)
T 3cmu_A          456 LARSGAVDVIVVDSVAA  472 (2050)
T ss_dssp             HHHHTCCSEEEESCGGG
T ss_pred             HHHhcCCcEEEECCHHH
Confidence            22345567999999853

>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=94.29  E-value=0.025  Score=48.34  Aligned_cols=28  Identities=29%  Similarity=0.264  Sum_probs=21.3

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..+.--|+|+|.+|+|||||...+.+..
T Consensus        27 ~~~~~ki~vvG~~~~GKSsLi~~l~~~~   54 (204)
T 4gzl_A           27 QGQAIKCVVVGDGAVGKTCLLISYTTNA   54 (204)
T ss_dssp             ---CEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             cCCeEEEEEECcCCCCHHHHHHHHHhCC
Confidence            3444568999999999999999888643

>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=94.29  E-value=0.022  Score=50.27  Aligned_cols=24  Identities=25%  Similarity=0.486  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||.+.+..-.
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            589999999999999999997643

>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=94.28  E-value=0.025  Score=50.30  Aligned_cols=23  Identities=30%  Similarity=0.436  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999874

>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=94.28  E-value=0.026  Score=51.58  Aligned_cols=23  Identities=30%  Similarity=0.394  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+|.|.|++|+||||+|+.+.+.
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999999874

>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=94.26  E-value=0.022  Score=50.82  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||.+.+..-.
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            589999999999999999987543

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.25  E-value=0.041  Score=49.19  Aligned_cols=109  Identities=17%  Similarity=0.138  Sum_probs=54.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHH--HhCCCccccCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAE--KLGLKIDQESESVRAWRLLEQL  247 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~--~l~~~~~~~~~~~~~~~l~~~l  247 (426)
                      .-.+++|+|+.|+|||||++.+.......  +...+++.-.. .+-.... ..+..  .++..     .......+...+
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~~~--~~G~I~~~g~~i~~~~~~~-~~~v~q~~~gl~-----~~~l~~~la~aL   95 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYINQT--KSYHIITIEDPIEYVFKHK-KSIVNQREVGED-----TKSFADALRAAL   95 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHHHH--CCCEEEEEESSCCSCCCCS-SSEEEEEEBTTT-----BSCHHHHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCCCC--CCCEEEEcCCcceeecCCc-ceeeeHHHhCCC-----HHHHHHHHHHHH
Confidence            44689999999999999999998765432  12222221110 0000000 00000  01100     011223445555


Q ss_pred             hcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          248 KKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       248 ~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                      .. ++=++++|+..+.+....+...   ...|..|++||.....
T Consensus        96 ~~-~p~illlDEp~D~~~~~~~l~~---~~~g~~vl~t~H~~~~  135 (261)
T 2eyu_A           96 RE-DPDVIFVGEMRDLETVETALRA---AETGHLVFGTLHTNTA  135 (261)
T ss_dssp             HH-CCSEEEESCCCSHHHHHHHHHH---HHTTCEEEEEECCSSH
T ss_pred             hh-CCCEEEeCCCCCHHHHHHHHHH---HccCCEEEEEeCcchH
Confidence            54 4668888999755433332211   1236668888876553

>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=94.25  E-value=0.02  Score=49.58  Aligned_cols=24  Identities=42%  Similarity=0.641  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||.+.+..-.
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            579999999999999999997654

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=94.24  E-value=0.16  Score=44.26  Aligned_cols=25  Identities=20%  Similarity=0.181  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..++|.|++|+||||+|+.+.+...
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~g   33 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKFG   33 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             cceeeECCCCCCHHHHHHHHHHHhC
Confidence            4589999999999999999988764

>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=94.23  E-value=0.098  Score=45.12  Aligned_cols=32  Identities=22%  Similarity=0.194  Sum_probs=26.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccce
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEK  204 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~  204 (426)
                      ...|.|.|+.|+||||+++.+.+..... .+..
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~v   37 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRER-GIEV   37 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTT-TCCE
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHc-CCCc
Confidence            3579999999999999999999887653 3444

>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=94.21  E-value=0.023  Score=51.00  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||++.+..-.
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCC
Confidence            3589999999999999999987543

>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=94.20  E-value=0.024  Score=49.68  Aligned_cols=26  Identities=27%  Similarity=0.376  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||.+.+..-..
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            35899999999999999999986543

>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=94.19  E-value=0.024  Score=50.30  Aligned_cols=24  Identities=42%  Similarity=0.631  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||.+.+..-.
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            579999999999999999987653

>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=94.17  E-value=0.026  Score=50.65  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999874

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=94.17  E-value=0.037  Score=51.10  Aligned_cols=28  Identities=29%  Similarity=0.458  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+|+|+|++|+||||++..+......
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~  131 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAE  131 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4578999999999999999999887664

>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=94.16  E-value=0.029  Score=47.36  Aligned_cols=24  Identities=25%  Similarity=0.454  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..|+|+|..|+|||||.+.+....
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            468999999999999999998754

>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=94.16  E-value=0.027  Score=50.38  Aligned_cols=25  Identities=24%  Similarity=0.333  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            4689999999999999999987643

>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=94.15  E-value=0.024  Score=50.11  Aligned_cols=25  Identities=28%  Similarity=0.325  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3589999999999999999987543

>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=94.08  E-value=0.026  Score=50.38  Aligned_cols=25  Identities=28%  Similarity=0.448  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCC
Confidence            3589999999999999999997643

>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=94.04  E-value=0.034  Score=50.78  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +-.+++|+|+.|+|||||++.+..-.
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            34689999999999999999998765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.02  E-value=0.031  Score=50.01  Aligned_cols=24  Identities=29%  Similarity=0.290  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            358999999999999999999754

>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=93.98  E-value=0.052  Score=48.28  Aligned_cols=27  Identities=37%  Similarity=0.474  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...++.+.|.+|+||||++..+.....
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            356789999999999999999987665

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.97  E-value=0.031  Score=50.27  Aligned_cols=25  Identities=20%  Similarity=0.228  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||++.+..-.
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3589999999999999999997643

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=93.97  E-value=0.028  Score=49.91  Aligned_cols=24  Identities=25%  Similarity=0.504  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||.+.+..-.
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            579999999999999999987643

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=93.97  E-value=0.04  Score=53.68  Aligned_cols=28  Identities=32%  Similarity=0.475  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...+++|+|+.|+|||||++.+......
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~  319 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQ  319 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhh
Confidence            3569999999999999999999887654

>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=93.93  E-value=0.2  Score=49.32  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=35.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .++.|.|.+|+||||||.++......+. -..++|++...  +..++...++.
T Consensus       243 ~l~li~G~pG~GKT~lal~~a~~~a~~~-g~~vl~~s~E~--s~~~l~~r~~~  292 (503)
T 1q57_A          243 EVIMVTSGSGMVMSTFVRQQALQWGTAM-GKKVGLAMLEE--SVEETAEDLIG  292 (503)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHTTTS-CCCEEEEESSS--CHHHHHHHHHH
T ss_pred             eEEEEeecCCCCchHHHHHHHHHHHHhc-CCcEEEEeccC--CHHHHHHHHHH
Confidence            5789999999999999999988765431 12466766543  45666665543

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.93  E-value=0.038  Score=48.68  Aligned_cols=26  Identities=23%  Similarity=0.285  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..|+|.|..|+||||+++.+.+...
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            46799999999999999999998763

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.93  E-value=0.028  Score=50.42  Aligned_cols=25  Identities=32%  Similarity=0.287  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3589999999999999999987543

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=93.92  E-value=0.032  Score=47.37  Aligned_cols=23  Identities=26%  Similarity=0.473  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..|+|+|..|+|||||.+.+...
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            45899999999999999999875

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.91  E-value=0.029  Score=49.96  Aligned_cols=25  Identities=28%  Similarity=0.489  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|+|+.|+|||||.+.+..-..
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            5799999999999999999986543

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=93.90  E-value=0.086  Score=49.20  Aligned_cols=29  Identities=38%  Similarity=0.450  Sum_probs=24.8

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +...+++.+.|.||+||||+|..+.....
T Consensus        15 ~~~~~i~~~~gkGGvGKTt~a~~lA~~la   43 (348)
T 3io3_A           15 HDSLKWIFVGGKGGVGKTTTSSSVAVQLA   43 (348)
T ss_dssp             CTTCSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHHHH
Confidence            45568999999999999999999887665

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.90  E-value=0.029  Score=50.74  Aligned_cols=25  Identities=32%  Similarity=0.442  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3579999999999999999987643

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=93.86  E-value=0.026  Score=47.29  Aligned_cols=22  Identities=32%  Similarity=0.498  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|+|+|.+|+|||||.+.+...
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            4789999999999999998763

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=93.84  E-value=0.044  Score=48.08  Aligned_cols=26  Identities=23%  Similarity=0.309  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...+|+|.|+.|+||||+++.+....
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            45689999999999999999998754

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.84  E-value=0.035  Score=49.91  Aligned_cols=23  Identities=39%  Similarity=0.540  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .++|+|+.|+|||||.+.++...
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

>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=93.83  E-value=0.039  Score=52.21  Aligned_cols=25  Identities=24%  Similarity=0.485  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++|+|.|+.|+||||||..+.....
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCC
Confidence            5899999999999999999987653

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=93.80  E-value=0.041  Score=44.54  Aligned_cols=23  Identities=17%  Similarity=0.408  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +-|.|+|.+|+|||||+..+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45889999999999999998765

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=93.79  E-value=0.038  Score=45.26  Aligned_cols=23  Identities=22%  Similarity=0.398  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..|+|+|.+|+|||||...+...
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            46899999999999999999764

>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=93.78  E-value=0.093  Score=48.69  Aligned_cols=30  Identities=37%  Similarity=0.439  Sum_probs=25.1

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +...+++.+.|.||+||||+|..+......
T Consensus        13 ~~~~~i~~~sgkGGvGKTt~a~~lA~~la~   42 (334)
T 3iqw_A           13 QRSLRWIFVGGKGGVGKTTTSCSLAIQLAK   42 (334)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHHHHHHHTT
T ss_pred             CCCeEEEEEeCCCCccHHHHHHHHHHHHHh
Confidence            445678899999999999999999877654

>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=93.76  E-value=0.032  Score=47.31  Aligned_cols=25  Identities=20%  Similarity=0.207  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+.|.|.|+.|+||||||..+....
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            3568999999999999999998764

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.76  E-value=0.08  Score=44.39  Aligned_cols=26  Identities=23%  Similarity=0.198  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ....|+|+|.+|+|||||...+....
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            34578999999999999999988653

>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=93.73  E-value=0.036  Score=50.07  Aligned_cols=26  Identities=23%  Similarity=0.278  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.++.|+|++|+|||||+.++.....
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            36899999999999999999987544

>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=93.69  E-value=0.029  Score=49.04  Aligned_cols=25  Identities=24%  Similarity=0.203  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +..+|+|.|+.|+||||+++.+...
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            3468999999999999999998875

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=93.64  E-value=0.043  Score=51.78  Aligned_cols=27  Identities=22%  Similarity=0.023  Sum_probs=23.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +...+++|+|+.|+|||||++.+....
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            345689999999999999999999753

>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=93.62  E-value=0.034  Score=51.36  Aligned_cols=26  Identities=27%  Similarity=0.387  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +.+++.|+|+.|+|||||.+.+....
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            46789999999999999999998653

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=93.60  E-value=0.073  Score=44.45  Aligned_cols=33  Identities=24%  Similarity=0.329  Sum_probs=25.2

Q ss_pred             HHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          162 GILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       162 ~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+.+ +...+..-|.|+|..|+|||||...+...
T Consensus         7 ~~~~-~~~~~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A            7 RIWR-LFNHQEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             HHHH-HHTTSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHH-hcCCCccEEEEECCCCCCHHHHHHHHhcC
Confidence            3444 33445567899999999999999999854

>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=93.58  E-value=0.046  Score=45.66  Aligned_cols=24  Identities=17%  Similarity=0.274  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+.+|+|+.|+|||||+..++--.
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            488999999999999999987654

>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=93.56  E-value=0.54  Score=41.07  Aligned_cols=38  Identities=18%  Similarity=0.054  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          156 RKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       156 R~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |....+.+..++.. +  -+.|+|+.|.|||.+|..+....
T Consensus        95 ~~~Q~~ai~~~~~~-~--~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A           95 RDYQEKALERWLVD-K--RGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             CHHHHHHHHHHTTT-S--EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHhC-C--CEEEEeCCCCCHHHHHHHHHHHc
Confidence            44444444444433 2  37789999999999998887654

>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=93.55  E-value=0.081  Score=51.94  Aligned_cols=45  Identities=9%  Similarity=-0.110  Sum_probs=32.5

Q ss_pred             cchHHHHHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          154 ESRKSTLKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       154 ~gR~~~~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +.|.+..+.+.+...  ..+..+|.+.|+.|+||||+|+.+......
T Consensus       375 f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          375 FSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             TSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             ccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            345444455555442  234568999999999999999999998764

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=93.52  E-value=0.043  Score=44.45  Aligned_cols=23  Identities=30%  Similarity=0.534  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -|.++|.+|+|||||+..+....
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            47899999999999999997653

>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=93.52  E-value=0.23  Score=48.75  Aligned_cols=47  Identities=17%  Similarity=0.270  Sum_probs=34.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC-HHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ-IKEIQREI  223 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~il~~i  223 (426)
                      .-++|.|..|+|||+|+.++.+...    -+.++++-+++..+ ..++++++
T Consensus       228 qr~~I~g~~g~GKT~L~~~ia~~~~----~~~~V~~~iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          228 GTAAIPGPAGSGKTVTQHQLAKWSD----AQVVIYIGCGERGNEMTDVLEEF  275 (588)
T ss_dssp             CEEEECSCCSHHHHHHHHHHHHHSS----CSEEEEEECCSSSSHHHHHHHHT
T ss_pred             CeEEeecCCCCCHHHHHHHHHhccC----CCEEEEEEecccHHHHHHHHHHH
Confidence            5689999999999999999876532    35677888876654 55555554

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.49  E-value=0.044  Score=45.79  Aligned_cols=23  Identities=22%  Similarity=0.398  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..|+|+|.+|+|||||...+...
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            46899999999999999999864

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.49  E-value=0.05  Score=44.88  Aligned_cols=25  Identities=24%  Similarity=0.348  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +...|+|+|.+|+|||||...+...
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999998764

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.49  E-value=0.038  Score=49.48  Aligned_cols=25  Identities=28%  Similarity=0.380  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            3589999999999999999997643

>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=93.48  E-value=0.041  Score=51.47  Aligned_cols=25  Identities=28%  Similarity=0.388  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcCC
Confidence            3589999999999999999998643

>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=93.44  E-value=0.045  Score=44.57  Aligned_cols=23  Identities=22%  Similarity=0.452  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|.|+|.+|+|||||...+...
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            35789999999999999999865

>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=93.43  E-value=0.054  Score=44.95  Aligned_cols=33  Identities=27%  Similarity=0.374  Sum_probs=24.6

Q ss_pred             HHHHHhcc-CCccEEEEEcCCCCcHHHHHHHHHH
Q 044858          162 GILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       162 ~l~~~l~~-~~~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      ++.+.+.. .+...|+|+|..|+|||||...+..
T Consensus         7 ~~~~~~~~~~~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A            7 SMFDKLWGSNKELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             HHHGGGTTCSSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             HHHHHhcCCCCccEEEEECCCCCCHHHHHHHHhc
Confidence            34443434 4556789999999999999998874

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=93.42  E-value=0.061  Score=45.25  Aligned_cols=109  Identities=16%  Similarity=0.059  Sum_probs=51.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .++.|+|+.|+||||++..+..+....+ .. ++.+....+.  ..-...+...++........ .....+.+.+. ++.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g-~~-v~~~~~~~d~--r~~~~~i~s~~g~~~~~~~~-~~~~~~~~~~~-~~~   77 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGK-KK-VAVFKPKIDS--RYHSTMIVSHSGNGVEAHVI-ERPEEMRKYIE-EDT   77 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTT-CE-EEEEEEC-------CCCEECC----CEECEEE-SSGGGGGGGCC-TTE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCC-Ce-EEEEeecccc--ccCcccEEecCCCceeeEEE-CCHHHHHHHhc-CCC
Confidence            4788999999999999977776654322 22 2233222110  00000011111111110000 00112222222 346


Q ss_pred             EEEEEeCCCCc-cChhhhcCCCCCCCCCeEEEEeecch
Q 044858          253 ILIILDDIWGS-LDLEAIGIPLADDNGGCKVLLTARSQ  289 (426)
Q Consensus       253 ~LlVlDdv~~~-~~~~~l~~~l~~~~~~s~iivTtr~~  289 (426)
                      -+|++|++... .+|......+.+  .+..|++|.+..
T Consensus        78 dvviIDE~Q~~~~~~~~~l~~l~~--~~~~Vi~~Gl~~  113 (184)
T 2orw_A           78 RGVFIDEVQFFNPSLFEVVKDLLD--RGIDVFCAGLDL  113 (184)
T ss_dssp             EEEEECCGGGSCTTHHHHHHHHHH--TTCEEEEEEESB
T ss_pred             CEEEEECcccCCHHHHHHHHHHHH--CCCCEEEEeecc
Confidence            69999999765 345443322222  277899988854

>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=93.40  E-value=0.23  Score=48.07  Aligned_cols=85  Identities=25%  Similarity=0.282  Sum_probs=50.2

Q ss_pred             cEEEEEcCCCCcHHHHH-HHHHHHhhhcCccc-eEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHHH---
Q 044858          173 NMIGVYGMGGIGKTTLV-KEVGRQAKENNLFE-KVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESVR---  239 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~~---  239 (426)
                      .-+.|.|..|+|||+|+ ..+.+..    +-+ .++++-+++.. .+.++.+++...-...       ...++....   
T Consensus       163 QR~~Ifg~~g~GKT~l~l~~I~n~~----~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~~a  238 (513)
T 3oaa_A          163 QRELIIGDRQTGKTALAIDAIINQR----DSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQYLA  238 (513)
T ss_dssp             CBCEEEESSSSSHHHHHHHHHHTTS----SSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHHHH
T ss_pred             CEEEeecCCCCCcchHHHHHHHhhc----cCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHHHH
Confidence            45789999999999996 5666642    233 35677777654 4566777665432111       111111111   


Q ss_pred             ---HHHHHHHHh-cCCeEEEEEeCCC
Q 044858          240 ---AWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       240 ---~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                         ...+-+++. ++++.||++||+-
T Consensus       239 ~~~a~tiAEyfrd~G~dVLli~Dslt  264 (513)
T 3oaa_A          239 PYAGCAMGEYFRDRGEDALIIYDDLS  264 (513)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHhcCCCEEEEecChH
Confidence               112333332 5899999999984

>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=93.35  E-value=0.066  Score=44.60  Aligned_cols=25  Identities=32%  Similarity=0.437  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ....|+|+|.+|+|||||...+...
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            4457899999999999999998764

>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=93.34  E-value=0.057  Score=46.41  Aligned_cols=26  Identities=23%  Similarity=0.198  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ....|.|+|++|+|||||+..+....
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            45678999999999999999998754

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=93.31  E-value=0.079  Score=45.94  Aligned_cols=37  Identities=16%  Similarity=0.203  Sum_probs=27.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      .|.+.|.||+||||+|..+......++ ++ +..+.+..
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G-~~-V~v~d~D~   44 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQG-VR-VMAGVVET   44 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTT-CC-EEEEECCC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCC-CC-EEEEEeCC
Confidence            478999999999999999988876543 33 33444443

>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=93.28  E-value=0.071  Score=49.95  Aligned_cols=111  Identities=13%  Similarity=0.091  Sum_probs=58.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH--HHHHHHHHHHhCCCccccCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI--KEIQREIAEKLGLKIDQESESVRAWRLLEQLK  248 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~--~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~  248 (426)
                      ...+++|+|+.|+|||||.+.+.......  ....+ +++..+...  ... ..+..+...   ..........+...+.
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~--~~~~i-~t~ed~~e~~~~~~-~~~v~q~~~---~~~~~~~~~~La~aL~  194 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNT--KYHHI-LTIEDPIEFVHESK-KCLVNQREV---HRDTLGFSEALRSALR  194 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHH--CCCEE-EEEESSCCSCCCCS-SSEEEEEEB---TTTBSCHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCC--CCcEE-EEccCcHHhhhhcc-ccceeeeee---ccccCCHHHHHHHHhh
Confidence            34589999999999999999998765432  11111 122221110  000 000000000   0011112234455555


Q ss_pred             cCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhh
Q 044858          249 KETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVL  292 (426)
Q Consensus       249 ~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va  292 (426)
                       ..+=+|++|++.+.+.++.+...   ...|..||+||.....+
T Consensus       195 -~~PdvillDEp~d~e~~~~~~~~---~~~G~~vl~t~H~~~~~  234 (356)
T 3jvv_A          195 -EDPDIILVGEMRDLETIRLALTA---AETGHLVFGTLHTTSAA  234 (356)
T ss_dssp             -SCCSEEEESCCCSHHHHHHHHHH---HHTTCEEEEEESCSSHH
T ss_pred             -hCcCEEecCCCCCHHHHHHHHHH---HhcCCEEEEEEccChHH
Confidence             46788999999876655543222   12366688888877654

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.27  E-value=0.12  Score=44.98  Aligned_cols=27  Identities=30%  Similarity=0.342  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...|.|.|+.|+||||+++.+.+....
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l~~   51 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRLQE   51 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            468999999999999999999988764

>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=93.22  E-value=0.04  Score=53.12  Aligned_cols=28  Identities=32%  Similarity=0.458  Sum_probs=24.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ++.+|.|+|++|+||||++..+......
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~l~~  125 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARYIQK  125 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3568999999999999999999877653

>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=93.22  E-value=0.065  Score=51.18  Aligned_cols=24  Identities=21%  Similarity=0.385  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            456899999999999999999987

>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=93.21  E-value=0.05  Score=49.42  Aligned_cols=26  Identities=27%  Similarity=0.376  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||.+.+..-..
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl~~   89 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGELE   89 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            35899999999999999999986543

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=93.19  E-value=0.17  Score=50.23  Aligned_cols=27  Identities=33%  Similarity=0.297  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      -.++.|.|+.|+|||||++.++.....
T Consensus       281 G~i~~i~G~~GsGKSTLl~~l~g~~~~  307 (525)
T 1tf7_A          281 DSIILATGATGTGKTLLVSRFVENACA  307 (525)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHT
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            358999999999999999999876554

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.17  E-value=0.063  Score=47.97  Aligned_cols=37  Identities=22%  Similarity=0.475  Sum_probs=27.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      ++|+|.|.||+||||+|..+.......+  ..++-+...
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la~~G--~~VlliD~D   38 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLHAMG--KTIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTT--CCEEEEEEC
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHHHCC--CcEEEEcCC
Confidence            5788899999999999999988776432  234555554

>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=93.16  E-value=0.056  Score=43.87  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |+|+|.+|+|||||...+....
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            7899999999999999997653

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.15  E-value=0.05  Score=50.88  Aligned_cols=25  Identities=32%  Similarity=0.550  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3589999999999999999997543

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.15  E-value=0.1  Score=48.76  Aligned_cols=27  Identities=26%  Similarity=0.404  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+|+|+|++|+|||||...+.....
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~~~   99 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKMLT   99 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            367899999999999999999987544

>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=93.15  E-value=0.045  Score=44.95  Aligned_cols=23  Identities=26%  Similarity=0.385  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|+|+|.+|+|||||...+...
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCccHHHHHHHHhcC
Confidence            45899999999999999998754

>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=93.14  E-value=0.039  Score=50.52  Aligned_cols=26  Identities=23%  Similarity=0.299  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-.+++|+|+.|+|||||++.+..-.
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            34689999999999999999987643

>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=93.11  E-value=0.051  Score=50.93  Aligned_cols=25  Identities=36%  Similarity=0.525  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEEcCCCchHHHHHHHHhcCC
Confidence            3689999999999999999987643

>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=93.10  E-value=0.054  Score=45.38  Aligned_cols=24  Identities=29%  Similarity=0.493  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|.|+|.+|+|||||+..+....
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            358899999999999999998653

>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=93.10  E-value=0.055  Score=43.94  Aligned_cols=24  Identities=25%  Similarity=0.440  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|.+|+|||||...+....
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            358899999999999999998653

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=93.08  E-value=0.054  Score=46.74  Aligned_cols=24  Identities=29%  Similarity=0.382  Sum_probs=21.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+|.|.|+.|+||||+++.+....
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            479999999999999999997754

>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=93.06  E-value=0.062  Score=45.14  Aligned_cols=25  Identities=16%  Similarity=0.407  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +...|+|+|..|+|||||...+...
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            4567899999999999999999765

>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=93.05  E-value=0.22  Score=49.11  Aligned_cols=48  Identities=17%  Similarity=0.260  Sum_probs=34.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREI  223 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i  223 (426)
                      -.-++|.|..|+|||+|+.++.+...    -+.++++-+.+. ....++++++
T Consensus       232 Gqr~~Ifgg~g~GKT~L~~~ia~~~~----~~v~V~~~iGER~~Ev~e~~~~~  280 (600)
T 3vr4_A          232 GGAAAVPGPFGAGKTVVQHQIAKWSD----VDLVVYVGCGERGNEMTDVVNEF  280 (600)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHSS----CSEEEEEEEEECHHHHHHHHHHT
T ss_pred             CCEEeeecCCCccHHHHHHHHHhccC----CCEEEEEEecccHHHHHHHHHHH
Confidence            35689999999999999999987643    356777777765 3455555543

>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=93.04  E-value=0.057  Score=43.81  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -|+|+|.+|+|||||...+....
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

>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=93.03  E-value=0.057  Score=43.89  Aligned_cols=22  Identities=32%  Similarity=0.549  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|+|+|.+|+|||||...+.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999999864

>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=93.01  E-value=0.053  Score=51.13  Aligned_cols=25  Identities=24%  Similarity=0.368  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+.--.
T Consensus        29 Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           29 GEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEEcCCCchHHHHHHHHHcCC
Confidence            3589999999999999999998644

>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=93.00  E-value=0.053  Score=44.19  Aligned_cols=23  Identities=17%  Similarity=0.333  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -|.|+|..|+|||||...+....
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            47899999999999999987654

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=92.99  E-value=0.053  Score=44.82  Aligned_cols=23  Identities=17%  Similarity=0.323  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35889999999999999999864

>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=92.99  E-value=0.035  Score=49.60  Aligned_cols=26  Identities=23%  Similarity=0.303  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +...|+|.|..|+||||+++.+.+..
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            45789999999999999999998765

>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=92.98  E-value=0.054  Score=50.72  Aligned_cols=25  Identities=24%  Similarity=0.284  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           29 GEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEEcCCCchHHHHHHHHHCCC
Confidence            3589999999999999999998643

>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=92.98  E-value=0.11  Score=46.21  Aligned_cols=37  Identities=19%  Similarity=0.297  Sum_probs=28.0

Q ss_pred             HHHHHHHhccC--CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          160 LKGILDALSNR--NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       160 ~~~l~~~l~~~--~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...+..++...  +...+.++|++|+|||.+|..+.+..
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            34456666543  24579999999999999999998853

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=92.96  E-value=0.059  Score=44.02  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|.|+|.+|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35889999999999999998865

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.95  E-value=0.054  Score=44.23  Aligned_cols=23  Identities=35%  Similarity=0.699  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|.|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999999864

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=92.94  E-value=0.054  Score=44.18  Aligned_cols=23  Identities=17%  Similarity=0.393  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -|.|+|.+|+|||||...+....
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            58899999999999999998654

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=92.93  E-value=0.055  Score=50.73  Aligned_cols=25  Identities=24%  Similarity=0.367  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcCC
Confidence            3589999999999999999997643

>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=92.91  E-value=0.11  Score=45.60  Aligned_cols=39  Identities=23%  Similarity=0.365  Sum_probs=28.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      |+|.|.||+||||+|..+.......+  ..++-+......+
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~g--~~VlliD~D~~~~   41 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASDY--DKIYAVDGDPDSC   41 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTTC--SCEEEEEECTTSC
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCcC
Confidence            66799999999999999998876543  3455666654444

>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=92.91  E-value=0.059  Score=44.94  Aligned_cols=23  Identities=30%  Similarity=0.339  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|+|+|.+|+|||||+..+...
T Consensus         8 ~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            8 CKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45789999999999999999865

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=92.87  E-value=0.036  Score=55.86  Aligned_cols=44  Identities=18%  Similarity=0.115  Sum_probs=30.1

Q ss_pred             ccchHHHHHHHHHHhccCCcc-----------EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          153 FESRKSTLKGILDALSNRNFN-----------MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~~~~~~-----------vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++|.+..+..+.-.+..+..+           -+.++|++|+|||+||+.+.+..
T Consensus       297 I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          297 IYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             TSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTC
T ss_pred             hcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhC
Confidence            456665555554444333211           58899999999999999998765

>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=92.87  E-value=0.061  Score=45.03  Aligned_cols=23  Identities=26%  Similarity=0.284  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|+|+|.+|+|||||+..+.+.
T Consensus        21 ~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           21 LKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45889999999999999887764

>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=92.86  E-value=0.056  Score=44.68  Aligned_cols=25  Identities=24%  Similarity=0.385  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..-|.|+|.+|+|||||...+....
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            4568999999999999999987653

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=92.86  E-value=0.056  Score=44.00  Aligned_cols=21  Identities=29%  Similarity=0.553  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      -|+|+|.+|+|||||...+.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            478999999999999999864

>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=92.85  E-value=0.053  Score=52.67  Aligned_cols=85  Identities=18%  Similarity=0.220  Sum_probs=48.5

Q ss_pred             cEEEEEcCCCCcHHHHH-HHHHHHhhhcCccc-eEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCc------
Q 044858          173 NMIGVYGMGGIGKTTLV-KEVGRQAKENNLFE-KVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESE------  236 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~------  236 (426)
                      .-+.|.|..|+|||+|| ..+.+...    -+ .++++-+++.. ...++.+.+...-...       ...++.      
T Consensus       164 QR~~Ifg~~g~GKT~Lal~~I~~~~~----~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a  239 (507)
T 1fx0_A          164 QRELIIGDRQTGKTAVATDTILNQQG----QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLA  239 (507)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCCT----TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHH
T ss_pred             CEEEEecCCCCCccHHHHHHHHHhhc----CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHH
Confidence            45789999999999995 56766543    34 34667776654 4555655554321110       001110      


Q ss_pred             HHHHHHHHHHHh-cCCeEEEEEeCCC
Q 044858          237 SVRAWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       237 ~~~~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                      ......+-+++. +++.+||++||+.
T Consensus       240 ~~~a~tiAEyfrd~G~dVLli~Dslt  265 (507)
T 1fx0_A          240 PYTGAALAEYFMYRERHTLIIYDDLS  265 (507)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEEecHH
Confidence            111222333332 4799999999973

>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=92.84  E-value=0.058  Score=50.83  Aligned_cols=24  Identities=25%  Similarity=0.410  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|.|+.|+|||||.+.+.--.
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCcHHHHHHHHHHcCC
Confidence            579999999999999999998643

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=92.81  E-value=0.061  Score=43.92  Aligned_cols=21  Identities=33%  Similarity=0.572  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      -|+|+|.+|+|||||...+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            478999999999999999863

>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=92.80  E-value=0.14  Score=46.28  Aligned_cols=38  Identities=29%  Similarity=0.469  Sum_probs=28.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      .++|+|.|.||+||||+|..+.......+  ..+.-+...
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~La~~G--~rVlliD~D   39 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAALAEMG--KKVMIVGCD   39 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHTT--CCEEEEEEC
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHHHHHCC--CeEEEEecC
Confidence            36788899999999999999988776432  234555554

>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=92.80  E-value=0.059  Score=50.74  Aligned_cols=25  Identities=24%  Similarity=0.344  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC
Confidence            3589999999999999999997543

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=92.79  E-value=0.064  Score=44.22  Aligned_cols=23  Identities=35%  Similarity=0.397  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|+|+|.+|+|||||...+...
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEEEECcCCCCHHHHHHHHHhC
Confidence            35889999999999999998764

>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=92.77  E-value=0.064  Score=44.16  Aligned_cols=23  Identities=26%  Similarity=0.457  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|+|+|.+|+|||||...+...
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45899999999999999999764

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=92.77  E-value=0.065  Score=43.69  Aligned_cols=23  Identities=26%  Similarity=0.352  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|+|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35889999999999999998754

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=92.76  E-value=0.073  Score=44.55  Aligned_cols=25  Identities=16%  Similarity=0.320  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...|+|+|..|+|||||...+....
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            4568999999999999999998764

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=92.75  E-value=0.077  Score=45.33  Aligned_cols=25  Identities=16%  Similarity=0.170  Sum_probs=23.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|.|.|+.|+||||+++.+.+...
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~lg   31 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHYN   31 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHhC
Confidence            5899999999999999999998765

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=92.69  E-value=0.11  Score=51.61  Aligned_cols=28  Identities=25%  Similarity=0.338  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+++|+|+.|+|||||++.+......
T Consensus       368 ~G~iI~LiG~sGSGKSTLar~La~~L~~  395 (552)
T 3cr8_A          368 QGFTVFFTGLSGAGKSTLARALAARLME  395 (552)
T ss_dssp             SCEEEEEEESSCHHHHHHHHHHHHHHHT
T ss_pred             cceEEEEECCCCChHHHHHHHHHHhhcc
Confidence            3468999999999999999999987753

>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=92.67  E-value=0.1  Score=47.67  Aligned_cols=33  Identities=18%  Similarity=0.400  Sum_probs=25.3

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++++.+.+..   .+++++|+.|+|||||.+.+. ..
T Consensus       156 i~~L~~~l~G---~i~~l~G~sG~GKSTLln~l~-~~  188 (302)
T 2yv5_A          156 IDELVDYLEG---FICILAGPSGVGKSSILSRLT-GE  188 (302)
T ss_dssp             HHHHHHHTTT---CEEEEECSTTSSHHHHHHHHH-SC
T ss_pred             HHHHHhhccC---cEEEEECCCCCCHHHHHHHHH-Hh
Confidence            3455555432   578999999999999999998 54

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=92.66  E-value=0.069  Score=43.47  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|+|+|..|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998864

>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=92.65  E-value=0.094  Score=44.42  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=20.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      +..-|+|+|.+|+|||||...+..
T Consensus        24 ~~~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           24 KTGKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            345688999999999999999875

>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=92.63  E-value=0.05  Score=50.78  Aligned_cols=25  Identities=20%  Similarity=0.236  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        26 Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           26 GEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCccHHHHHHHHHcCC
Confidence            3589999999999999999998644

>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=92.63  E-value=0.082  Score=43.58  Aligned_cols=24  Identities=29%  Similarity=0.440  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|+|+|..|+|||||...+...
T Consensus         9 ~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            9 THKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346899999999999999998875

>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=92.62  E-value=0.1  Score=49.24  Aligned_cols=110  Identities=19%  Similarity=0.162  Sum_probs=55.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEE-EEEecCCcCHHHHHHHHHHH--hCCCccccCcHHHHHHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVI-SSRVSQTPQIKEIQREIAEK--LGLKIDQESESVRAWRLLEQ  246 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~-wv~v~~~~~~~~il~~i~~~--l~~~~~~~~~~~~~~~l~~~  246 (426)
                      ....+++|+|+.|+|||||++.+.......  ....+ ++...-......- ..+..|  ++.  +.   ......+...
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~~~--~~g~I~~~e~~~e~~~~~~-~~~v~Q~~~g~--~~---~~~~~~l~~~  205 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYINQT--KSYHIITIEDPIEYVFKHK-KSIVNQREVGE--DT---KSFADALRAA  205 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHHHH--SCCEEEEEESSCCSCCCCS-SSEEEEEEBTT--TB---SCSHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcCcC--CCcEEEEecccHhhhhccC-ceEEEeeecCC--CH---HHHHHHHHHH
Confidence            345689999999999999999998765432  11222 2221110000000 000000  000  00   1112344555


Q ss_pred             HhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhh
Q 044858          247 LKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDV  291 (426)
Q Consensus       247 l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~v  291 (426)
                      +.. .+=+|++|++.+.+.........   ..|..|+.|+....+
T Consensus       206 L~~-~pd~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~~~  246 (372)
T 2ewv_A          206 LRE-DPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTA  246 (372)
T ss_dssp             TTS-CCSEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCCSH
T ss_pred             hhh-CcCEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcchH
Confidence            554 56789999998655443322211   235567777776543

>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=92.61  E-value=0.063  Score=45.01  Aligned_cols=24  Identities=21%  Similarity=0.328  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|.|+|.+|+|||||...+....
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            458899999999999999987653

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=92.61  E-value=0.069  Score=44.93  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ...|+|+|.+|+|||||...+.+.
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            346899999999999999998864

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=92.55  E-value=0.21  Score=43.03  Aligned_cols=27  Identities=22%  Similarity=0.241  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...|.+.|+.|+||||+++.+.+....
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHHCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            468999999999999999999988764

>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=92.53  E-value=0.068  Score=44.85  Aligned_cols=24  Identities=38%  Similarity=0.286  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|.|+|.+|+|||||++.+.+..
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            358899999999999997766543

>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=92.51  E-value=0.073  Score=43.79  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..-|.|+|..|+|||||...+....
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            3468899999999999999998654

>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=92.51  E-value=0.076  Score=44.79  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=19.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .-|+|+|.+|+|||||...+..
T Consensus         7 ~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            7 YRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3588999999999999999874

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=92.50  E-value=0.11  Score=49.74  Aligned_cols=28  Identities=29%  Similarity=0.274  Sum_probs=23.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ....+++|+|+.|+|||||.+.+.....
T Consensus       165 ~~ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          165 RPHGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             hcCCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            4456899999999999999999987654

>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=92.49  E-value=0.066  Score=50.40  Aligned_cols=26  Identities=19%  Similarity=0.349  Sum_probs=22.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..++|+|+.|+|||||++.+......
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L~gl~~~  196 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKLAAVFNT  196 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            57899999999999999999876543

>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=92.48  E-value=0.083  Score=52.25  Aligned_cols=27  Identities=26%  Similarity=0.325  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+|.++|++|+||||+|+.+.....
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999987664

>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=92.48  E-value=0.067  Score=44.48  Aligned_cols=24  Identities=25%  Similarity=0.303  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|..|+|||||...+.+..
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            458899999999999999988653

>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=92.44  E-value=0.058  Score=44.56  Aligned_cols=22  Identities=27%  Similarity=0.422  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|+|+|.+|+|||||...+.+.
T Consensus         9 ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            9 RLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEECCGGGCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5789999999999999998864

>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=92.43  E-value=0.069  Score=43.95  Aligned_cols=23  Identities=22%  Similarity=0.281  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|.|+|..|+|||||...+...
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35889999999999999998754

>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=92.41  E-value=0.075  Score=44.21  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|+|+|.+|+|||||...+.+..
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            358899999999999999998654

>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=92.40  E-value=0.064  Score=44.77  Aligned_cols=22  Identities=27%  Similarity=0.395  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|+|+|.+|+|||||...+...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            4789999999999999998764

>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=92.40  E-value=0.07  Score=44.27  Aligned_cols=23  Identities=30%  Similarity=0.469  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|.|+|.+|+|||||...+.+.
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45889999999999999999865

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=92.39  E-value=0.083  Score=49.14  Aligned_cols=28  Identities=25%  Similarity=0.493  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..+++|+|++|+|||||.+.+.....
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~~   80 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLLT   80 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhhh
Confidence            4557899999999999999999986654

>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=92.39  E-value=0.095  Score=42.76  Aligned_cols=23  Identities=30%  Similarity=0.430  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..|.|+|.+|+|||||...+...
T Consensus         8 ~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            8 MRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            46889999999999999999764

>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=92.37  E-value=0.077  Score=44.32  Aligned_cols=24  Identities=21%  Similarity=0.270  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|+|+|..|+|||||...+....
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            458899999999999999998643

>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=92.34  E-value=0.047  Score=51.09  Aligned_cols=25  Identities=28%  Similarity=0.457  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+.--.
T Consensus        31 Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           31 GERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3589999999999999999998543

>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=92.32  E-value=0.074  Score=50.42  Aligned_cols=24  Identities=33%  Similarity=0.451  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaGl   70 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLRL   70 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            358999999999999999999753

>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=92.29  E-value=0.084  Score=44.30  Aligned_cols=24  Identities=17%  Similarity=0.278  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|+|+|..|+|||||...+....
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            358899999999999999998754

>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=92.28  E-value=0.08  Score=44.43  Aligned_cols=24  Identities=29%  Similarity=0.482  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|+|+|..|+|||||...+....
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            458999999999999999988643

>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=92.24  E-value=0.18  Score=42.80  Aligned_cols=43  Identities=19%  Similarity=0.265  Sum_probs=30.1

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHH
Q 044858          173 NMIGVY-GMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIK  217 (426)
Q Consensus       173 ~vi~I~-G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  217 (426)
                      ++|+|+ +.||+||||+|..+.......+  ..++.+......+..
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~~g--~~vlliD~D~~~~~~   45 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSRSG--YNIAVVDTDPQMSLT   45 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHHTT--CCEEEEECCTTCHHH
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHHCC--CeEEEEECCCCCCHH
Confidence            567776 7799999999999988776532  245666665544433

>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=92.23  E-value=0.061  Score=45.51  Aligned_cols=22  Identities=32%  Similarity=0.530  Sum_probs=19.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVG  193 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~  193 (426)
                      ..-|+|+|.+|+|||||...+.
T Consensus        23 ~~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           23 IFKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHTC
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
Confidence            3468999999999999999985

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.22  E-value=0.065  Score=50.37  Aligned_cols=25  Identities=40%  Similarity=0.478  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|+|+.|+|||||++.+.....
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            5799999999999999999987654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=92.21  E-value=0.26  Score=50.23  Aligned_cols=63  Identities=25%  Similarity=0.263  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          157 KSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       157 ~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      +...+.+...|...  .+..|+||+|+|||+.+.++....-.+   ...+.++...+..+..++..+.
T Consensus       192 ~~Q~~AV~~al~~~--~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~  254 (646)
T 4b3f_X          192 TSQKEAVLFALSQK--ELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLA  254 (646)
T ss_dssp             HHHHHHHHHHHHCS--SEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCC--CceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHH
Confidence            34455566555433  467899999999996555544433222   2356666666666666666654

>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=92.21  E-value=0.076  Score=44.04  Aligned_cols=24  Identities=25%  Similarity=0.440  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|..|+|||||...+....
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            458899999999999999998653

>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=92.21  E-value=0.083  Score=43.80  Aligned_cols=22  Identities=32%  Similarity=0.369  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|+|+|.+|+|||||...+.+.
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5789999999999999998754

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=92.18  E-value=0.27  Score=42.06  Aligned_cols=25  Identities=36%  Similarity=0.434  Sum_probs=22.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.|+|-|.-|+||||+++.+.+...
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~   27 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLV   27 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHH
Confidence            4689999999999999999998875

>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=92.17  E-value=0.085  Score=43.61  Aligned_cols=24  Identities=29%  Similarity=0.350  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .--|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            8 FIKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            345889999999999999998764

>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=92.15  E-value=0.076  Score=44.75  Aligned_cols=25  Identities=24%  Similarity=0.312  Sum_probs=21.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+..-|+|+|.+|+|||||...+..
T Consensus        27 ~~~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           27 KKQMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHCS
T ss_pred             CCccEEEEECCCCCCHHHHHHHHHh
Confidence            3445689999999999999999864

>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=92.15  E-value=0.086  Score=43.64  Aligned_cols=24  Identities=21%  Similarity=0.351  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|+|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            346899999999999999999854

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=92.12  E-value=0.24  Score=42.37  Aligned_cols=43  Identities=19%  Similarity=0.148  Sum_probs=30.7

Q ss_pred             EEEE-EcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHH
Q 044858          174 MIGV-YGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEI  219 (426)
Q Consensus       174 vi~I-~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~i  219 (426)
                      +|+| .+.||+||||+|..+.......+   .+.-+......+....
T Consensus         2 vI~v~s~KGGvGKTT~a~~LA~~la~~g---~VlliD~D~q~~~~~~   45 (209)
T 3cwq_A            2 IITVASFKGGVGKTTTAVHLSAYLALQG---ETLLIDGDPNRSATGW   45 (209)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHTTS---CEEEEEECTTCHHHHH
T ss_pred             EEEEEcCCCCCcHHHHHHHHHHHHHhcC---CEEEEECCCCCCHHHH
Confidence            4555 57899999999999998877542   5667776655544433

>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=92.12  E-value=0.078  Score=44.92  Aligned_cols=25  Identities=24%  Similarity=0.449  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..-|+|+|.+|+|||||...+....
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            3468999999999999999987653

>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=92.12  E-value=0.067  Score=48.91  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      -|+|+|+.|+|||||.+.++.
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            459999999999999999764

>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=92.12  E-value=0.087  Score=43.46  Aligned_cols=24  Identities=29%  Similarity=0.361  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|+|+|..|+|||||...+....
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            358999999999999999987653

>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=92.12  E-value=0.087  Score=43.52  Aligned_cols=24  Identities=25%  Similarity=0.340  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|.+|+|||||...+....
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            358899999999999999988653

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=92.12  E-value=0.078  Score=43.72  Aligned_cols=24  Identities=21%  Similarity=0.416  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|+|+|.+|+|||||...+...
T Consensus         9 ~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            9 LFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            346899999999999999998754

>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=92.11  E-value=0.085  Score=43.93  Aligned_cols=27  Identities=22%  Similarity=0.321  Sum_probs=22.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+..-|.|+|.+|+|||||...+....
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            345578999999999999999998654

>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=92.09  E-value=0.054  Score=46.24  Aligned_cols=25  Identities=16%  Similarity=0.198  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ....|+|+|..|+|||||.+.+...
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3457999999999999999988754

>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=92.06  E-value=0.087  Score=44.85  Aligned_cols=23  Identities=35%  Similarity=0.489  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|+|+|.+|+|||||+..+...
T Consensus        27 ~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           27 FKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            46889999999999999998764

>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=92.01  E-value=0.089  Score=44.93  Aligned_cols=25  Identities=28%  Similarity=0.275  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..-|+|+|.+|+|||||+..+....
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            3468899999999999999998753

>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=91.99  E-value=0.09  Score=45.64  Aligned_cols=25  Identities=24%  Similarity=0.376  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +...|+|+|.+|+|||||...+...
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            4467899999999999999998765

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=91.95  E-value=0.091  Score=44.50  Aligned_cols=25  Identities=20%  Similarity=0.399  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..-|+|+|.+|+|||||...+....
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

>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=91.95  E-value=0.099  Score=44.71  Aligned_cols=25  Identities=20%  Similarity=0.138  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...|+|+|.+|+|||||...+....
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            4568999999999999999998654

>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=91.94  E-value=0.091  Score=44.57  Aligned_cols=25  Identities=24%  Similarity=0.426  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..-|+|+|.+|+|||||...+....
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            3468999999999999999987653

>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=91.94  E-value=0.093  Score=43.90  Aligned_cols=24  Identities=25%  Similarity=0.308  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|+|+|..|+|||||...+....
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            458899999999999999998643

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=91.93  E-value=0.093  Score=48.98  Aligned_cols=26  Identities=31%  Similarity=0.502  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||.+.+.....
T Consensus        71 Gq~~gIiG~nGaGKTTLl~~I~g~~~   96 (347)
T 2obl_A           71 GQRIGIFAGSGVGKSTLLGMICNGAS   96 (347)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            35799999999999999999998865

>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=91.93  E-value=0.092  Score=44.11  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|+|+|..|+|||||...+....
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            458999999999999999998654

>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=91.92  E-value=0.085  Score=45.61  Aligned_cols=22  Identities=23%  Similarity=0.341  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|.|+|.+|+|||+|+..+.+.
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            3789999999999999998754

>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=91.90  E-value=0.14  Score=51.21  Aligned_cols=28  Identities=14%  Similarity=0.099  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+|.|.|++|+||||+|+.+.+....
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~~L~~  422 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQVTLNQ  422 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHHHhcc
Confidence            4568999999999999999999887653

>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=91.90  E-value=0.11  Score=43.72  Aligned_cols=25  Identities=24%  Similarity=0.452  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ...-|+|+|.+|+|||||...+...
T Consensus        27 ~~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           27 AEVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3456889999999999999998865

>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=91.89  E-value=0.088  Score=44.05  Aligned_cols=24  Identities=17%  Similarity=0.267  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|..|+|||||...+....
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            458999999999999999987653

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=91.87  E-value=0.094  Score=44.15  Aligned_cols=25  Identities=16%  Similarity=0.308  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .--|+|+|..|+|||||...+....
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            3458899999999999999998763

>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=91.84  E-value=0.097  Score=43.90  Aligned_cols=23  Identities=22%  Similarity=0.310  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|.|+|..|+|||||...+...
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           22 FKYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            35889999999999999998764

>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=91.84  E-value=0.22  Score=46.94  Aligned_cols=40  Identities=15%  Similarity=0.199  Sum_probs=29.4

Q ss_pred             CCccEEEEEc-CCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          170 RNFNMIGVYG-MGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       170 ~~~~vi~I~G-~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      ++.++|+|+| -||+||||+|..+.......  -..++.+...
T Consensus       141 ~~~kvIav~s~KGGvGKTT~a~nLA~~La~~--g~rVlliD~D  181 (373)
T 3fkq_A          141 DKSSVVIFTSPCGGVGTSTVAAACAIAHANM--GKKVFYLNIE  181 (373)
T ss_dssp             TSCEEEEEECSSTTSSHHHHHHHHHHHHHHH--TCCEEEEECC
T ss_pred             CCceEEEEECCCCCChHHHHHHHHHHHHHhC--CCCEEEEECC
Confidence            3567888875 99999999999998776543  2245666654

>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=91.83  E-value=0.097  Score=43.98  Aligned_cols=24  Identities=33%  Similarity=0.419  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|.|+|.+|+|||||...+....
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            458899999999999999998754

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=91.83  E-value=7.9  Score=35.81  Aligned_cols=26  Identities=23%  Similarity=0.399  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ....|+|+|.+|+|||||...+....
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            45689999999999999999987643

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=91.82  E-value=0.1  Score=43.11  Aligned_cols=23  Identities=22%  Similarity=0.209  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-+.|.|++|+||||||..+...
T Consensus        17 ~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45889999999999999998874

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=91.79  E-value=0.086  Score=44.51  Aligned_cols=24  Identities=25%  Similarity=0.232  Sum_probs=20.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|.|+|.+|+|||||.+.+.+.
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhc
Confidence            346889999999999999877664

>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=91.75  E-value=0.12  Score=41.71  Aligned_cols=24  Identities=21%  Similarity=0.277  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..+.+|+|+.|+|||||...++--
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            357899999999999999988754

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=91.74  E-value=0.092  Score=44.04  Aligned_cols=24  Identities=21%  Similarity=0.354  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|..|+|||||...+....
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            458999999999999999998654

>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=91.74  E-value=0.099  Score=43.98  Aligned_cols=24  Identities=33%  Similarity=0.555  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|+|+|.+|+|||||...+...
T Consensus         8 ~~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            8 DYRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCcHHHHHHHHHcC
Confidence            346899999999999999999764

>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=91.73  E-value=0.17  Score=47.11  Aligned_cols=29  Identities=31%  Similarity=0.393  Sum_probs=24.4

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+..+|+|+|.+|+|||||+..+.....
T Consensus        53 ~~~~~~i~i~G~~g~GKSTl~~~l~~~~~   81 (341)
T 2p67_A           53 CGNTLRLGVTGTPGAGKSTFLEAFGMLLI   81 (341)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            34567899999999999999999976654

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=91.73  E-value=0.28  Score=45.37  Aligned_cols=30  Identities=33%  Similarity=0.401  Sum_probs=24.1

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ++...++.+.|.||+||||+|..+......
T Consensus        16 ~~~~~i~v~sgkGGvGKTTva~~LA~~lA~   45 (329)
T 2woo_A           16 QTSLKWIFVGGKGGVGKTTTSCSLAIQMSK   45 (329)
T ss_dssp             CTTCCEEEEECSSSSSHHHHHHHHHHHHHT
T ss_pred             CCCCEEEEEeCCCCCcHHHHHHHHHHHHHH
Confidence            334567778999999999999999877654

>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=91.73  E-value=0.093  Score=44.43  Aligned_cols=24  Identities=21%  Similarity=0.302  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|.+|+|||||...+....
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            358999999999999999987653

>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=91.70  E-value=0.15  Score=46.50  Aligned_cols=34  Identities=21%  Similarity=0.476  Sum_probs=25.6

Q ss_pred             HHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          161 KGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       161 ~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +++...+..   .+++|+|+.|+|||||.+.+.....
T Consensus       161 ~~lf~~l~g---eiv~l~G~sG~GKSTll~~l~g~~~  194 (301)
T 1u0l_A          161 EELKEYLKG---KISTMAGLSGVGKSSLLNAINPGLK  194 (301)
T ss_dssp             HHHHHHHSS---SEEEEECSTTSSHHHHHHHHSTTCC
T ss_pred             HHHHHHhcC---CeEEEECCCCCcHHHHHHHhccccc
Confidence            445554432   5789999999999999999976543

>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=91.68  E-value=0.1  Score=43.61  Aligned_cols=24  Identities=29%  Similarity=0.235  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|.|+|..|+|||||...+...
T Consensus        20 ~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           20 IFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            356899999999999999998764

>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=91.68  E-value=0.14  Score=43.56  Aligned_cols=93  Identities=10%  Similarity=0.051  Sum_probs=51.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH-HHHHhCCCcccc------------CcH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE-IAEKLGLKIDQE------------SES  237 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~-i~~~l~~~~~~~------------~~~  237 (426)
                      ...+|+|+|+.|+||+|+|..+.+....    ....      ..++.+.+++ .+...+.+.+..            ...
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~~~g~----~~~~------vv~msD~iK~~~a~~~gl~~~~~l~~~~ykE~~R~~m~   79 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQSRLGA----DVCA------VLRLSGPLKEQYAQEHGLNFQRLLDTSTYKEAFRKDMI   79 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHHHHCT----TTEE------EECTHHHHHHHHHHTTTCCCC-------CCSSHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHHHcCC----CCce------EEEccHHHHHHHHHHcCCCchhhcchhhhHHHHHHHHH
Confidence            4568999999999999999998764421    1111      1245666663 455555443221            000


Q ss_pred             HHHHHHHHH--------Hh-cCCeEEEEEeCCCCccChhhhcCCC
Q 044858          238 VRAWRLLEQ--------LK-KETKILIILDDIWGSLDLEAIGIPL  273 (426)
Q Consensus       238 ~~~~~l~~~--------l~-~~k~~LlVlDdv~~~~~~~~l~~~l  273 (426)
                      .....+++.        .. .-..-.+|+||+.+..+.+.+...+
T Consensus        80 ~~g~~~R~~d~~~~~~~~~~~~~~~~vII~dvR~~~Ev~~fr~~~  124 (202)
T 3ch4_B           80 RWGEEKRQADPGFFCRKIVEGISQPIWLVSDTRRVSDIQWFREAY  124 (202)
T ss_dssp             HHHHHHHHHCTTTTHHHHSBTCCCSEEEECCCCSHHHHHHHHHHH
T ss_pred             HHHHHHHhcCchHHHHHHHHhcCCCcEEEeCCCCHHHHHHHHHhC
Confidence            011111111        11 1112278999999888777665443

>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=91.68  E-value=0.11  Score=50.72  Aligned_cols=27  Identities=26%  Similarity=0.306  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+|.++|++|+||||+++.+.....
T Consensus        38 ~~~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           38 CPTLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999987654

>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=91.63  E-value=0.099  Score=45.00  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=19.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .-|+|+|.+|+|||||...+..
T Consensus        38 ~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           38 YRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4589999999999999999873

>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=91.63  E-value=0.09  Score=44.56  Aligned_cols=24  Identities=25%  Similarity=0.336  Sum_probs=20.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|+|+|..|+|||||...+...
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            346889999999999999998754

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=91.62  E-value=0.091  Score=44.41  Aligned_cols=24  Identities=29%  Similarity=0.270  Sum_probs=20.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|.|+|.+|+|||||...+.+.
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            345889999999999999998754

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=91.60  E-value=0.089  Score=51.10  Aligned_cols=26  Identities=23%  Similarity=0.175  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||++.+..-..
T Consensus       138 Ge~v~IvGpnGsGKSTLlr~L~Gl~~  163 (460)
T 2npi_A          138 GPRVVIVGGSQTGKTSLSRTLCSYAL  163 (460)
T ss_dssp             CCCEEEEESTTSSHHHHHHHHHHTTH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCccc
Confidence            35799999999999999999987543

>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=91.59  E-value=0.11  Score=44.00  Aligned_cols=25  Identities=16%  Similarity=0.301  Sum_probs=21.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ...-|+|+|..|+|||||...+...
T Consensus        27 ~~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           27 KAYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             -CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhC
Confidence            3456899999999999999998754

>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=91.57  E-value=0.076  Score=49.24  Aligned_cols=105  Identities=23%  Similarity=0.199  Sum_probs=53.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .+++|+|+.|+|||||++.+.......   ...+.+.-......... +   +.++.-..  ........+...+. .++
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~---~g~i~i~~~~e~~~~~~-~---~~i~~~~g--gg~~~r~~la~aL~-~~p  241 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKE---ERIISIEDTEEIVFKHH-K---NYTQLFFG--GNITSADCLKSCLR-MRP  241 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTT---SCEEEEESSCCCCCSSC-S---SEEEEECB--TTBCHHHHHHHHTT-SCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCC---CcEEEECCeeccccccc-h---hEEEEEeC--CChhHHHHHHHHhh-hCC
Confidence            479999999999999999998765432   23444432211110000 0   00000000  11112233444454 367


Q ss_pred             EEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchh
Q 044858          253 ILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQD  290 (426)
Q Consensus       253 ~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~  290 (426)
                      =+|++|++.+.+.++.+.. +..  .+..+|+||....
T Consensus       242 ~ilildE~~~~e~~~~l~~-~~~--g~~tvi~t~H~~~  276 (330)
T 2pt7_A          242 DRIILGELRSSEAYDFYNV-LCS--GHKGTLTTLHAGS  276 (330)
T ss_dssp             SEEEECCCCSTHHHHHHHH-HHT--TCCCEEEEEECSS
T ss_pred             CEEEEcCCChHHHHHHHHH-Hhc--CCCEEEEEEcccH
Confidence            7899999987544443322 211  1223677776554

>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=91.55  E-value=0.1  Score=43.75  Aligned_cols=24  Identities=25%  Similarity=0.409  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|+|+|.+|+|||||...+.+..
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            358899999999999999998653

>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=91.55  E-value=0.34  Score=45.23  Aligned_cols=28  Identities=36%  Similarity=0.377  Sum_probs=22.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +...++...|.||+||||+|..+.....
T Consensus        16 ~~~~i~v~sgKGGvGKTTvaanLA~~lA   43 (354)
T 2woj_A           16 TTHKWIFVGGKGGVGKTTSSCSIAIQMA   43 (354)
T ss_dssp             SSCCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHHHH
Confidence            3345677789999999999999887665

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=91.54  E-value=0.31  Score=44.88  Aligned_cols=27  Identities=26%  Similarity=0.365  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ..++...|.||+||||+|..+......
T Consensus        14 ~~i~v~sgKGGvGKTTvA~~LA~~lA~   40 (324)
T 3zq6_A           14 TTFVFIGGKGGVGKTTISAATALWMAR   40 (324)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCchHHHHHHHHHHHHHH
Confidence            356778899999999999998877654

>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=91.53  E-value=0.11  Score=44.18  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|.+|+|||||...+....
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            458899999999999999987643

>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=91.47  E-value=0.11  Score=47.58  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ...|+|+|.+|+|||||...+...
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            457999999999999999999865

>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=91.46  E-value=0.29  Score=49.24  Aligned_cols=40  Identities=20%  Similarity=0.274  Sum_probs=29.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      +..+++.+.|.||+||||+|..+.......+  ..+..|+..
T Consensus         6 ~~~~i~~~sgkGGvGKTT~a~~lA~~lA~~G--~rVLlvd~D   45 (589)
T 1ihu_A            6 NIPPYLFFTGKGGVGKTSISCATAIRLAEQG--KRVLLVSTD   45 (589)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEECC
T ss_pred             CCCEEEEEeCCCcCHHHHHHHHHHHHHHHCC--CcEEEEECC
Confidence            4567889999999999999999987765432  234555544

>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=91.39  E-value=0.09  Score=43.65  Aligned_cols=23  Identities=22%  Similarity=0.407  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|.|+|..|+|||||...+...
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            46889999999999999999864

>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=91.32  E-value=0.1  Score=44.86  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|+|+|.+|+|||||...+...
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            46889999999999999998754

>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=91.30  E-value=0.12  Score=44.10  Aligned_cols=23  Identities=30%  Similarity=0.414  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|+|+|.+|+|||||...+...
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHhcC
Confidence            46899999999999999998864

>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=91.30  E-value=0.11  Score=48.44  Aligned_cols=24  Identities=21%  Similarity=0.336  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|++|+|||||.+.+....
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            578999999999999999988543

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=91.29  E-value=0.31  Score=45.50  Aligned_cols=28  Identities=36%  Similarity=0.453  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ...++.+.|.||+||||+|..+......
T Consensus        25 ~~~i~v~sgKGGvGKTTvA~~LA~~lA~   52 (349)
T 3ug7_A           25 GTKYIMFGGKGGVGKTTMSAATGVYLAE   52 (349)
T ss_dssp             SCEEEEEECSSSTTHHHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCccHHHHHHHHHHHHHH
Confidence            3456677899999999999998877654

>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=91.29  E-value=0.13  Score=51.74  Aligned_cols=27  Identities=22%  Similarity=0.228  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+|.|.|+.|+||||+|+.+.+...
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~   77 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLV   77 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            456899999999999999999988763

>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=91.28  E-value=0.12  Score=45.30  Aligned_cols=26  Identities=19%  Similarity=0.156  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ....|+|+|.+|+|||||...+....
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            44578999999999999999988643

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=91.26  E-value=0.12  Score=43.44  Aligned_cols=26  Identities=23%  Similarity=0.340  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ....|+|+|..|+|||||...+....
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            34678999999999999999987643

>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=91.25  E-value=0.12  Score=43.35  Aligned_cols=23  Identities=30%  Similarity=0.354  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|.|+|..|+|||||...+.+.
T Consensus        19 ~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           19 LKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35889999999999999999865

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=91.23  E-value=0.088  Score=44.27  Aligned_cols=24  Identities=25%  Similarity=0.447  Sum_probs=19.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|.|+|..|+|||||...+....
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

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=91.17  E-value=0.1  Score=49.95  Aligned_cols=22  Identities=32%  Similarity=0.394  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .++|+|+.|+|||||.+.++..
T Consensus        44 ~vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           44 NILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            3999999999999999998754

>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=91.14  E-value=0.13  Score=46.11  Aligned_cols=23  Identities=22%  Similarity=0.398  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..|+|+|.+|+|||||...+...
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            56899999999999999998765

>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=91.13  E-value=0.11  Score=47.50  Aligned_cols=25  Identities=20%  Similarity=0.421  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ....|+|+|.+|+|||||...+...
T Consensus         9 ~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            9 KVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3568999999999999999998764

>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=91.12  E-value=0.12  Score=43.73  Aligned_cols=24  Identities=21%  Similarity=0.307  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ..-|.|+|.+|+|||||+..+...
T Consensus        29 ~~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           29 LFKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhhC
Confidence            346899999999999999998754

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=91.10  E-value=0.13  Score=43.97  Aligned_cols=23  Identities=22%  Similarity=0.200  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|+|+|.+|+|||||+..+...
T Consensus        10 ~ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A           10 IKCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45889999999999999998864

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=91.09  E-value=0.27  Score=48.84  Aligned_cols=44  Identities=11%  Similarity=0.171  Sum_probs=30.6

Q ss_pred             chHHHHHHHHHHh--ccCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          155 SRKSTLKGILDAL--SNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       155 gR~~~~~~l~~~l--~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|.+....+.+..  ......+|.+.|+.|+||||+|+.+......
T Consensus       353 ~r~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~~  398 (546)
T 2gks_A          353 TRPEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQA  398 (546)
T ss_dssp             SCHHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhhh
Confidence            3444444444444  1234568999999999999999999887653

>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=91.07  E-value=0.13  Score=43.60  Aligned_cols=24  Identities=25%  Similarity=0.390  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|+|+|.+|+|||||...+....
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            458899999999999999988643

>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=91.06  E-value=0.13  Score=43.84  Aligned_cols=25  Identities=24%  Similarity=0.332  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ..-|+|+|.+|+|||||...+....
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            3468899999999999999988543

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=91.06  E-value=0.16  Score=44.04  Aligned_cols=26  Identities=15%  Similarity=0.095  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+|.|.|+.|+||||+++.+.....
T Consensus        14 ~~iI~i~g~~gsGk~~i~~~la~~lg   39 (223)
T 3hdt_A           14 NLIITIEREYGSGGRIVGKKLAEELG   39 (223)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999998765

>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=91.01  E-value=0.12  Score=43.13  Aligned_cols=34  Identities=24%  Similarity=0.140  Sum_probs=24.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      +.|+|.+|+||||+|.++... .     ..++++.-+..+
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~-----~~~~yiaT~~~~   35 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-A-----PQVLYIATSQIL   35 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-C-----SSEEEEECCCC-
T ss_pred             EEEECCCCCcHHHHHHHHHhc-C-----CCeEEEecCCCC
Confidence            689999999999999998855 1     124555554443

>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=91.00  E-value=0.072  Score=44.22  Aligned_cols=23  Identities=22%  Similarity=0.335  Sum_probs=9.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|.|+|.+|+|||||...+.+.
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            45899999999999999988754

>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=90.99  E-value=0.13  Score=44.14  Aligned_cols=24  Identities=17%  Similarity=0.261  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      --|.|+|.+|+|||||...+....
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            458899999999999999987653

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=90.88  E-value=0.13  Score=49.55  Aligned_cols=28  Identities=21%  Similarity=0.472  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +-..++|+|+.|+|||||++.+......
T Consensus       156 ~Gq~~~IvG~sGsGKSTLl~~Iag~~~~  183 (438)
T 2dpy_A          156 RGQRMGLFAGSGVGKSVLLGMMARYTRA  183 (438)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcccCC
Confidence            3467999999999999999999987643

>3geh_A MNME, tRNA modification GTPase MNME; G protein, U34, GTP-binding, HYDR magnesium, metal-binding, nucleotide-binding, potassium, TR processing; HET: GDP FON; 3.20A {Nostoc SP}

Probab=90.86  E-value=1.7  Score=42.04  Aligned_cols=88  Identities=16%  Similarity=0.218  Sum_probs=55.1

Q ss_pred             CcHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccccccCCChHHHhHHHHHHHHHHHHHHHhhhcCCcceecccCCCcccc
Q 044858           64 IQQPVEEWLITVDEAINEVETLIADKEKSNNRCLKGLCPNLKTRYQLSKKAEREANAIVGLHEKGRFDSVSFRTIPEETW  143 (426)
Q Consensus        64 ~~~~~~~Wl~~l~~~~yd~ed~ld~~~~~~~~~~~~~~~~~~~r~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~  143 (426)
                      ....+..|..++.++.-.+|-.+|.-. .-         ....+..+..++..+.+.+.++....               
T Consensus       161 ~~~~~~~~r~~l~~~~a~iEa~iDf~e-d~---------~~~~~~~~~~~i~~l~~~l~~~~~~~---------------  215 (462)
T 3geh_A          161 LAHPIRQLRANCLDILAEIEARIDFEE-DL---------PPLDDEAIISDIENIAAEISQLLATK---------------  215 (462)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHTTSSS-SS---------CCCCTTTHHHHHHHHHHHHHHHTTTH---------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccccc-cC---------ChhhHHHHHHHHHHHHHHHHHHHHHh---------------
Confidence            467788899999999888888887322 10         01122345566666666666652210               


Q ss_pred             ccccCCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          144 LKSTQDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       144 ~~~~~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                                     ...+...    ++. .|+|+|.+|+|||||...+....
T Consensus       216 ---------------~~~~~~r----~~~-kV~ivG~~nvGKSSLln~L~~~~  248 (462)
T 3geh_A          216 ---------------DKGELLR----TGL-KVAIVGRPNVGKSSLLNAWSQSD  248 (462)
T ss_dssp             ---------------HHHHHHH----HCE-EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             ---------------hhhhhhc----CCC-EEEEEcCCCCCHHHHHHHHhCCC
Confidence                           0011111    122 38999999999999999988753

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=90.84  E-value=0.087  Score=44.13  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .-|+|+|..|+|||||...+....
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            468899999999999999988664

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=90.83  E-value=0.14  Score=49.82  Aligned_cols=25  Identities=20%  Similarity=0.163  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|+|+.|+|||||.+.+..-..
T Consensus        30 e~~~liG~nGsGKSTLl~~l~Gl~~   54 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVTALI   54 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEECCCCCcHHHHHHHHhcCCC
Confidence            7899999999999999999986543

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=90.70  E-value=0.94  Score=47.04  Aligned_cols=23  Identities=26%  Similarity=0.279  Sum_probs=18.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .++.|+|+.|+||||++..+...
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999976666443

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=90.63  E-value=0.097  Score=45.06  Aligned_cols=26  Identities=23%  Similarity=0.215  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ....|+|+|..|+|||||...+....
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~~   53 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQK   53 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTCS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            45678999999999999999998764

---

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	426
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	3e-32
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	4e-04

>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 =  121 bits (304), Expect = 3e-32
 Identities = 33/255 (12%), Positives = 84/255 (32%), Gaps = 26/255 (10%)

Query: 154 ESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN--NLFEKVISSRVS 211
           E     +   LD + + +   + ++G  G GK+ +  +   ++ +     ++ ++  + S
Sbjct: 26  EYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDS 85

Query: 212 QTPQIKEIQREIAEKLGLKIDQESESVRAWR----------LLEQLKKETKILIILDDIW 261
            T             L LK + +  +  +            +   L      L + DD+ 
Sbjct: 86  GTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVV 145

Query: 262 GSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKEAWSLFKKMTG 321
               +              + L+T R  ++ +      +   V  L   E +   +    
Sbjct: 146 QEETIRWA------QELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGM 199

Query: 322 DCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLRSFSGTQ 381
                 + + V+ + ++  +G P  ++   K+ + K+  +      +L+   L    G +
Sbjct: 200 PMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGL---VGVE 256

Query: 382 AVAAYSTIQLSYNQL 396
            +        SY  L
Sbjct: 257 CI-----TPYSYKSL 266

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 39.7 bits (91), Expect = 4e-04
 Identities = 10/104 (9%), Positives = 37/104 (35%)

Query: 164 LDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI 223
           ++ L      +  V G+   GK++++K    +     ++  +           K+   E+
Sbjct: 21  IEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLEL 80

Query: 224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLDLE 267
            +++   + +    ++A + ++ +      +    +    L   
Sbjct: 81  QKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFA 124

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	426
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.4
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.14
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.1
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.05
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.02
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.02
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.01
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.97
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.91
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.8
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.77
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.76
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.72
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.66
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.65
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.65
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.65
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.61
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.56
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.43
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.36
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.26
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.65
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.28
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.24
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.19
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.14
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.12
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.11
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.09
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.05
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.03
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.99
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.98
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.98
d1okkd2	207	GTPase domain of the signal recognition particle r	96.97
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.96
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.94
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.92
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.85
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.84
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.82
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.82
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.81
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.81
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.79
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.78
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.76
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.75
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.72
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.72
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.72
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.7
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.69
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.68
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.63
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.59
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.58
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.58
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.55
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.53
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.5
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.48
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.44
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.41
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.4
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.4
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.37
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.36
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.35
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.34
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.31
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.25
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.23
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.1
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.07
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.06
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	96.03
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.0
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.93
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.93
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.92
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.82
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.81
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.8
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.79
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	95.74
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.71
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.66
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.63
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.63
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.52
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.5
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.48
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.45
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.4
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.27
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.23
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	95.18
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.13
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.13
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.09
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.07
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.04
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.01
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.9
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	94.89
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.87
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.83
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.8
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	94.78
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.77
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.75
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	94.74
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	94.69
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.61
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.6
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	94.6
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	94.6
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	94.57
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.51
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.48
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.48
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.46
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	94.39
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.35
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.34
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.34
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.34
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.32
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.25
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	94.24
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.23
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.22
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.21
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.17
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.17
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.15
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.08
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.07
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.06
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.03
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.02
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.99
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.92
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	93.84
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.83
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.82
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.82
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.81
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.79
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.78
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.78
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	93.74
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.72
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.71
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.69
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.67
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	93.66
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.65
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.61
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.61
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.56
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	93.54
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.54
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.52
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.48
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.48
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	93.45
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.42
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.42
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.41
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	93.38
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.37
d2fh5b1	207	Signal recognition particle receptor beta-subunit	93.36
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.36
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.3
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.28
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	93.25
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	93.18
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.14
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.13
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.11
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.09
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	93.08
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	92.99
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	92.97
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	92.93
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.92
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.86
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	92.86
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.84
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	92.84
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.8
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	92.79
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	92.75
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.75
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.58
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	92.58
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.56
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.52
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	92.51
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.5
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	92.49
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	92.35
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	92.29
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	92.25
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.15
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	92.14
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	92.09
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.05
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	91.9
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	91.73
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	91.56
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.46
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	91.33
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	91.31
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	91.31
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	91.19
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	91.16
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	90.86
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	90.61
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.21
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	89.59
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	89.53
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	89.17
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	88.82
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	88.55
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	88.34
d1tuea_	205	Replication protein E1 helicase domain {Human papi	88.32
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	87.78
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	86.94
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	86.83
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.27
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	86.17
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	85.25
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	85.2
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	84.7
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	84.35
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	84.03
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.24
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	82.8
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	82.62
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	82.04

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=2.4e-44  Score=329.94  Aligned_cols=243  Identities=14%  Similarity=0.135  Sum_probs=195.2

Q ss_pred             ccccchHHHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhh--hcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          151 MHFESRKSTLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAK--ENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       151 ~~~~gR~~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~--~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      ..++||+.++++|+++|.   +....+|+|+||||+||||||+++|++..  ...+|++++|+++++.++...+...+..
T Consensus        20 ~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~   99 (277)
T d2a5yb3          20 MTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDI   99 (277)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHH
T ss_pred             CceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHH
Confidence            347799999999999985   45578999999999999999999998854  5678999999999999988877766644


Q ss_pred             Hh---CCCc------cc-cCcHHHHHHHHHHHhcCCeEEEEEeCCCCccChhhhcCCCCCCCCCeEEEEeecchhhhhcc
Q 044858          226 KL---GLKI------DQ-ESESVRAWRLLEQLKKETKILIILDDIWGSLDLEAIGIPLADDNGGCKVLLTARSQDVLSCE  295 (426)
Q Consensus       226 ~l---~~~~------~~-~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~iivTtr~~~va~~~  295 (426)
                      .+   +...      .. ................++|+|+||||+|+...|+.+..      .||+||||||+..++...
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~------~~srilvTTR~~~v~~~~  173 (277)
T d2a5yb3         100 LLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQE------LRLRCLVTTRDVEISNAA  173 (277)
T ss_dssp             HHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHH------TTCEEEEEESBGGGGGGC
T ss_pred             HHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcc------cCceEEEEeehHHHHHhc
Confidence            33   2211      11 11122223344444457899999999999988876532      389999999999997544


Q ss_pred             CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHhhcCCHHHHHHHHHHHhhcccc
Q 044858          296 MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKALKNKSPYEWRNALRQLKRNFLR  375 (426)
Q Consensus       296 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~~w~~~l~~l~~~~~~  375 (426)
                      ....+.|++++|+.+|||+||.+.++.....+..++++++|+++|+|+||||+++|+.|+.++.+.|.+..+.+..... 
T Consensus       174 ~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~~~~~-  252 (277)
T d2a5yb3         174 SQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGL-  252 (277)
T ss_dssp             CSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHHHHCS-
T ss_pred             CCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHHHHhcCcH-
Confidence            4556789999999999999999998866666677889999999999999999999999999999999999888865322 


Q ss_pred             CCCCcchhhhhhhHHhhhcCCCCChhHHHHHHh
Q 044858          376 SFSGTQAVAAYSTIQLSYNQLGGEELRKTFLLI  408 (426)
Q Consensus       376 ~~~~~~~~~~~~~l~~sy~~L~~~~lk~cfl~~  408 (426)
                             .++..++.+||++||++ +|+||.++
T Consensus       253 -------~~v~~il~~sY~~L~~~-lk~c~~~l  277 (277)
T d2a5yb3         253 -------VGVECITPYSYKSLAMA-LQRCVEVL  277 (277)
T ss_dssp             -------STTCCCSSSSSSSHHHH-HHHHHHTS
T ss_pred             -------HHHHHHHHHHHhcccHH-HHHHHHhC
Confidence                   56788999999999998 99999874

>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=99.40  E-value=6.5e-13  Score=119.69  Aligned_cols=194  Identities=14%  Similarity=0.183  Sum_probs=114.5

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec-----CCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS-----QTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~-----~~~~~~~il~~  222 (426)
                      .....|+||++++++|.+.    ..+++.|+|++|+|||+|++++.+.....     ..|+.+.     .......+...
T Consensus         9 ~~~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~~~~-----~~~i~~~~~~~~~~~~~~~~~~~   79 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINELNLP-----YIYLDLRKFEERNYISYKDFLLE   79 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHHTCC-----EEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             CChhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHCCCC-----eEEEEeccccccccccHHHHHHH
Confidence            3567899999999998764    34688999999999999999998776432     3344432     22234444444


Q ss_pred             HHHHhC--------------CCc---------c---ccCcHHHHHHHHHHHh--cCCeEEEEEeCCCCccC------hhh
Q 044858          223 IAEKLG--------------LKI---------D---QESESVRAWRLLEQLK--KETKILIILDDIWGSLD------LEA  268 (426)
Q Consensus       223 i~~~l~--------------~~~---------~---~~~~~~~~~~l~~~l~--~~k~~LlVlDdv~~~~~------~~~  268 (426)
                      +.....              ...         .   ..........+.+.+.  .++++++++|++.....      +..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~  159 (283)
T d2fnaa2          80 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  159 (283)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHH
Confidence            433221              000         0   0000011222333332  36789999999853311      111


Q ss_pred             hcCCCCCCCCCeEEEEeecchhhh----hc-------cCCceeeEEccCCCHHHHHHHHHHhhCCC-CCCCchHHHHHHH
Q 044858          269 IGIPLADDNGGCKVLLTARSQDVL----SC-------EMDCQQNFVVDVLNDKEAWSLFKKMTGDC-IENGELKSVVTEV  336 (426)
Q Consensus       269 l~~~l~~~~~~s~iivTtr~~~va----~~-------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~-~~~~~~~~~~~~i  336 (426)
                      +.... ........+++++.....    ..       .......+.|.+|+.+++.+++.+.+... ...++    .++|
T Consensus       160 l~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~~----~~~i  234 (283)
T d2fnaa2         160 LAYAY-DNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKD----YEVV  234 (283)
T ss_dssp             HHHHH-HHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCC----HHHH
T ss_pred             HHHHH-HhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHHH----HHHH
Confidence            11111 122345556655543221    00       01124678999999999999998876421 22222    4689


Q ss_pred             HHHcCCchHHHHHHHHHhh
Q 044858          337 VKECAGLPIAIVPIAKALK  355 (426)
Q Consensus       337 ~~~c~GlPlai~~~~~~l~  355 (426)
                      ++.++|+|..+..++..+.
T Consensus       235 ~~~~~G~P~~L~~~~~~~~  253 (283)
T d2fnaa2         235 YEKIGGIPGWLTYFGFIYL  253 (283)
T ss_dssp             HHHHCSCHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHH
Confidence            9999999999999987665

>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=99.14  E-value=2.1e-10  Score=99.73  Aligned_cols=187  Identities=14%  Similarity=0.131  Sum_probs=116.5

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      ....+++|.++.++.|..++.++..+.+.++|++|+||||+|+.+.+.......-....-++.+...+...+...+....
T Consensus        12 ~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~   91 (224)
T d1sxjb2          12 QVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFA   91 (224)
T ss_dssp             SSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHHHHH
Confidence            45678999999999999999988777788999999999999999988765432111234455555544444333322211


Q ss_pred             CCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecch-hhhhccCCceeeEEc
Q 044858          228 GLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMDCQQNFVV  304 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~~~~~~~l  304 (426)
                      .....              ....+.-++|+|+++...  ....+...+......+++++||.+. .+.....+....+++
T Consensus        92 ~~~~~--------------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~  157 (224)
T d1sxjb2          92 QKKLH--------------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRY  157 (224)
T ss_dssp             HBCCC--------------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             Hhhcc--------------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhh
Confidence            10000              012356688999997542  1222222222233456666666554 332222344578999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVP  349 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~  349 (426)
                      .+++.++...++.+.+....-.-+ .+..+.|++.|+|.+..+..
T Consensus       158 ~~~~~~~i~~~l~~i~~~e~~~i~-~~~l~~I~~~s~Gd~R~ai~  201 (224)
T d1sxjb2         158 SKLSDEDVLKRLLQIIKLEDVKYT-NDGLEAIIFTAEGDMRQAIN  201 (224)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCCBC-HHHHHHHHHHHTTCHHHHHH
T ss_pred             cccchhhhHHHHHHHHHhcccCCC-HHHHHHHHHHcCCcHHHHHH
Confidence            999999999999887742211111 34678999999998765443

>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=99.10  E-value=4.4e-10  Score=97.77  Aligned_cols=182  Identities=13%  Similarity=0.105  Sum_probs=113.3

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      ....+++|.++.++.|..++.++..+.+.++|++|+||||+|+.+++............-.+.+...+.......+....
T Consensus        11 ~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~   90 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFA   90 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhcc
Confidence            35677999999999999999887777788999999999999999998765433222333334444333332222111110


Q ss_pred             CCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEeecchh-hhhccCCceeeEEc
Q 044858          228 GLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLTARSQD-VLSCEMDCQQNFVV  304 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivTtr~~~-va~~~~~~~~~~~l  304 (426)
                      ..               ..+..+++-++|+|++....  .-..+...+......+.++++|.... +..........+++
T Consensus        91 ~~---------------~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~  155 (227)
T d1sxjc2          91 ST---------------RQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRF  155 (227)
T ss_dssp             HB---------------CCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             cc---------------ccccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhcc
Confidence            00               00112345688899997552  22223333333345677777776643 22222344578999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI  345 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl  345 (426)
                      .+++.++...++.+.+....-.-+ .+..+.|++.++|..-
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            999999999999987743322111 3567889999998653

>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=99.05  E-value=5.7e-10  Score=97.33  Aligned_cols=181  Identities=12%  Similarity=0.096  Sum_probs=110.0

Q ss_pred             CcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCHHHHHHHHHHHh
Q 044858          149 DFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      ...+++|.++.++.|..++.+++.+.+.++|++|+||||+|+.+.+..... .+. ..+-++.+...+...+...+....
T Consensus        22 ~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~-~~~~~~~e~n~s~~~~~~~~~~~~~~~~  100 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKEFA  100 (231)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG-GHHHHEEEEETTCHHHHHTTHHHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhc-ccCCCeeEEecCcccchhHHHHHHHHHH
Confidence            567899999999999999998888888999999999999999998875431 122 122333332211111111111110


Q ss_pred             CCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecch-hhhhccCCceeeEEc
Q 044858          228 GLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQ-DVLSCEMDCQQNFVV  304 (426)
Q Consensus       228 ~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~-~va~~~~~~~~~~~l  304 (426)
                      .               .......++.++++||+...  ..+..+...+......+.+|+||... .+..........+.+
T Consensus       101 ~---------------~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~  165 (231)
T d1iqpa2         101 R---------------TKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRF  165 (231)
T ss_dssp             H---------------SCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEEC
T ss_pred             h---------------hhhccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccc
Confidence            0               00011246788999998644  23333332232223345566666543 332212234578999


Q ss_pred             cCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH
Q 044858          305 DVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIA  346 (426)
Q Consensus       305 ~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla  346 (426)
                      .+.+.++....+.+.+....-. --.+..+.|++.|+|.+-.
T Consensus       166 ~~~~~~~~~~~l~~~~~~e~i~-i~~~~l~~I~~~~~gdiR~  206 (231)
T d1iqpa2         166 RPLRDEDIAKRLRYIAENEGLE-LTEEGLQAILYIAEGDMRR  206 (231)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCE-ECHHHHHHHHHHHTTCHHH
T ss_pred             cccchhhHHHHHHHHHHHhCCC-CCHHHHHHHHHHcCCCHHH
Confidence            9999999999998887533221 1245678899999987543

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.02  E-value=4.9e-09  Score=92.26  Aligned_cols=157  Identities=18%  Similarity=0.232  Sum_probs=103.8

Q ss_pred             cccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEE-EecCCcCHHHHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISS-RVSQTPQIKEIQREIA  224 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv-~v~~~~~~~~il~~i~  224 (426)
                      ..+.+||++++++++..|.......+.++|++|+|||+|+..+++.....+    .....+|. +.+.-           
T Consensus        17 ld~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~l-----------   85 (268)
T d1r6bx2          17 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL-----------   85 (268)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-------------
T ss_pred             CCcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechH-----------
Confidence            446789999999999999866667788999999999999999988755321    12234443 22210           


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------ChhhhcCCCCCCCCCeEEEEeecchhhhh-
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL----------DLEAIGIPLADDNGGCKVLLTARSQDVLS-  293 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~----------~~~~l~~~l~~~~~~s~iivTtr~~~va~-  293 (426)
                        +............+..+.+.+....+.++++|++...-          +...+..|... .+.-++|.||..+.... 
T Consensus        86 --iag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~-rg~i~vIgatT~eey~~~  162 (268)
T d1r6bx2          86 --LAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS-SGKIRVIGSTTYQEFSNI  162 (268)
T ss_dssp             ---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS-SCCCEEEEEECHHHHHCC
T ss_pred             --hccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh-CCCCeEEEeCCHHHHHHH
Confidence              01111122333455666777766678999999987541          12233333322 34578888888776531 


Q ss_pred             -----ccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          294 -----CEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       294 -----~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                           ........+.+++.+.+++..++....
T Consensus       163 ~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         163 FEKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             CCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             HhhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence                 123456899999999999999997654

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.02  E-value=6.7e-09  Score=90.86  Aligned_cols=185  Identities=12%  Similarity=0.173  Sum_probs=111.9

Q ss_pred             CCcccccchHHHHHHHHHHhccCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-------------------eEEE
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNF-NMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-------------------KVIS  207 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~-~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-------------------~~~w  207 (426)
                      ..+.+++|.++.++.+..++..++. +.+.++|++|+||||+|+.+.+.........                   .++.
T Consensus         9 ~~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   88 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIE   88 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEE
T ss_pred             CCHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEEE
Confidence            3567889999999999999886654 5688999999999999999887654321111                   1122


Q ss_pred             EEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ChhhhcCCCCCCCCCeEEEEe
Q 044858          208 SRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL--DLEAIGIPLADDNGGCKVLLT  285 (426)
Q Consensus       208 v~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~iivT  285 (426)
                      +..+....... .+++.+.+....                ..+++.++|||+++...  .-..+...+.....++++|++
T Consensus        89 ~~~~~~~~i~~-ir~~~~~~~~~~----------------~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~  151 (239)
T d1njfa_          89 IDAASRTKVED-TRDLLDNVQYAP----------------ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLA  151 (239)
T ss_dssp             EETTCSSSHHH-HHHHHHSCCCSC----------------SSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEE
T ss_pred             ecchhcCCHHH-HHHHHHHHHhcc----------------ccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEE
Confidence            22222222211 112222211100                12456689999997652  222333333233456777777


Q ss_pred             ecchhh-hhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH-HHHHH
Q 044858          286 ARSQDV-LSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI-AIVPI  350 (426)
Q Consensus       286 tr~~~v-a~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl-ai~~~  350 (426)
                      |.+..- ..........+.+.+++.++..+.+.+.+...... --.+....|++.++|.+- |+..+
T Consensus       152 tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~-~~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         152 TTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA-HEPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             ESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             cCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            766432 22223345789999999999999888877422211 124567889999999885 44433

>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=99.01  E-value=1e-09  Score=95.94  Aligned_cols=192  Identities=15%  Similarity=0.170  Sum_probs=114.5

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCc-cceEEEEEecCCcCHHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNL-FEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~-f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      ....+++|+++.++.+..++.++..+.+.++|++|+||||+++.+++....... ......+..+.......+...+-..
T Consensus         9 ~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (237)
T d1sxjd2           9 KNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNF   88 (237)
T ss_dssp             SSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHH
Confidence            356678899988999999998877777899999999999999999987532211 2233445555555544433333221


Q ss_pred             hCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchh-hhhccCCceeeEE
Q 044858          227 LGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQD-VLSCEMDCQQNFV  303 (426)
Q Consensus       227 l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~-va~~~~~~~~~~~  303 (426)
                      ..........     .........+.-++|+|++...  ..+..+...+......+++|+|+.... ...........++
T Consensus        89 ~~~~~~~~~~-----~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~  163 (237)
T d1sxjd2          89 ARLTVSKPSK-----HDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFR  163 (237)
T ss_dssp             HHSCCCCCCT-----THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEE
T ss_pred             hhhhhhhhhH-----HHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhc
Confidence            1111111100     0111222334447899998754  223333222222334566777665532 2211222346899


Q ss_pred             ccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH
Q 044858          304 VDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI  345 (426)
Q Consensus       304 l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl  345 (426)
                      +.+++.++...++.+.+....-.- -.+..+.|++.++|.+.
T Consensus       164 f~~~~~~~~~~~L~~i~~~e~i~i-~~~~l~~ia~~s~gd~R  204 (237)
T d1sxjd2         164 FKALDASNAIDRLRFISEQENVKC-DDGVLERILDISAGDLR  204 (237)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHTSSCHH
T ss_pred             cccccccccchhhhhhhhhhcCcC-CHHHHHHHHHHcCCCHH
Confidence            999999999999998875332221 24567889999988653

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.97  E-value=2.3e-08  Score=88.75  Aligned_cols=171  Identities=14%  Similarity=0.171  Sum_probs=109.5

Q ss_pred             CcccccchHHHHHHHHHHhc------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          149 DFMHFESRKSTLKGILDALS------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      .+..++||+.+++++.++|.      ...++.+.|+|++|+|||++|+.+++.......+ ..+++..............
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~   92 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTA-RFVYINGFIYRNFTAIIGE   92 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCC-EEEEEETTTCCSHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCC-cEEEecchhhhhhhhhhhh
Confidence            34468999999999998885      2345789999999999999999999988654322 3457777777788888888


Q ss_pred             HHHHhCCCcccc--CcHHHHHHHHHHHh-cCCeEEEEEeCCCCccC-----hhhhcCCCC-CCCCCeEEEEeecchhhhh
Q 044858          223 IAEKLGLKIDQE--SESVRAWRLLEQLK-KETKILIILDDIWGSLD-----LEAIGIPLA-DDNGGCKVLLTARSQDVLS  293 (426)
Q Consensus       223 i~~~l~~~~~~~--~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~~-----~~~l~~~l~-~~~~~s~iivTtr~~~va~  293 (426)
                      +....+......  ........+.+.+. .....++++|++++...     ...+..... .......+|.++.......
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  172 (276)
T d1fnna2          93 IARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLN  172 (276)
T ss_dssp             HHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHH
T ss_pred             hHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhh
Confidence            888876554332  23333444444443 24567788888765421     111211111 1123344555555433211


Q ss_pred             c------cCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          294 C------EMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       294 ~------~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                      .      .......+.+.+.+.++.++++.+.+
T Consensus       173 ~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         173 NLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             TSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             hcchhhhhhhcchhccccchhHHHHHHHHHHHH
Confidence            0      00122468899999999999998776

>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=98.91  E-value=1.4e-09  Score=96.09  Aligned_cols=193  Identities=8%  Similarity=0.033  Sum_probs=101.2

Q ss_pred             CcccccchHHHHHHHHHHhccC-CccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEEEecCC----------
Q 044858          149 DFMHFESRKSTLKGILDALSNR-NFNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISSRVSQT----------  213 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~~-~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~----------  213 (426)
                      ...+++|+++..+.|..++..+ ..+.+.|+|++|+||||+|+.+++......    .++...+...+..          
T Consensus         9 ~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (252)
T d1sxje2           9 SLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSP   88 (252)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECS
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhhhhhccCC
Confidence            5677899999888888887644 345578999999999999999998752111    1111111111100          


Q ss_pred             -----------cCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCe
Q 044858          214 -----------PQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGC  280 (426)
Q Consensus       214 -----------~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s  280 (426)
                                 .....................     ... ......++.-+++||+++..  ..+..+...+......+
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~-~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~  162 (252)
T d1sxje2          89 YHLEITPSDMGNNDRIVIQELLKEVAQMEQVD-----FQD-SKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNI  162 (252)
T ss_dssp             SEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTE
T ss_pred             ccceeeecccccCCcceeeehhhhhhhhhhhh-----hhh-cccccCCCceEEEeccccccccccchhhhcccccccccc
Confidence                       001111111111111000000     000 00001234558999999764  22333333332234567


Q ss_pred             EEEEeecchh-hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHH
Q 044858          281 KVLLTARSQD-VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAI  347 (426)
Q Consensus       281 ~iivTtr~~~-va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai  347 (426)
                      ++|+||.+.. +.....+....+++.+++.++..+++.+.+......-..++..+.|++.+.|.+..+
T Consensus       163 ~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~a  230 (252)
T d1sxje2         163 RLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVS  230 (252)
T ss_dssp             EEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHH
T ss_pred             cceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHHH
Confidence            7777776543 211111223688999999999999998776321111111346678999999987543

>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=98.80  E-value=1.2e-08  Score=84.79  Aligned_cols=153  Identities=14%  Similarity=0.184  Sum_probs=93.9

Q ss_pred             cccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEEEecCCcCHHHHHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      ..+.+||++++++++..|.......+.++|++|+|||+++..++.+....+    ..+..+|.-     +...++.    
T Consensus        21 ld~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~l-----d~~~LiA----   91 (195)
T d1jbka_          21 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL-----DMGALVA----   91 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE-----CHHHHHT----
T ss_pred             CCCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEe-----eHHHHhc----
Confidence            345789999999999999976666788999999999999999998765321    223444431     2222110    


Q ss_pred             HhCCCccccCcHHHHHHHHHHHh-cCCeEEEEEeCCCCcc---------Chhhh-cCCCCCCCCCeEEEEeecchhhhh-
Q 044858          226 KLGLKIDQESESVRAWRLLEQLK-KETKILIILDDIWGSL---------DLEAI-GIPLADDNGGCKVLLTARSQDVLS-  293 (426)
Q Consensus       226 ~l~~~~~~~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~---------~~~~l-~~~l~~~~~~s~iivTtr~~~va~-  293 (426)
                         .......-...+..+++.+. ...+.+|++||+...-         +...+ ...+.  ...-++|.||..+.... 
T Consensus        92 ---g~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~--rg~l~~IgatT~eey~~~  166 (195)
T d1jbka_          92 ---GAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQY  166 (195)
T ss_dssp             ---TTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECHHHHHHH
T ss_pred             ---cCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHh--CCCceEEecCCHHHHHHH
Confidence               00011112234445555553 3457999999997541         11122 22221  23567888887665331 


Q ss_pred             -----ccCCceeeEEccCCCHHHHHHHH
Q 044858          294 -----CEMDCQQNFVVDVLNDKEAWSLF  316 (426)
Q Consensus       294 -----~~~~~~~~~~l~~L~~~e~~~Lf  316 (426)
                           ........+.++..+.+++..++
T Consensus       167 ~e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         167 IEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             TTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             HHcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence                 12345688999999998887543

>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=98.77  E-value=2.5e-07  Score=82.33  Aligned_cols=197  Identities=16%  Similarity=0.135  Sum_probs=114.6

Q ss_pred             CcccccchHHHHHHHHHHhc----cC----C-ccEEEEEcCCCCcHHHHHHHHHHHhhhc----CccceEEEEEecCCcC
Q 044858          149 DFMHFESRKSTLKGILDALS----NR----N-FNMIGVYGMGGIGKTTLVKEVGRQAKEN----NLFEKVISSRVSQTPQ  215 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~----~~----~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~  215 (426)
                      .+..+.||+.++++|.+.+.    ++    . ..++.|+|++|+|||++++.+.+.....    .......++......+
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            34568899999999988763    11    1 1245678999999999999999875421    1123456777777778


Q ss_pred             HHHHHHHHHHHhCCCccc--cCcHHHHHHHHHHHh-cCCeEEEEEeCCCCcc-----C------hhhhc---CCCCCCCC
Q 044858          216 IKEIQREIAEKLGLKIDQ--ESESVRAWRLLEQLK-KETKILIILDDIWGSL-----D------LEAIG---IPLADDNG  278 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~--~~~~~~~~~l~~~l~-~~k~~LlVlDdv~~~~-----~------~~~l~---~~l~~~~~  278 (426)
                      .......+...++.....  .........+..... .+...++++|.+....     .      +..+.   ........
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~  173 (287)
T d1w5sa2          94 LYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNR  173 (287)
T ss_dssp             HHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCB
T ss_pred             hhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccc
Confidence            888888888877654432  222223333333332 3567888888875331     1      11111   11111222


Q ss_pred             CeEEEEeecchhhh-------hccCCceeeEEccCCCHHHHHHHHHHhhCCC-CCCCchHHHHHHHHHHc------CCch
Q 044858          279 GCKVLLTARSQDVL-------SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDC-IENGELKSVVTEVVKEC------AGLP  344 (426)
Q Consensus       279 ~s~iivTtr~~~va-------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~-~~~~~~~~~~~~i~~~c------~GlP  344 (426)
                      ...|++++......       .........+.+++.+.++..+++...+... ....--.+..+.|+++.      .|.|
T Consensus       174 ~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~  253 (287)
T d1w5sa2         174 IGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSA  253 (287)
T ss_dssp             EEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCH
T ss_pred             eeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCH
Confidence            23344444443221       1112234689999999999999999876311 11111134555666554      5666


Q ss_pred             H
Q 044858          345 I  345 (426)
Q Consensus       345 l  345 (426)
                      -
T Consensus       254 R  254 (287)
T d1w5sa2         254 R  254 (287)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.76  E-value=4.4e-07  Score=78.78  Aligned_cols=175  Identities=15%  Similarity=0.165  Sum_probs=101.8

Q ss_pred             CCcccccchHHHHHHHHHHhc-----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALS-----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      ....+++|.++.+++|..++.     ....+.+.++|++|+||||+|+.+.+.....     ...++.+......++. .
T Consensus         6 ~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~-----~~~~~~~~~~~~~~~~-~   79 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN-----IHVTSGPVLVKQGDMA-A   79 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC-----EEEEETTTCCSHHHHH-H
T ss_pred             CcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCCC-----cccccCcccccHHHHH-H
Confidence            356788999999888888775     2335568899999999999999999876532     2233333333332221 1


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC---------hhhhc--C---------CCCCCCCCeEE
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD---------LEAIG--I---------PLADDNGGCKV  282 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~---------~~~l~--~---------~l~~~~~~s~i  282 (426)
                      ++..                      .+++..+++|++.....         .+...  .         ......+...+
T Consensus        80 ~~~~----------------------~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (238)
T d1in4a2          80 ILTS----------------------LERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTL  137 (238)
T ss_dssp             HHHH----------------------CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEE
T ss_pred             HHHh----------------------hccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEE
Confidence            2111                      12345666666643310         00000  0         00001123445


Q ss_pred             EEeecchhhh--hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHH
Q 044858          283 LLTARSQDVL--SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIA  351 (426)
Q Consensus       283 ivTtr~~~va--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~  351 (426)
                      |++|......  .........+.+++.+.++...++......... ....+....|++.++|.+-.+..+.
T Consensus       138 I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~~~l~~i~~~s~gd~R~ai~~l  207 (238)
T d1in4a2         138 VGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV-EIEDAAAEMIAKRSRGTPRIAIRLT  207 (238)
T ss_dssp             EEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-CBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             EEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccc-hhhHHHHHHHHHhCCCCHHHHHHHH
Confidence            5555544322  112234467899999999999999887753222 2224568889999999877665443

>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=98.72  E-value=2.9e-08  Score=87.33  Aligned_cols=185  Identities=12%  Similarity=0.094  Sum_probs=105.4

Q ss_pred             CcccccchHHHHHHHHHHhcc-----------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          149 DFMHFESRKSTLKGILDALSN-----------------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~~l~~-----------------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      .+..++|.++.+++|..++..                 +..+.+.++|++|+||||+|+.+++....     ...++..+
T Consensus        12 ~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~-----~~~~~~~~   86 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY-----DILEQNAS   86 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC-----EEEEECTT
T ss_pred             CHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHh-----hhhccccc
Confidence            567789999999998888742                 23467999999999999999999987643     24456665


Q ss_pred             CCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC-----hhhhcCCCCCCCCCeEEEEee
Q 044858          212 QTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD-----LEAIGIPLADDNGGCKVLLTA  286 (426)
Q Consensus       212 ~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~-----~~~l~~~l~~~~~~s~iivTt  286 (426)
                      ...+...+-. .................  ........++..++++|++.....     +..+.....  .....+++|+
T Consensus        87 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~--~~~~~ii~i~  161 (253)
T d1sxja2          87 DVRSKTLLNA-GVKNALDNMSVVGYFKH--NEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCR--KTSTPLILIC  161 (253)
T ss_dssp             SCCCHHHHHH-TGGGGTTBCCSTTTTTC------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHH--HCSSCEEEEE
T ss_pred             cchhhHHHHH-HHHHHhhcchhhhhhhh--hhhcccccccceEEEeeeccccccchhhhhHHHhhhhc--cccccccccc
Confidence            5555443322 22222111110000000  000111235678999999864321     222211111  1123355554


Q ss_pred             cchh--hhhccCCceeeEEccCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCchHH
Q 044858          287 RSQD--VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTG--DCIENGELKSVVTEVVKECAGLPIA  346 (426)
Q Consensus       287 r~~~--va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~--~~~~~~~~~~~~~~i~~~c~GlPla  346 (426)
                      ....  ...........+++.+.+.++....+...+.  +-.-++   +....|++.++|....
T Consensus       162 ~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~---~~l~~i~~~s~GDiR~  222 (253)
T d1sxja2         162 NERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NVIDRLIQTTRGDIRQ  222 (253)
T ss_dssp             SCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHTTTCHHH
T ss_pred             ccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCH---HHHHHHHHhCCCcHHH
Confidence            3322  1122234457899999999999999888763  111122   2467899999997633

>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=9.2e-07  Score=76.76  Aligned_cols=177  Identities=11%  Similarity=0.044  Sum_probs=100.1

Q ss_pred             CCcccccchHHHHHHHHHHhc-----cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALS-----NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQRE  222 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~-----~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~  222 (426)
                      ..+.+++|.++.+++|..++.     ...++-+.++|++|+||||+|+.+++.....     ..+++.+...........
T Consensus         6 ~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~-----~~~~~~~~~~~~~~~~~~   80 (239)
T d1ixsb2           6 KTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVN-----LRVTSGPAIEKPGDLAAI   80 (239)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCC-----EEEEETTTCCSHHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC-----eEeccCCccccchhhHHH
Confidence            356778999988888777764     2235667899999999999999999876532     233443333222221111


Q ss_pred             HHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCccC---------hhh----hcCCC-------CCCCCCeEE
Q 044858          223 IAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSLD---------LEA----IGIPL-------ADDNGGCKV  282 (426)
Q Consensus       223 i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~~---------~~~----l~~~l-------~~~~~~s~i  282 (426)
                      +..                     .. +.+.++++|++.....         .+.    .....       ....+...+
T Consensus        81 ~~~---------------------~~-~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (239)
T d1ixsb2          81 LAN---------------------SL-EEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTL  138 (239)
T ss_dssp             HHT---------------------TC-CTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEE
T ss_pred             HHh---------------------hc-cCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEE
Confidence            111                     11 1234556676653310         000    00000       001123344


Q ss_pred             EEeecc-hhhh-hccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHH
Q 044858          283 LLTARS-QDVL-SCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAK  352 (426)
Q Consensus       283 ivTtr~-~~va-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~  352 (426)
                      +.+|-+ .... .........+.+.+.+.++...++.+.+..... ....+....|++.++|.+-.+..+..
T Consensus       139 i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i-~~~~~~l~~ia~~s~gd~R~a~~~l~  209 (239)
T d1ixsb2         139 IGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGV-RITEEAALEIGRRSRGTMRVAKRLFR  209 (239)
T ss_dssp             EEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCC-CBCHHHHHHHHHHTTSSHHHHHHHHH
T ss_pred             EeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCC-ccchHHHHHHHHHcCCCHHHHHHHHH
Confidence            444433 2221 222334578889999999999888877653222 22255788999999998876654443

>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=3.5e-07  Score=77.61  Aligned_cols=168  Identities=10%  Similarity=0.090  Sum_probs=102.2

Q ss_pred             HHHHHHHHHHhccCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------ccceEEEEEecCCcCH
Q 044858          157 KSTLKGILDALSNRN-FNMIGVYGMGGIGKTTLVKEVGRQAKENN-------------------LFEKVISSRVSQTPQI  216 (426)
Q Consensus       157 ~~~~~~l~~~l~~~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~v~~~~~~  216 (426)
                      +...+++...+..++ ++.+.++|+.|+||||+|+.+.+..-...                   ......++.....   
T Consensus         8 ~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~---   84 (207)
T d1a5ta2           8 RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG---   84 (207)
T ss_dssp             HHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT---
T ss_pred             HHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhc---
Confidence            445677777777666 45689999999999999999887642110                   0011111111110   


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchh
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLK----KETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQD  290 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~  290 (426)
                                     ...-..+.+..+.+.+.    .+++-++|+||++..  .....+...+-....++.+|+||++..
T Consensus        85 ---------------~~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~  149 (207)
T d1a5ta2          85 ---------------KNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPE  149 (207)
T ss_dssp             ---------------CSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGG
T ss_pred             ---------------ccccccchhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChh
Confidence                           00011222333333332    246679999999765  234444433333345788888777754


Q ss_pred             -hhhccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHH
Q 044858          291 -VLSCEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIV  348 (426)
Q Consensus       291 -va~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~  348 (426)
                       +.....+....+.+.+++.++....+.+....      .++....|++.++|.|-.+.
T Consensus       150 ~ll~tI~SRc~~i~~~~~~~~~~~~~L~~~~~~------~~~~~~~i~~~s~Gs~r~al  202 (207)
T d1a5ta2         150 RLLATLRSRCRLHYLAPPPEQYAVTWLSREVTM------SQDALLAALRLSAGSPGAAL  202 (207)
T ss_dssp             GSCHHHHTTSEEEECCCCCHHHHHHHHHHHCCC------CHHHHHHHHHHTTTCHHHHH
T ss_pred             hhhhhhcceeEEEecCCCCHHHHHHHHHHcCCC------CHHHHHHHHHHcCCCHHHHH
Confidence             33222234579999999999999998765421      13567889999999986553

>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=98.65  E-value=1.1e-07  Score=88.17  Aligned_cols=156  Identities=15%  Similarity=0.208  Sum_probs=92.4

Q ss_pred             cccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhc----CccceEEE-EEecCCcCHHHHHHHHH
Q 044858          150 FMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN----NLFEKVIS-SRVSQTPQIKEIQREIA  224 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~w-v~v~~~~~~~~il~~i~  224 (426)
                      ..+++||+.++++++..|.......+.++|++|+|||+|+..++++....    ...+.++| ++++.      ++..  
T Consensus        21 ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~------l~ag--   92 (387)
T d1qvra2          21 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS------LLAG--   92 (387)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC--------------
T ss_pred             CCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh------hhcc--
Confidence            45678999999999999985555556788999999999998877765432    22334454 33321      1100  


Q ss_pred             HHhCCCccccCcHHHHHHHHHHHhcC-CeEEEEEeCCCCcc---------Chhh-hcCCCCCCCCCeEEEEeecchhhh-
Q 044858          225 EKLGLKIDQESESVRAWRLLEQLKKE-TKILIILDDIWGSL---------DLEA-IGIPLADDNGGCKVLLTARSQDVL-  292 (426)
Q Consensus       225 ~~l~~~~~~~~~~~~~~~l~~~l~~~-k~~LlVlDdv~~~~---------~~~~-l~~~l~~~~~~s~iivTtr~~~va-  292 (426)
                           ..........+..+...+... .+++|++|++...-         +... +...|  ..+.-++|.+|..+... 
T Consensus        93 -----~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L--~rg~~~~I~~tT~~ey~~  165 (387)
T d1qvra2          93 -----AKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL--ARGELRLIGATTLDEYRE  165 (387)
T ss_dssp             ----------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH--HTTCCCEEEEECHHHHHH
T ss_pred             -----cCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHH--hCCCcceeeecCHHHHHH
Confidence                 000112223444555555443 47999999997651         1111 12222  12345777777665443 


Q ss_pred             ----hccCCceeeEEccCCCHHHHHHHHHHhh
Q 044858          293 ----SCEMDCQQNFVVDVLNDKEAWSLFKKMT  320 (426)
Q Consensus       293 ----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  320 (426)
                          ......++.+.+++.+.+++..++....
T Consensus       166 ~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         166 IEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             HTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             hcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence                1123457899999999999999987654

>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=98.65  E-value=1.4e-07  Score=82.28  Aligned_cols=176  Identities=15%  Similarity=0.203  Sum_probs=98.7

Q ss_pred             CCcccccchHHHHHHHHH---Hhcc---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcC
Q 044858          148 QDFMHFESRKSTLKGILD---ALSN---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQ  215 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~---~l~~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  215 (426)
                      ..+.+++|-++.++.|.+   .+..         ..++-+.++|++|+|||+||+.+.+.....     .+.++.     
T Consensus         6 ~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~-----~~~i~~-----   75 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVP-----FITASG-----   75 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCC-----EEEEEH-----
T ss_pred             CcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCC-----EEEEEh-----
Confidence            345667787766555443   3321         234568999999999999999999876432     223322     


Q ss_pred             HHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------------ChhhhcCCCC--CCC
Q 044858          216 IKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL----------------DLEAIGIPLA--DDN  277 (426)
Q Consensus       216 ~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~----------------~~~~l~~~l~--~~~  277 (426)
                       .++..        .... .....+..+++......+++|+|||++...                ....+...+.  ...
T Consensus        76 -~~l~~--------~~~g-~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~  145 (247)
T d1ixza_          76 -SDFVE--------MFVG-VGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKD  145 (247)
T ss_dssp             -HHHHH--------SCTT-HHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTT
T ss_pred             -HHhhh--------cccc-HHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCC
Confidence             22211        0000 111234455666656678999999985320                0111111111  122


Q ss_pred             CCeEEEEeecchhhhhcc----CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH
Q 044858          278 GGCKVLLTARSQDVLSCE----MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI  345 (426)
Q Consensus       278 ~~s~iivTtr~~~va~~~----~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl  345 (426)
                      .+.-||.||....-....    ..-.+.+++.+.+.++-.++|+..+.......+.  ....+++.|.|+.-
T Consensus       146 ~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~--~~~~la~~t~g~s~  215 (247)
T d1ixza_         146 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV--DLALLAKRTPGFVG  215 (247)
T ss_dssp             CCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCCH
T ss_pred             CCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCcccc--CHHHHHHHCCCCCH
Confidence            333344466554322111    1234689999999999999999888643322221  13567788888643

>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=3e-07  Score=80.55  Aligned_cols=175  Identities=18%  Similarity=0.198  Sum_probs=101.7

Q ss_pred             CcccccchHHHHHHHHH---Hhc---------cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          149 DFMHFESRKSTLKGILD---ALS---------NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       149 ~~~~~~gR~~~~~~l~~---~l~---------~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      .+.++.|-++.+++|.+   ++.         ...++.+.++|++|+|||++|+.+.+.....     .+.+..+.-.+ 
T Consensus        10 t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~-----~~~i~~~~l~~-   83 (256)
T d1lv7a_          10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP-----FFTISGSDFVE-   83 (256)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCC-----EEEECSCSSTT-
T ss_pred             CHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCC-----EEEEEhHHhhh-
Confidence            45677787776666544   332         1235678899999999999999999876532     22233222111 


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc------------cC----hhhhcCCCC--CCCC
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS------------LD----LEAIGIPLA--DDNG  278 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~------------~~----~~~l~~~l~--~~~~  278 (426)
                                   ..... ....+..+++......+++|+|||++..            ..    ...+...+.  ....
T Consensus        84 -------------~~~g~-~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~  149 (256)
T d1lv7a_          84 -------------MFVGV-GASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNE  149 (256)
T ss_dssp             -------------SCCCC-CHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSS
T ss_pred             -------------cchhH-HHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCC
Confidence                         11111 1234556666666678899999998531            00    111211111  2233


Q ss_pred             CeEEEEeecchhhh-hcc---CCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchH
Q 044858          279 GCKVLLTARSQDVL-SCE---MDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPI  345 (426)
Q Consensus       279 ~s~iivTtr~~~va-~~~---~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPl  345 (426)
                      +.-||.||...... ...   ..-.+.+.+.+.+.++-.++|+.........++.  ....+++.+.|+.-
T Consensus       150 ~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~--~~~~la~~t~G~s~  218 (256)
T d1lv7a_         150 GIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI--DAAIIARGTPGFSG  218 (256)
T ss_dssp             CEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCCH
T ss_pred             CEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCccc--CHHHHHHhCCCCCH
Confidence            45566677764432 111   1234789999999999999999887643322221  13567788888653

>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=98.56  E-value=5.9e-07  Score=78.98  Aligned_cols=173  Identities=13%  Similarity=0.155  Sum_probs=100.5

Q ss_pred             cccccchHHHHHHHHHHh----cc---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH
Q 044858          150 FMHFESRKSTLKGILDAL----SN---------RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI  216 (426)
Q Consensus       150 ~~~~~gR~~~~~~l~~~l----~~---------~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  216 (426)
                      +.++.|-++.+++|.+.+    ..         ..++-+.++|++|+|||++|+.+.+.....     .+.++.+     
T Consensus         3 ~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~-----~~~i~~~-----   72 (258)
T d1e32a2           3 YDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGP-----   72 (258)
T ss_dssp             GGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCE-----EEEECHH-----
T ss_pred             hhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCe-----EEEEEch-----
Confidence            345667777666665543    21         235678999999999999999999876532     2222211     


Q ss_pred             HHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCcc---------Chh----hhcCCC--CCCCCCeE
Q 044858          217 KEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGSL---------DLE----AIGIPL--ADDNGGCK  281 (426)
Q Consensus       217 ~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~~---------~~~----~l~~~l--~~~~~~s~  281 (426)
                       +        +....... ....+..+++......+++|+|||++...         ...    .+...+  .....+.-
T Consensus        73 -~--------l~~~~~g~-~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vl  142 (258)
T d1e32a2          73 -E--------IMSKLAGE-SESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVI  142 (258)
T ss_dssp             -H--------HTTSCTTH-HHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEE
T ss_pred             -h--------hccccccc-HHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCcc
Confidence             1        11111111 12233344555545689999999997541         111    111111  12234555


Q ss_pred             EEEeecchhhhh----ccCCceeeEEccCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCch
Q 044858          282 VLLTARSQDVLS----CEMDCQQNFVVDVLNDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLP  344 (426)
Q Consensus       282 iivTtr~~~va~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlP  344 (426)
                      ||.||.......    ....-.+.++++..+.++-.++|...+......++.  ....|++.|.|+-
T Consensus       143 vi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~--~~~~la~~t~G~s  207 (258)
T d1e32a2         143 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDV--DLEQVANETHGHV  207 (258)
T ss_dssp             EEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTC--CHHHHHHHCTTCC
T ss_pred             EEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCccccccc--chhhhhhcccCCC
Confidence            666887654321    111345789999999999999999887643322221  1467889998863

>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=98.43  E-value=6e-06  Score=71.69  Aligned_cols=72  Identities=15%  Similarity=0.185  Sum_probs=43.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .++-|.++|++|+|||++|+.+++.....  |   +.++.+....              ..........+..+++...+.
T Consensus        39 p~~~vLL~GppGtGKT~la~alA~~~~~~--~---~~i~~~~~~~--------------g~~~~~~~~~i~~if~~A~~~   99 (246)
T d1d2na_          39 PLVSVLLEGPPHSGKTALAAKIAEESNFP--F---IKICSPDKMI--------------GFSETAKCQAMKKIFDDAYKS   99 (246)
T ss_dssp             SEEEEEEECSTTSSHHHHHHHHHHHHTCS--E---EEEECGGGCT--------------TCCHHHHHHHHHHHHHHHHTS
T ss_pred             CCeEEEEECcCCCCHHHHHHHHhhccccc--c---cccccccccc--------------cccccchhhhhhhhhhhhhhc
Confidence            34568899999999999999999876532  2   2233221110              000111112334455555556


Q ss_pred             CeEEEEEeCCC
Q 044858          251 TKILIILDDIW  261 (426)
Q Consensus       251 k~~LlVlDdv~  261 (426)
                      .+++|+|||++
T Consensus       100 ~p~il~iDEid  110 (246)
T d1d2na_         100 QLSCVVVDDIE  110 (246)
T ss_dssp             SEEEEEECCHH
T ss_pred             ccceeehhhhh
Confidence            78999999985

>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=98.36  E-value=9.9e-07  Score=77.76  Aligned_cols=154  Identities=13%  Similarity=0.163  Sum_probs=87.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcC
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKE  250 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  250 (426)
                      .++-|.++|++|+|||+||+.+++.....       ++.++    ..++.       + ... ......+..++......
T Consensus        40 ~~~giLL~Gp~GtGKT~l~~ala~~~~~~-------~~~~~----~~~l~-------~-~~~-~~~~~~l~~~f~~A~~~   99 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLLAKAIANECQAN-------FISIK----GPELL-------T-MWF-GESEANVREIFDKARQA   99 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHHHHHHHHHTTCE-------EEEEC----HHHHH-------T-SCT-TTHHHHHHHHHHHHHHT
T ss_pred             CCCeEEEECCCCCcchhHHHHHHHHhCCc-------EEEEE----HHHhh-------h-ccc-cchHHHHHHHHHHHHhc
Confidence            34578899999999999999999887542       12221    11111       0 111 11223344555555556


Q ss_pred             CeEEEEEeCCCCcc--------C--------hhhhcCCCC--CCCCCeEEEEeecchhhhh----ccCCceeeEEccCCC
Q 044858          251 TKILIILDDIWGSL--------D--------LEAIGIPLA--DDNGGCKVLLTARSQDVLS----CEMDCQQNFVVDVLN  308 (426)
Q Consensus       251 k~~LlVlDdv~~~~--------~--------~~~l~~~l~--~~~~~s~iivTtr~~~va~----~~~~~~~~~~l~~L~  308 (426)
                      .+++|+|||++...        .        ...+...+.  ...++.-||.||....-..    ....-...+++++.+
T Consensus       100 ~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~  179 (265)
T d1r7ra3         100 APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD  179 (265)
T ss_dssp             CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCC
T ss_pred             CCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchH
Confidence            78999999996431        1        112222221  1223445666776554321    112345789999999


Q ss_pred             HHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHH
Q 044858          309 DKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIA  346 (426)
Q Consensus       309 ~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPla  346 (426)
                      .++-.++|+..+.......+.  ...+|++++.|+..+
T Consensus       180 ~~~R~~il~~~l~~~~~~~~~--~l~~la~~t~g~s~~  215 (265)
T d1r7ra3         180 EKSRVAILKANLRKSPVAKDV--DLEFLAKMTNGFSGA  215 (265)
T ss_dssp             CHHHHHHHHHHTTCC----CC--CCHHHHHHHCSSCCH
T ss_pred             HHHHHHHHHHHhccCCchhhh--hHHHHHhcCCCCCHH
Confidence            999999999877543221111  135677788886543

>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=98.26  E-value=4.6e-06  Score=70.72  Aligned_cols=130  Identities=20%  Similarity=0.198  Sum_probs=77.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      ..+.|+|++|+|||.|++.+++....+  ...+++++.      .++...+...+...        ......+.+..  -
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~--~~~~~~~~~------~~~~~~~~~~~~~~--------~~~~~~~~~~~--~   98 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKR--GYRVIYSSA------DDFAQAMVEHLKKG--------TINEFRNMYKS--V   98 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHT--TCCEEEEEH------HHHHHHHHHHHHHT--------CHHHHHHHHHT--C
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhccC--ccceEEech------HHHHHHHHHHHHcc--------chhhHHHHHhh--c
Confidence            347899999999999999999988754  334555543      34444444443211        11233344432  4


Q ss_pred             EEEEEeCCCCc---cChhh-hcCCCC-CCCCCeEEEEeecchhhhh--------ccCCceeeEEccCCCHHHHHHHHHHh
Q 044858          253 ILIILDDIWGS---LDLEA-IGIPLA-DDNGGCKVLLTARSQDVLS--------CEMDCQQNFVVDVLNDKEAWSLFKKM  319 (426)
Q Consensus       253 ~LlVlDdv~~~---~~~~~-l~~~l~-~~~~~s~iivTtr~~~va~--------~~~~~~~~~~l~~L~~~e~~~Lf~~~  319 (426)
                      -+|+|||++..   ..|+. +...+. ....|.+||+||+.....-        ........+.++ .++++-.+++++.
T Consensus        99 dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~  177 (213)
T d1l8qa2          99 DLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEK  177 (213)
T ss_dssp             SEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHH
T ss_pred             cchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHH
Confidence            69999999744   34443 221111 1235778999998764321        012234567775 4777777788777


Q ss_pred             hC
Q 044858          320 TG  321 (426)
Q Consensus       320 ~~  321 (426)
                      +.
T Consensus       178 a~  179 (213)
T d1l8qa2         178 LK  179 (213)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>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=97.65  E-value=0.00014  Score=60.55  Aligned_cols=130  Identities=15%  Similarity=0.078  Sum_probs=73.5

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhc--CccceEEEEEecC-CcCHHHHHHHHHHHhCCCccccCc
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN--NLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKIDQESE  236 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~--~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~~~~~  236 (426)
                      ++.+..++..+..+.+.++|++|+|||++|..+.+.....  .|.| ..++.... ...+.++- ++.+.+.....    
T Consensus         3 ~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~~~~~~I~Id~IR-~i~~~~~~~~~----   76 (198)
T d2gnoa2           3 LETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDIR-TIKDFLNYSPE----   76 (198)
T ss_dssp             HHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHHH-HHHHHHTSCCS----
T ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEeCCcCCCCHHHHH-HHHHHHhhCcc----
Confidence            4445555556778899999999999999999998865432  2333 33443221 22344332 34433332211    


Q ss_pred             HHHHHHHHHHHhcCCeEEEEEeCCCCc--cChhhhcCCCCCCCCCeEEEEeecchh-hhhccCCceeeEEccCC
Q 044858          237 SVRAWRLLEQLKKETKILIILDDIWGS--LDLEAIGIPLADDNGGCKVLLTARSQD-VLSCEMDCQQNFVVDVL  307 (426)
Q Consensus       237 ~~~~~~l~~~l~~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~iivTtr~~~-va~~~~~~~~~~~l~~L  307 (426)
                                  .+++=++|+|+++..  ...+.+...+-.-.+++.+|++|.+.. +.....+....+.+.+.
T Consensus        77 ------------~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p  138 (198)
T d2gnoa2          77 ------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVP  138 (198)
T ss_dssp             ------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCC
T ss_pred             ------------cCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCc
Confidence                        245569999999755  344444444433334677766666643 33222333456777643

>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=97.28  E-value=7.9e-05  Score=60.03  Aligned_cols=28  Identities=25%  Similarity=0.329  Sum_probs=24.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .+|+.|+|+.|+|||||++.+.+....+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            4799999999999999999999876653

>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=97.24  E-value=0.0015  Score=56.59  Aligned_cols=85  Identities=19%  Similarity=0.243  Sum_probs=58.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~~~l~~~  246 (426)
                      -+++-|.|+.|+||||||.+++......+  ..++|++....++...     +++++...+.     ....+.+-.+.+.
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~~  132 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIADM  132 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHHH
Confidence            46899999999999999998887665443  3588999999888654     5566765432     1222333334444


Q ss_pred             H-hcCCeEEEEEeCCCCc
Q 044858          247 L-KKETKILIILDDIWGS  263 (426)
Q Consensus       247 l-~~~k~~LlVlDdv~~~  263 (426)
                      + .+++.-|||+|.+-..
T Consensus       133 l~~~~~~~liIiDSi~al  150 (269)
T d1mo6a1         133 LIRSGALDIVVIDSVAAL  150 (269)
T ss_dssp             HHHTTCEEEEEEECSTTC
T ss_pred             HHhcCCCCEEEEeccccc
Confidence            4 3466789999998543

>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=97.19  E-value=0.00025  Score=58.43  Aligned_cols=32  Identities=25%  Similarity=0.453  Sum_probs=26.7

Q ss_pred             ccCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          168 SNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       168 ~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ...++-+|+|.|+.|+||||||+.+.+.....
T Consensus        18 ~~~~~~iIgI~G~~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          18 KTAGRLVLGIDGLSRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             CCSSSEEEEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             cCCCCEEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            34556689999999999999999999877653

>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=97.14  E-value=0.00022  Score=57.83  Aligned_cols=37  Identities=14%  Similarity=-0.024  Sum_probs=28.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEE
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISS  208 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv  208 (426)
                      +..+|.|+|++|+||||+|+.+....... .++...+.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~~-~~~~~~~~   41 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQQ-GGRSVSLL   41 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHH-CSSCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhc-CCCchhhh
Confidence            34689999999999999999999887643 24444443

>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=97.12  E-value=0.00014  Score=60.10  Aligned_cols=29  Identities=28%  Similarity=0.263  Sum_probs=25.6

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++.+|.|.|++|+||||+|+.+.+...
T Consensus         3 ~~kp~iI~i~G~pGSGKsT~a~~La~~~g   31 (194)
T d1qf9a_           3 KSKPNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CCCCEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            45778999999999999999999998753

>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=97.11  E-value=0.00012  Score=59.72  Aligned_cols=26  Identities=19%  Similarity=0.321  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.|+|.|+.|+||||||+.+.+...
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            47899999999999999999998754

>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=97.09  E-value=0.00012  Score=58.39  Aligned_cols=25  Identities=28%  Similarity=0.373  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.|.++|++|+||||+|+.+.....
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4688999999999999999998764

>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=97.05  E-value=0.0019  Score=53.51  Aligned_cols=90  Identities=17%  Similarity=0.209  Sum_probs=52.0

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCH--HHHHHHHHHHhCCCcccc----CcHHHHHH
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQI--KEIQREIAEKLGLKIDQE----SESVRAWR  242 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~--~~il~~i~~~l~~~~~~~----~~~~~~~~  242 (426)
                      .+.+.||.++|+.|+||||.+..+.......+   ..+.+-..+.+..  .+-++...+.++.+....    +....+..
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~g---~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~   82 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQG---KSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFD   82 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTTT---CCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC---CcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHH
Confidence            34578999999999999988888887765332   2334434445544  455667777777665322    11222223


Q ss_pred             HHHHHhcCCeEEEEEeCCC
Q 044858          243 LLEQLKKETKILIILDDIW  261 (426)
Q Consensus       243 l~~~l~~~k~~LlVlDdv~  261 (426)
                      ..+.......=++++|=.-
T Consensus        83 ~~~~a~~~~~d~ilIDTaG  101 (211)
T d2qy9a2          83 AIQAAKARNIDVLIADTAG  101 (211)
T ss_dssp             HHHHHHHTTCSEEEECCCC
T ss_pred             HHHHHHHcCCCEEEeccCC
Confidence            3332222223367777654

>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=97.03  E-value=0.00017  Score=56.89  Aligned_cols=24  Identities=29%  Similarity=0.373  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++|.|+|++|+||||||+.+....
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            578899999999999999987643

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.99  E-value=0.002  Score=55.71  Aligned_cols=85  Identities=20%  Similarity=0.250  Sum_probs=59.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRAWRLLE  245 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~~~l~~  245 (426)
                      ..+++-|.|++|+|||+||.++.......+  ..++|++....+++.     ++++++...+.     ....+..-.+.+
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~  128 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  128 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHH
Confidence            346899999999999999999887765432  357899999888874     66777776542     122333334444


Q ss_pred             HHh-cCCeEEEEEeCCCC
Q 044858          246 QLK-KETKILIILDDIWG  262 (426)
Q Consensus       246 ~l~-~~k~~LlVlDdv~~  262 (426)
                      .+. ++..-|||+|-+-.
T Consensus       129 ~l~~~~~~~liIiDSi~a  146 (268)
T d1xp8a1         129 LLVRSGAIDVVVVDSVAA  146 (268)
T ss_dssp             HHHTTTCCSEEEEECTTT
T ss_pred             HHHhcCCCcEEEEecccc
Confidence            443 34567999999854

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.98  E-value=0.00019  Score=57.71  Aligned_cols=24  Identities=29%  Similarity=0.463  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++|.|.|++|+||||+|+.+....
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            579999999999999999998764

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.98  E-value=0.00026  Score=57.52  Aligned_cols=27  Identities=30%  Similarity=0.437  Sum_probs=23.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      +.|.|+|++|+|||||++.+.......
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            468999999999999999999887543

>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=96.97  E-value=0.002  Score=53.35  Aligned_cols=60  Identities=22%  Similarity=0.295  Sum_probs=43.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKI  231 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~  231 (426)
                      ++.++|.++|+.|+||||.+..+.......+  ..+..++... .....+-++...+.++.+.
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   64 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNLG--KKVMFCAGDTFRAAGGTQLSEWGKRLSIPV   64 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTTT--CCEEEECCCCSSTTHHHHHHHHHHHHTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEEeccccccchhhHhhcccccCceE
Confidence            4678999999999999998888887765432  3466666543 3455667777777777654

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.96  E-value=0.0002  Score=57.71  Aligned_cols=25  Identities=40%  Similarity=0.486  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.|.|.|++|+||||+|+.+.+...
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Confidence            4578999999999999999987754

>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=96.94  E-value=0.0018  Score=53.78  Aligned_cols=61  Identities=21%  Similarity=0.318  Sum_probs=36.9

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCc
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKI  231 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~  231 (426)
                      +..+.||.++|+.|+||||.+..++...+.++ . .+..++... .....+-++...+.++.+.
T Consensus         9 ~k~p~vi~lvGptGvGKTTTiAKLA~~~~~~g-~-kV~lit~Dt~R~ga~eQL~~~a~~l~v~~   70 (211)
T d1j8yf2           9 DKIPYVIMLVGVQGTGKATTAGKLAYFYKKKG-F-KVGLVGADVYRPAALEQLQQLGQQIGVPV   70 (211)
T ss_dssp             SSSSEEEEEECSCCC----HHHHHHHHHHHTT-C-CEEEEECCCSSHHHHHHHHHHHHHHTCCE
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC-C-ceEEEEeeccccchhHHHHHhccccCcce
Confidence            34678999999999999988887777665432 2 355565542 2233455566677777664

>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=96.92  E-value=0.00029  Score=56.60  Aligned_cols=28  Identities=25%  Similarity=0.495  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...+++.|.|++|+||||+|+.+.....
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4578999999999999999999988764

>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=96.85  E-value=0.00086  Score=59.84  Aligned_cols=101  Identities=13%  Similarity=0.189  Sum_probs=54.4

Q ss_pred             ccchHHHHHHHHHHhc-------c-C-CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          153 FESRKSTLKGILDALS-------N-R-NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~-------~-~-~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ++|.++.++.+...+.       + + ...++.++|+.|+|||.||+.+.....     ...+-++.+.-.+...+    
T Consensus        24 viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~-----~~~i~~d~s~~~~~~~~----   94 (315)
T d1r6bx3          24 VFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG-----IELLRFDMSEYMERHTV----   94 (315)
T ss_dssp             SCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT-----CEEEEEEGGGCSSSSCC----
T ss_pred             ecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc-----CCeeEeccccccchhhh----
Confidence            4666777776655542       1 2 234788999999999999999998653     23344444432211100    


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                      .+-++.+. ..........+...+......+++||+++..
T Consensus        95 ~~l~g~~~-gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa  133 (315)
T d1r6bx3          95 SRLIGAPP-GYVGFDQGGLLTDAVIKHPHAVLLLDEIEKA  133 (315)
T ss_dssp             SSSCCCCS-CSHHHHHTTHHHHHHHHCSSEEEEEETGGGS
T ss_pred             hhhcccCC-CccccccCChhhHHHHhCccchhhhcccccc
Confidence            00011111 1100111112334444456789999999754

>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=96.84  E-value=0.0027  Score=54.77  Aligned_cols=83  Identities=23%  Similarity=0.308  Sum_probs=55.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccc-----cCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQ-----ESESVRAWRLLEQ  246 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~-----~~~~~~~~~l~~~  246 (426)
                      -+++-|+|++|+|||||+.++.......+  ..++|++....++..     .++.++...+.     ....+..-.+.+.
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~  126 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDA  126 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHH
Confidence            36899999999999999999988765442  357899998888864     35667765432     1222223333333


Q ss_pred             H-hcCCeEEEEEeCCC
Q 044858          247 L-KKETKILIILDDIW  261 (426)
Q Consensus       247 l-~~~k~~LlVlDdv~  261 (426)
                      + ..++.-|+|+|-+-
T Consensus       127 l~~~~~~~liViDSi~  142 (263)
T d1u94a1         127 LARSGAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHTCCSEEEEECGG
T ss_pred             HHhcCCCCEEEEECcc
Confidence            3 33455688999884

>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=96.82  E-value=0.00048  Score=55.17  Aligned_cols=27  Identities=33%  Similarity=0.311  Sum_probs=24.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ++++|+|..|+|||||+..+......+
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~   28 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhC
Confidence            689999999999999999999887764

>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=96.82  E-value=0.00037  Score=56.10  Aligned_cols=28  Identities=21%  Similarity=0.249  Sum_probs=23.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++...|.|.|++|+||||+|+.+.+...
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~   30 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELD   30 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhC
Confidence            3455799999999999999999998753

>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=96.81  E-value=0.0031  Score=52.36  Aligned_cols=60  Identities=20%  Similarity=0.256  Sum_probs=41.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCC-cCHHHHHHHHHHHhCCCc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQT-PQIKEIQREIAEKLGLKI  231 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~il~~i~~~l~~~~  231 (426)
                      .++.||.++|+.|+||||.+.+++.....++  ..+..++.... ....+-++...+.++.+.
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   69 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDEG--KSVVLAAADTFRAAAIEQLKIWGERVGATV   69 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEECTTCHHHHHHHHHHHHHHTCEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--CceEEEeecccccchhHHHHHHhhhcCccc
Confidence            4577999999999999988888887765432  34556655432 234456677777777654

>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=96.81  E-value=0.00035  Score=57.46  Aligned_cols=28  Identities=21%  Similarity=0.184  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +..+|.++|++|+||||+|+.+......
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~l~~   45 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEYLVC   45 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3468899999999999999999887764

>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=96.79  E-value=0.0028  Score=52.49  Aligned_cols=60  Identities=23%  Similarity=0.321  Sum_probs=39.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC-CcCHHHHHHHHHHHhCCCcc
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ-TPQIKEIQREIAEKLGLKID  232 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~il~~i~~~l~~~~~  232 (426)
                      +.+||.++|+.|+||||.+..+......++  ..+..++... .....+-++...+.++.+..
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~   69 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAADTQRPAAREQLRLLGEKVGVPVL   69 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTT--CCEEEEECCSSCHHHHHHHHHHHHHHTCCEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEecccccchHHHHHHHHHHhcCCccc
Confidence            457899999999999998888877766432  2344554432 22344566667777776543

>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=96.78  E-value=0.0031  Score=53.50  Aligned_cols=85  Identities=19%  Similarity=0.155  Sum_probs=53.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCc----------------cccC
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKI----------------DQES  235 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~----------------~~~~  235 (426)
                      -.++.|+|++|+|||+++.++......  ....++|++....  ...+.+ .+..++...                ....
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~--~~~~~~~is~e~~--~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACA--NKERAILFAYEES--RAQLLR-NAYSWGMDFEEMERQNLLKIVCAYPESAG  100 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHT--TTCCEEEEESSSC--HHHHHH-HHHTTSCCHHHHHHTTSEEECCCCGGGSC
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHH--hccccceeeccCC--HHHHHH-HHHHcCCChHHHhhcCceEEEEeecchhh
Confidence            468999999999999999999988653  3556778776543  333332 223332211                1112


Q ss_pred             cHHHHHHHHHHHhcCCeEEEEEeCCC
Q 044858          236 ESVRAWRLLEQLKKETKILIILDDIW  261 (426)
Q Consensus       236 ~~~~~~~l~~~l~~~k~~LlVlDdv~  261 (426)
                      .......+...+.+.+.-++|+|.+.
T Consensus       101 ~~~~~~~i~~~i~~~~~~~vviDs~~  126 (242)
T d1tf7a2         101 LEDHLQIIKSEINDFKPARIAIDSLS  126 (242)
T ss_dssp             HHHHHHHHHHHHHTTCCSEEEEECHH
T ss_pred             HHHHHHHHHHHHHhcCCceeeeecch
Confidence            33445566666666677789999863

>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=96.76  E-value=0.00041  Score=55.90  Aligned_cols=26  Identities=23%  Similarity=0.243  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++|.|.|++|+||||+|+.+.+...
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~   28 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999998764

>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=96.75  E-value=0.00043  Score=57.22  Aligned_cols=28  Identities=25%  Similarity=0.293  Sum_probs=24.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++.++|.|.|++|+||||+|+.+.+...
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~g   33 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDYS   33 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4678999999999999999999988763

>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=96.72  E-value=0.003  Score=54.45  Aligned_cols=88  Identities=19%  Similarity=0.334  Sum_probs=56.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------------ccccCcHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------------IDQESESV  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------------~~~~~~~~  238 (426)
                      +-+.|.|..|+|||+|+.++.+.... .+-+.++++-+.+.. ...++.+++.+.--..             ...++...
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~~~-~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~~~  147 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGA  147 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTT-TCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHH
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHHHh-hCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEEEEEECCCCCHHH
Confidence            45899999999999999999877433 224567788777654 5667777776642111             00111111


Q ss_pred             ------HHHHHHHHHh--cCCeEEEEEeCCC
Q 044858          239 ------RAWRLLEQLK--KETKILIILDDIW  261 (426)
Q Consensus       239 ------~~~~l~~~l~--~~k~~LlVlDdv~  261 (426)
                            ....+-+++.  +++++|+++||+-
T Consensus       148 r~~~~~~a~~iAEyf~~~~G~~VLv~~Dslt  178 (276)
T d2jdid3         148 RARVALTGLTVAEYFRDQEGQDVLLFIDNIF  178 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSCEEEEEECTH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCeEEEEEcchh
Confidence                  1224556664  3899999999984

>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=96.72  E-value=0.0006  Score=54.88  Aligned_cols=25  Identities=24%  Similarity=0.363  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .++|.|.|++|+||||+|+.+.+..
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            4689999999999999999997654

>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=96.72  E-value=0.00047  Score=56.05  Aligned_cols=27  Identities=22%  Similarity=0.346  Sum_probs=24.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ++|+|.|+.|+||||+++.+.+.....
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            689999999999999999999887643

>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=96.70  E-value=0.00047  Score=55.75  Aligned_cols=27  Identities=26%  Similarity=0.365  Sum_probs=23.1

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+++.+|.++|++|+||||+|+.+...
T Consensus        11 ~~~p~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          11 SPNPEVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             CSSCCEEEEECCTTSSHHHHHHHHTGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            346789999999999999999988654

>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=96.69  E-value=0.001  Score=59.30  Aligned_cols=104  Identities=16%  Similarity=0.274  Sum_probs=52.4

Q ss_pred             ccchHHHHHHHHHHhc-------c-CC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          153 FESRKSTLKGILDALS-------N-RN-FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~-------~-~~-~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ++|.++.++.+...+.       + .+ ..++.++|+.|+|||.||+.+.+..-..  -...+-++.+...+...+. .+
T Consensus        25 v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~--~~~~~~~~~~~~~~~~~~~-~L  101 (315)
T d1qvra3          25 VVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKHAVS-RL  101 (315)
T ss_dssp             SCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS--GGGEEEECTTTCCSSGGGG-GC
T ss_pred             EeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCC--CcceEEEeccccccchhhh-hh
Confidence            4566666666555442       2 22 3378899999999999999999876211  1122333333322211110 00


Q ss_pred             HHHhCCCccccCcHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 044858          224 AEKLGLKIDQESESVRAWRLLEQLKKETKILIILDDIWGS  263 (426)
Q Consensus       224 ~~~l~~~~~~~~~~~~~~~l~~~l~~~k~~LlVlDdv~~~  263 (426)
                         +|.+..-.. ......+.+.+.+....+++||+++..
T Consensus       102 ---~g~~~gyvG-~~~~~~l~~~~~~~p~~Vvl~DEieK~  137 (315)
T d1qvra3         102 ---IGAPPGYVG-YEEGGQLTEAVRRRPYSVILFDEIEKA  137 (315)
T ss_dssp             ------------------CHHHHHHHCSSEEEEESSGGGS
T ss_pred             ---cCCCCCCcC-cccCChHHHHHHhCCCcEEEEehHhhc
Confidence               011110000 001123445555556789999999754

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.68  E-value=0.00079  Score=58.44  Aligned_cols=28  Identities=21%  Similarity=0.208  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .++.|.++|++|+||||||+.+++....
T Consensus        31 ~P~~ilL~GpPGtGKT~la~~la~~~~~   58 (273)
T d1gvnb_          31 SPTAFLLGGQPGSGKTSLRSAIFEETQG   58 (273)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHTTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhhc
Confidence            4667899999999999999999987653

>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=96.63  E-value=0.00056  Score=56.99  Aligned_cols=27  Identities=26%  Similarity=0.281  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +.+|.++|.+|+||||+|+++.+....
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~   28 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNF   28 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            457999999999999999999987653

>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=96.59  E-value=0.0036  Score=55.39  Aligned_cols=71  Identities=20%  Similarity=0.297  Sum_probs=43.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHHHHHHHHHHhcCCe
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVRAWRLLEQLKKETK  252 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~k~  252 (426)
                      .++.++|++|+|||.||+.+......+..|-   -+..+.-.+              ..- ......+..+++...+  +
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~~~~~~---~~~~~~~~~--------------~~~-G~~e~~~~~~f~~a~~--~  183 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGGKDKYA---TVRFGEPLS--------------GYN-TDFNVFVDDIARAMLQ--H  183 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHTTSCCE---EEEBSCSST--------------TCB-CCHHHHHHHHHHHHHH--C
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcCCCCeE---EEEhhHhhh--------------ccc-chHHHHHHHHHHHHhh--c
Confidence            3556689999999999999999875332231   233332221              111 1123344556665543  6


Q ss_pred             EEEEEeCCCCc
Q 044858          253 ILIILDDIWGS  263 (426)
Q Consensus       253 ~LlVlDdv~~~  263 (426)
                      ++|++|+++..
T Consensus       184 ~ilf~DEid~~  194 (321)
T d1w44a_         184 RVIVIDSLKNV  194 (321)
T ss_dssp             SEEEEECCTTT
T ss_pred             cEEEeehhhhh
Confidence            79999999754

>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=96.58  E-value=0.00052  Score=55.01  Aligned_cols=24  Identities=21%  Similarity=0.365  Sum_probs=20.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      |.+.|++|+||||+++.+++....
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~   27 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGV   27 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            456699999999999999988753

>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=96.58  E-value=0.0014  Score=57.14  Aligned_cols=50  Identities=22%  Similarity=0.414  Sum_probs=36.7

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      +..+.+.+..+..++|.++|-||+||||++..+.......+  ..+.-+...
T Consensus         8 ~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G--~rVllvD~D   57 (279)
T d1ihua2           8 LSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMG--FDVHLTTSD   57 (279)
T ss_dssp             HHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESC
T ss_pred             HHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEeCC
Confidence            45566667778889999999999999999988877765442  234444444

>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=96.55  E-value=0.00059  Score=54.48  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=21.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |.|.|++|+||||+++.+.....
T Consensus         3 I~liG~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            77889999999999999999875

>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=96.53  E-value=0.00073  Score=54.59  Aligned_cols=24  Identities=42%  Similarity=0.565  Sum_probs=21.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      |+|+|+.|+|||||++.+......
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCC
Confidence            789999999999999999987653

>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=96.50  E-value=0.00075  Score=55.50  Aligned_cols=26  Identities=23%  Similarity=0.148  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.+|.|.|++|+||||+|+.+++...
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~~g   26 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEKYG   26 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999998653

>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=96.48  E-value=0.00067  Score=54.64  Aligned_cols=26  Identities=31%  Similarity=0.322  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +.|.++|++|+||||+|+.+++....
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~   28 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGY   28 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34678899999999999999988753

>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=96.44  E-value=0.00084  Score=56.38  Aligned_cols=41  Identities=27%  Similarity=0.254  Sum_probs=32.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAE  225 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~  225 (426)
                      .++|+|.||+|+||||+|+.+.++..-.       +      .+..+++++++.
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~gl~-------~------iStGdLlR~~a~   43 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQWH-------L------LDSGAIYRVLAL   43 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHTCE-------E------EEHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCc-------E------ECHHHHHHHHHH
Confidence            4699999999999999999999987532       1      245677777654

>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=96.41  E-value=0.00096  Score=55.80  Aligned_cols=27  Identities=22%  Similarity=0.288  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      |-+|+|.|..|+||||+|+.+.+....
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhch
Confidence            568999999999999999999887653

>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=96.40  E-value=0.0024  Score=56.07  Aligned_cols=42  Identities=19%  Similarity=0.250  Sum_probs=31.1

Q ss_pred             ccCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          168 SNRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       168 ~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      .++.+++|.+.|-||+||||+|..+.......+  ..+.-++..
T Consensus         4 ~~~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G--~rVLlvD~D   45 (296)
T d1ihua1           4 LQNIPPYLFFTGKGGVGKTSISCATAIRLAEQG--KRVLLVSTD   45 (296)
T ss_dssp             GSSCCSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEECC
T ss_pred             CCCCCeEEEEECCCcChHHHHHHHHHHHHHHCC--CCEEEEeCC
Confidence            355688999999999999999999887766542  234455544

>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=96.40  E-value=0.003  Score=56.28  Aligned_cols=55  Identities=22%  Similarity=0.363  Sum_probs=37.1

Q ss_pred             HHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc
Q 044858          160 LKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP  214 (426)
Q Consensus       160 ~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  214 (426)
                      ..++++.+.  .++..+|+|+|++|+|||||...+.......++=-.++-++.+.++
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~   93 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTR   93 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGS
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccHH
Confidence            445555543  4567899999999999999999999876543322234445444444

>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=96.37  E-value=0.0015  Score=58.16  Aligned_cols=27  Identities=26%  Similarity=0.413  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++.+.++||+|+|||.||+.+++...
T Consensus        48 ~~~~iLl~GPpG~GKT~lAkalA~~~~   74 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIARRLAKLAN   74 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCceEEEECCCCCCHHHHHHHHhhccc
Confidence            456788999999999999999998754

>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=96.36  E-value=0.006  Score=53.66  Aligned_cols=28  Identities=18%  Similarity=0.200  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .+-+|+|.|..|+||||+|+.+......
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL~~  106 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALLSR  106 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHTT
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHHhh
Confidence            4668999999999999999999887653

>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=96.35  E-value=0.0033  Score=56.06  Aligned_cols=63  Identities=27%  Similarity=0.273  Sum_probs=35.1

Q ss_pred             HHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHH
Q 044858          161 KGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       161 ~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      .++++.+.  .++..+|+|+|++|+|||||...+......+++=-.++-++-+.+++-..++.+-
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~ggailgdr  105 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVTGGSILGDK  105 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC------------
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceeeeccccccch
Confidence            34444443  4567899999999999999999998877654332234444444445544455443

>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=96.34  E-value=0.002  Score=53.56  Aligned_cols=29  Identities=31%  Similarity=0.305  Sum_probs=25.4

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..+..+|.+.|++|+||||||+.+.....
T Consensus        21 ~~kg~vIwltGlsGsGKTTia~~L~~~l~   49 (208)
T d1m7ga_          21 NQRGLTIWLTGLSASGKSTLAVELEHQLV   49 (208)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45678999999999999999999987654

>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=96.31  E-value=0.0011  Score=54.29  Aligned_cols=27  Identities=15%  Similarity=0.106  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++..|.|.|++|+||||+|+.+.+...
T Consensus         2 ~Pm~I~i~GppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1           2 DPLKVMISGAPASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHC
Confidence            345688999999999999999987764

>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=96.25  E-value=0.0018  Score=52.65  Aligned_cols=26  Identities=27%  Similarity=0.414  Sum_probs=23.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ++|.|.|+.|+||||+++.+......
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            57899999999999999999988764

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.23  E-value=0.008  Score=50.72  Aligned_cols=46  Identities=13%  Similarity=0.010  Sum_probs=32.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC----ccceEEEEEecCCcCHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENN----LFEKVISSRVSQTPQIK  217 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~  217 (426)
                      -+++.|.|++|+|||||+.++........    .-...+|++....++..
T Consensus        34 G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   83 (251)
T d1szpa2          34 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPV   83 (251)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGG
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHH
Confidence            46899999999999999999876543211    12357788777666533

>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=96.10  E-value=0.0018  Score=53.25  Aligned_cols=27  Identities=26%  Similarity=0.251  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.++|.|.|++|+||||+|+.+.+...
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~g   33 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKYG   33 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            457899999999999999999988653

>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=96.07  E-value=0.011  Score=51.18  Aligned_cols=80  Identities=14%  Similarity=0.016  Sum_probs=47.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccc-eEEEEEecCCcCHHHHHHHHHHHhCC-------CccccCcHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFE-KVISSRVSQTPQIKEIQREIAEKLGL-------KIDQESESVRAWR  242 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~il~~i~~~l~~-------~~~~~~~~~~~~~  242 (426)
                      .+-+|+|.|..|+|||||+..+.........+. .++.++...-+-..+-...+.+....       ..+..-+...+.+
T Consensus        26 ~P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~ll~~  105 (286)
T d1odfa_          26 CPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLLQE  105 (286)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHHHHH
T ss_pred             CCEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhHHHHHH
Confidence            355899999999999999999887765432222 34445544433222323344444321       1234456677777


Q ss_pred             HHHHHhcC
Q 044858          243 LLEQLKKE  250 (426)
Q Consensus       243 l~~~l~~~  250 (426)
                      .+..+.++
T Consensus       106 ~l~~l~~~  113 (286)
T d1odfa_         106 VLNTIFNN  113 (286)
T ss_dssp             HHHHHTC-
T ss_pred             HHHHHHhh
Confidence            77777653

>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=96.06  E-value=0.0047  Score=53.56  Aligned_cols=96  Identities=20%  Similarity=0.199  Sum_probs=51.8

Q ss_pred             HHHHHhcc-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEE-EEecCCcCHHHHHHHHHHHhCC----CccccC
Q 044858          162 GILDALSN-RNFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVIS-SRVSQTPQIKEIQREIAEKLGL----KIDQES  235 (426)
Q Consensus       162 ~l~~~l~~-~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~w-v~v~~~~~~~~il~~i~~~l~~----~~~~~~  235 (426)
                      ++++.+.. .+-+-++|.|..|+|||+|+.++.+...... -++++. ..+.....  + ..++.+....    .....+
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~~-~~~v~~~~~iger~~--e-v~~~~~~~~~~vv~~t~d~~  107 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNH-PDCVLMVLLIDERPE--E-VTEMQRLVKGEVVASTFDEP  107 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHHHC-TTSEEEEEEEEECHH--H-HHHHHHHCSSEEEEEETTSC
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhhcC-CCeEEEEEeeceeHH--H-HHhHHhhcceEEEeccCCCc
Confidence            45666652 2335689999999999999999998776432 333333 33333322  1 1222222211    111111


Q ss_pred             cH------HHHHHHHHHH-hcCCeEEEEEeCCC
Q 044858          236 ES------VRAWRLLEQL-KKETKILIILDDIW  261 (426)
Q Consensus       236 ~~------~~~~~l~~~l-~~~k~~LlVlDdv~  261 (426)
                      ..      .....+-+++ .+++.+||++||+-
T Consensus       108 ~~~r~~~~~~a~~iAEyfrd~G~dVLli~Dslt  140 (289)
T d1xpua3         108 ASRHVQVAEMVIEKAKRLVEHKKDVIILLDSIT  140 (289)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTCEEEEEESCHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHhccCceeecCcHH
Confidence            11      1122334444 35799999999984

>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=96.03  E-value=0.0018  Score=58.27  Aligned_cols=47  Identities=19%  Similarity=0.263  Sum_probs=35.1

Q ss_pred             CCcccccchHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHH
Q 044858          148 QDFMHFESRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       148 ~~~~~~~gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .++..++|.+..+..|.-.....+..-+.+.|++|+||||||+.+..
T Consensus         4 ~~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_           4 FPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             CChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHH
Confidence            35677899998777655443332334588999999999999999875

>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=96.00  E-value=0.0019  Score=54.21  Aligned_cols=41  Identities=17%  Similarity=0.141  Sum_probs=31.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEK  226 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~  226 (426)
                      -+|+|-|++|+||||+|+.+.....-.       +      .+..++++.++..
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~lg~~-------~------istGdl~R~~a~~   44 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKDFGFT-------Y------LDTGAMYRAATYM   44 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCCE-------E------EEHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCc-------E------ECHHHHHHHHHHH
Confidence            368899999999999999999887532       1      2456777776543

>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=95.93  E-value=0.0022  Score=52.08  Aligned_cols=25  Identities=20%  Similarity=0.398  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ++|.|+|++|+|||||++.+.+...
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5789999999999999999987653

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.93  E-value=0.002  Score=52.06  Aligned_cols=23  Identities=22%  Similarity=0.328  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |.|.|++|+||||+|+.+.+...
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~   25 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYG   25 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC
Confidence            77999999999999999988763

>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=95.92  E-value=0.0019  Score=52.90  Aligned_cols=23  Identities=30%  Similarity=0.482  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |+|+|++|+|||||++.+.+...
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~~~   25 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQEHS   25 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHhCC
Confidence            77999999999999999988754

>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=95.82  E-value=0.0024  Score=51.69  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|.|++|+||||+|+.+++...
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            378899999999999999998864

>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=95.81  E-value=0.0022  Score=52.27  Aligned_cols=25  Identities=32%  Similarity=0.424  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|.|+|++|+|||||++.+.+....
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~~~   27 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEYPD   27 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHCTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCc
Confidence            4789999999999999999887653

>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=95.80  E-value=0.0025  Score=51.66  Aligned_cols=24  Identities=25%  Similarity=0.317  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|.|++|+||||+|+.+++...
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~g   25 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKYG   25 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            377999999999999999998764

>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=95.79  E-value=0.0029  Score=54.84  Aligned_cols=37  Identities=22%  Similarity=0.434  Sum_probs=28.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      +.|+|+|-||+||||+|..+.......+ + .+.-++..
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~G-~-rVllID~D   38 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAMG-K-TIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTT-C-CEEEEEEC
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHhCC-C-cEEEEecC
Confidence            5799999999999999999988876542 3 34445543

>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=95.74  E-value=0.013  Score=49.30  Aligned_cols=166  Identities=14%  Similarity=0.156  Sum_probs=78.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh--hcC-----------ccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCc
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAK--ENN-----------LFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESE  236 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~--~~~-----------~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~  236 (426)
                      ++.+++.|+|+.+.||||+.+.+.-..-  .-+           .|+ .++..+....++..-....          ..+
T Consensus        39 ~~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d-~I~~~~~~~d~~~~~~S~F----------~~E  107 (234)
T d1wb9a2          39 PQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPID-RIFTRVGAADDLASGRSTF----------MVE  107 (234)
T ss_dssp             SSSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCC-EEEEEEC-----------C----------HHH
T ss_pred             CCceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccch-hheeEEccCcccccchhHH----------HHH
Confidence            3457899999999999999999875432  111           122 2233333322221100000          011


Q ss_pred             HHHHHHHHHHHhcCCeEEEEEeCCCCccChh---hh----cCCCCCCCCCeEEEEeecchhhhh--ccCCceeeEEccCC
Q 044858          237 SVRAWRLLEQLKKETKILIILDDIWGSLDLE---AI----GIPLADDNGGCKVLLTARSQDVLS--CEMDCQQNFVVDVL  307 (426)
Q Consensus       237 ~~~~~~l~~~l~~~k~~LlVlDdv~~~~~~~---~l----~~~l~~~~~~s~iivTtr~~~va~--~~~~~~~~~~l~~L  307 (426)
                      ...+..+.+.  ..++.|+++|++-....-.   .+    ...+ ....++.+|+||.......  ........+.+...
T Consensus       108 ~~~~~~il~~--~~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l-~~~~~~~~i~tTH~~~l~~~~~~~~~v~~~~~~~~  184 (234)
T d1wb9a2         108 MTETANILHN--ATEYSLVLMDEIGRGTSTYDGLSLAWACAENL-ANKIKALTLFATHYFELTQLPEKMEGVANVHLDAL  184 (234)
T ss_dssp             HHHHHHHHHH--CCTTEEEEEESCCCCSSSSHHHHHHHHHHHHH-HHTTCCEEEEECSCGGGGGHHHHSTTEEEEEEEEE
T ss_pred             HHHHHHHHHh--cccccEEeecccccCCChhhhhHHHHHhhhhh-hccccceEEEecchHHHhhhhhcccceEEEEEEEe
Confidence            1222233332  2467899999997542211   11    1112 1234678999998876542  12223334555544


Q ss_pred             CHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          308 NDKEAWSLFKKMTGDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       308 ~~~e~~~Lf~~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      ..++...+..+...+....    ..+-++++.+| +|-.+..-|..+
T Consensus       185 ~~~~~i~f~YkL~~G~~~~----s~ai~iA~~~G-lp~~ii~~A~~i  226 (234)
T d1wb9a2         185 EHGDTIAFMHSVQDGAASK----SYGLAVAALAG-VPKEVIKRARQK  226 (234)
T ss_dssp             EETTEEEEEEEEEESCCSS----CCHHHHHHHTT-CCHHHHHHHHHH
T ss_pred             eccCcceEEEEecCCCCCC----cHHHHHHHHhC-cCHHHHHHHHHH
Confidence            3332211111111111111    24566777664 877776665433

>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=95.71  E-value=0.0035  Score=51.24  Aligned_cols=26  Identities=19%  Similarity=0.339  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .-.|.|.|++|+||||+|+.+.....
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~~~g   31 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITKHFE   31 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHBC
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHHC
Confidence            34577889999999999999998653

>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=95.66  E-value=0.0031  Score=51.45  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=20.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVG  193 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~  193 (426)
                      .+-+|+|+|..|+||||+|..+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            35689999999999999999874

>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=95.63  E-value=0.0025  Score=52.29  Aligned_cols=28  Identities=21%  Similarity=0.179  Sum_probs=23.8

Q ss_pred             cCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          169 NRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       169 ~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +.++-+|+|-|..|+||||+++.+.+..
T Consensus         6 ~~kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           6 GTQPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3456689999999999999999988654

>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=95.63  E-value=0.0034  Score=50.72  Aligned_cols=25  Identities=12%  Similarity=0.315  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +.|.|+||+|+|||||++.+..+..
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~~   28 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKHP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhCC
Confidence            5789999999999999999987654

>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=95.52  E-value=0.0037  Score=50.54  Aligned_cols=23  Identities=22%  Similarity=0.287  Sum_probs=20.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |.|.|++|+||||+|+.+.+...
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g   27 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFH   27 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            55779999999999999988754

>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=95.50  E-value=0.0038  Score=50.36  Aligned_cols=24  Identities=21%  Similarity=0.076  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|.|++|+||||+|+.+++...
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~~   25 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKYG   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            367899999999999999997754

>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=95.48  E-value=0.0096  Score=51.59  Aligned_cols=28  Identities=21%  Similarity=0.376  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +.++|+|.|.+|+||||+++.+.+....
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~   30 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRR   30 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            4679999999999999999998877654

>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=95.45  E-value=0.012  Score=48.68  Aligned_cols=27  Identities=19%  Similarity=0.228  Sum_probs=24.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ..|+|.|+.|+||||+++.+.+.....
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            578999999999999999999987764

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=95.40  E-value=0.0054  Score=49.94  Aligned_cols=25  Identities=20%  Similarity=0.320  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .++| |.|++|+||||+|+.+.+...
T Consensus         4 ~rii-l~G~pGSGKsT~a~~La~~~g   28 (190)
T d1ak2a1           4 VRAV-LLGPPGAGKGTQAPKLAKNFC   28 (190)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHHHHT
T ss_pred             cEEE-EECCCCCCHHHHHHHHHHHhC
Confidence            4455 789999999999999997653

>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=95.27  E-value=0.0058  Score=50.56  Aligned_cols=25  Identities=20%  Similarity=0.329  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+|.|+||+|+|||||.+.+.....
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5789999999999999999988754

>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=95.23  E-value=0.0061  Score=51.51  Aligned_cols=24  Identities=42%  Similarity=0.606  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ||+|.|+.|+|||||...+.+...
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~   25 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLE   25 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Confidence            789999999999999999987654

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=95.18  E-value=0.034  Score=46.26  Aligned_cols=160  Identities=19%  Similarity=0.240  Sum_probs=76.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh--hcC-----------ccceEEEEEecCCcCHHHHHHHHHHHhCCCccccCcHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK--ENN-----------LFEKVISSRVSQTPQIKEIQREIAEKLGLKIDQESESVR  239 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~--~~~-----------~f~~~~wv~v~~~~~~~~il~~i~~~l~~~~~~~~~~~~  239 (426)
                      +++.|+|+...||||+.+.+.-..-  .-+           .|+. ++.......++..             ....-...
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~-I~~~~~~~d~~~~-------------~~StF~~e  101 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDG-IYTRIGASDDLAG-------------GKSTFMVE  101 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSE-EEEECCC-------------------CCSHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecce-EEEEECCCccccC-------------CccHHHHh
Confidence            4788999999999999999865431  111           2222 2333332222111             00011112


Q ss_pred             HHHHHHHHh-cCCeEEEEEeCCCCccChh-------hhcCCCCCCCCCeEEEEeecchhhhhccCCceeeEEccCCCHHH
Q 044858          240 AWRLLEQLK-KETKILIILDDIWGSLDLE-------AIGIPLADDNGGCKVLLTARSQDVLSCEMDCQQNFVVDVLNDKE  311 (426)
Q Consensus       240 ~~~l~~~l~-~~k~~LlVlDdv~~~~~~~-------~l~~~l~~~~~~s~iivTtr~~~va~~~~~~~~~~~l~~L~~~e  311 (426)
                      +.++...+. .+++.|+++|++-...+-.       .+...|  ...++.+++||....+..........+.+.....++
T Consensus       102 l~~~~~il~~~~~~sLvliDE~~~gT~~~eg~ala~aile~L--~~~~~~~i~tTH~~eL~~l~~~~~~~~~~~~~~~~~  179 (224)
T d1ewqa2         102 MEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEAL--HERRAYTLFATHYFELTALGLPRLKNLHVAAREEAG  179 (224)
T ss_dssp             HHHHHHHHHHCCTTEEEEEESTTTTSCHHHHHHHHHHHHHHH--HHHTCEEEEECCCHHHHTCCCTTEEEEEEEEECCSS
T ss_pred             HHHHHHHhccCCCCcEEeecccccCcchhhhcchHHHHHHHH--hhcCcceEEeeechhhhhhhhcccceEEEEEEEeCC
Confidence            223333332 2568999999997553211       111122  123678899998876643222333344443322222


Q ss_pred             HHHHHHHhh-CCCCCCCchHHHHHHHHHHcCCchHHHHHHHHHh
Q 044858          312 AWSLFKKMT-GDCIENGELKSVVTEVVKECAGLPIAIVPIAKAL  354 (426)
Q Consensus       312 ~~~Lf~~~~-~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  354 (426)
                      ... |...+ .+....    ..+-++++++ |+|-.+..-|..+
T Consensus       180 ~~~-f~Ykl~~G~~~~----s~ai~iA~~~-Glp~~II~rA~~i  217 (224)
T d1ewqa2         180 GLV-FYHQVLPGPASK----SYGVEVAAMA-GLPKEVVARARAL  217 (224)
T ss_dssp             SCE-EEEEEEESCCSS----CCHHHHHHHT-TCCHHHHHHHHHH
T ss_pred             CeE-EEEEEeeCCCCc----cHHHHHHHHh-CcCHHHHHHHHHH
Confidence            111 11111 111111    2466677766 6887776655543

>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=95.13  E-value=0.0062  Score=51.58  Aligned_cols=27  Identities=22%  Similarity=0.279  Sum_probs=24.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +++.|+|-|.-|+||||+++.+.+...
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHh
Confidence            368899999999999999999998754

>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=95.13  E-value=0.0065  Score=53.12  Aligned_cols=38  Identities=29%  Similarity=0.414  Sum_probs=28.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecC
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQ  212 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  212 (426)
                      +.|+|+|-||+||||+|..+.......+ . .+.-+....
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA~~G-~-rVLlID~Dp   40 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALAEMG-K-KVMIVGCDP   40 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTT-C-CEEEEEECS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCC-C-CEEEEecCC
Confidence            5788999999999999999887766432 2 355566543

>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=95.09  E-value=0.049  Score=45.58  Aligned_cols=55  Identities=16%  Similarity=0.142  Sum_probs=36.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCc--------------cceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNL--------------FEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~--------------f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      -.++.|.|.+|+|||+++.++.......+.              ...+.|++.....+.. ....+...+
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~~-~~~~~~~~~  102 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPE-RIMQMAEHA  102 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHH-HHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCHH-HHHHHHhhc
Confidence            368999999999999999999876543211              1246677766555533 334444444

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=95.07  E-value=0.078  Score=45.40  Aligned_cols=52  Identities=21%  Similarity=0.176  Sum_probs=35.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      .++.|.|.+|+|||+++.++..+......+ .+++++.  ..+..++...++...
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s~--E~~~~~~~~r~~~~~   87 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAML--EESVEETAEDLIGLH   87 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEES--SSCHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhccc-ceeEeee--ccchhhHHhHHHHHh
Confidence            478899999999999999998765433223 3444443  455666666666544

>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=95.04  E-value=0.024  Score=47.91  Aligned_cols=48  Identities=25%  Similarity=0.222  Sum_probs=34.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc----CccceEEEEEecCCcCHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN----NLFEKVISSRVSQTPQIKEI  219 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~i  219 (426)
                      -.++.|.|++|+|||+++.++......+    ......+|+......+...+
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            4689999999999999999998765422    22345778877766665433

>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=95.01  E-value=0.013  Score=48.16  Aligned_cols=26  Identities=31%  Similarity=0.575  Sum_probs=23.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .|+|-|.-|+||||+++.+.+....+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            58999999999999999999887654

>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=94.90  E-value=0.0063  Score=51.08  Aligned_cols=25  Identities=24%  Similarity=0.470  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCcchhhHhccCCC
Confidence            3589999999999999999887543

>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=94.89  E-value=0.027  Score=46.38  Aligned_cols=51  Identities=24%  Similarity=0.291  Sum_probs=32.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIA  224 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~  224 (426)
                      +.|+|-|+.|+||||+++.+.+.....+ +..+.+..-+......+.+++..
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~g-~~~~~~~~ep~~~~~g~~i~~~~   53 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQLG-IRDMVFTREPGGTQLAEKLRSLL   53 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTT-CCCEEEEESSCSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhCC-CCeEEEecCCCCccchhhhHHHH
Confidence            5789999999999999999998876532 33344333222223344444443

>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=94.87  E-value=0.0076  Score=47.04  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.|+|++|+|||||...+..+.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            6799999999999999987654

>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=94.83  E-value=0.0075  Score=50.91  Aligned_cols=24  Identities=25%  Similarity=0.410  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+++|+|+.|+|||||++.++.-.
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhcCC
Confidence            589999999999999999997643

>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=94.80  E-value=0.0077  Score=50.56  Aligned_cols=25  Identities=24%  Similarity=0.368  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCC
Confidence            3589999999999999999987543

>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=94.78  E-value=0.036  Score=46.12  Aligned_cols=39  Identities=18%  Similarity=-0.024  Sum_probs=26.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      -.++.|.|++|+|||+||.++........ -..++|++..
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~~~~~-~~~~~~~s~e   64 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEF-DEPGVFVTFE   64 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCccccccc
Confidence            46899999999999999988654432211 2235565544

>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=94.77  E-value=0.007  Score=51.10  Aligned_cols=25  Identities=36%  Similarity=0.525  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||++.+.--.
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCc
Confidence            3589999999999999999997644

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.75  E-value=0.0062  Score=50.12  Aligned_cols=26  Identities=42%  Similarity=0.566  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||.+.+..-.+
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCChHHHHHHHHhcccc
Confidence            35799999999999999999987543

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.74  E-value=0.02  Score=48.59  Aligned_cols=44  Identities=16%  Similarity=0.347  Sum_probs=31.4

Q ss_pred             ccchHHHHHHHHHHhc---cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          153 FESRKSTLKGILDALS---NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       153 ~~gR~~~~~~l~~~l~---~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      |+|....++++.+.+.   ..+. -|.|.|+.|+|||++|+.+++...
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~~~-pvlI~Ge~GtGK~~~A~~ih~~s~   48 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCAEC-PVLITGESGVGKEVVARLIHKLSD   48 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTCCS-CEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEecCHHHHHHHHHHHHHhCCCC-CEEEECCCCcCHHHHHHHHHHhcC
Confidence            5666666666665554   2222 368999999999999999987543

>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=94.69  E-value=0.027  Score=46.64  Aligned_cols=28  Identities=21%  Similarity=0.236  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      +-+.|+|-|+-|+||||+++.+.+....
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L~~   29 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKLQP   29 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHTTT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            3468999999999999999999987654

>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=94.61  E-value=0.0086  Score=50.69  Aligned_cols=26  Identities=38%  Similarity=0.489  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -..++|+|+.|+|||||++.+..-..
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            35799999999999999999976543

>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=94.60  E-value=0.0091  Score=50.29  Aligned_cols=25  Identities=24%  Similarity=0.344  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||.+.+..-.
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC
Confidence            3589999999999999999987654

>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=94.60  E-value=0.066  Score=46.07  Aligned_cols=89  Identities=17%  Similarity=0.198  Sum_probs=48.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCc-c-----ceEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCcHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKENNL-F-----EKVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESESV  238 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~~~~-f-----~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~~~  238 (426)
                      +-+.|.|.+|+|||+|+..+......... -     ..++++-+.... ...++...+...-...       ...++...
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvvv~~ts~~~~~~  148 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPL  148 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHH
T ss_pred             CEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceEEEEECCCCCHHH
Confidence            44789999999999999888765432111 1     134555565544 3455555554432111       11111111


Q ss_pred             ------HHHHHHHHHh-cCCeEEEEEeCCC
Q 044858          239 ------RAWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       239 ------~~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                            ....+-+++. ++|++|+++||+-
T Consensus       149 r~~~~~~a~tiAEyfrd~G~~VLll~Dslt  178 (285)
T d2jdia3         149 QYLAPYSGCSMGEYFRDNGKHALIIYDDLS  178 (285)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCcEEEEEcChH
Confidence                  1112333332 5899999999984

>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=94.60  E-value=0.12  Score=43.97  Aligned_cols=25  Identities=24%  Similarity=0.359  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+..|+|.+|+|||||+.+++....
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            5788999999999999999887654

>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=94.57  E-value=0.041  Score=47.24  Aligned_cols=86  Identities=16%  Similarity=0.183  Sum_probs=48.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCc-CHHHHHHHHHHHhCCC-------ccccCc------HHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTP-QIKEIQREIAEKLGLK-------IDQESE------SVR  239 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~il~~i~~~l~~~-------~~~~~~------~~~  239 (426)
                      -+.|.|..|+|||+|+.........  +-+.++++-+.... ...++..++.+.-...       ...++.      ...
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~~~~--~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~  146 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILNQQG--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYT  146 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHTCCT--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHH
T ss_pred             eEeeccCCCCChHHHHHHHHhhhcc--cCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHHH
Confidence            4789999999999999886554432  23456677666554 3334444443321000       001111      112


Q ss_pred             HHHHHHHHh-cCCeEEEEEeCCC
Q 044858          240 AWRLLEQLK-KETKILIILDDIW  261 (426)
Q Consensus       240 ~~~l~~~l~-~~k~~LlVlDdv~  261 (426)
                      ...+-+++. ++++.|+++||+-
T Consensus       147 a~tiAEyfrd~G~~Vlll~Dslt  169 (276)
T d1fx0a3         147 GAALAEYFMYRERHTLIIYDDLS  169 (276)
T ss_dssp             HHHHHHHHHHTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHcCCceeEEeeccH
Confidence            233444443 4789999999984

>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=50.02  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|.|+.|+|||||.+.+..-.+
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~~   49 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEECCCCChHHHHHHHHHcCCC
Confidence            4788999999999999999987553

>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=94.48  E-value=0.0093  Score=46.90  Aligned_cols=22  Identities=32%  Similarity=0.508  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |+|+|.+|+|||||...+....
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7899999999999999987653

>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=94.48  E-value=0.01  Score=50.69  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||++.+..-.
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhccc
Confidence            3579999999999999999997544

>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=94.46  E-value=0.011  Score=48.03  Aligned_cols=26  Identities=15%  Similarity=0.378  Sum_probs=22.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ++.+.|+|+|.+|+|||||...+.+.
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            34567999999999999999999753

>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=94.39  E-value=0.034  Score=43.35  Aligned_cols=28  Identities=29%  Similarity=0.255  Sum_probs=24.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      .-+|.+.|.=|+||||+++.+.+.....
T Consensus        33 g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          33 AIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            3489999999999999999999887653

>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=94.35  E-value=0.0098  Score=50.87  Aligned_cols=25  Identities=24%  Similarity=0.425  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|+|+.|+|||||++.+.--.
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            3589999999999999999997543

>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=94.34  E-value=0.012  Score=50.10  Aligned_cols=25  Identities=20%  Similarity=0.230  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -..++|+|+.|+|||||++.+..-.
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhccc
Confidence            4689999999999999999987644

>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=94.34  E-value=0.011  Score=49.56  Aligned_cols=25  Identities=28%  Similarity=0.405  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +.+|..|.|+-|+|||||.+.+.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5689999999999999999998875

>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=94.34  E-value=0.011  Score=49.97  Aligned_cols=25  Identities=28%  Similarity=0.325  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -..++|+|+.|+|||||++.+..-.
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3689999999999999999987543

>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=94.32  E-value=0.016  Score=46.27  Aligned_cols=26  Identities=23%  Similarity=0.380  Sum_probs=21.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ++..-|+|+|.+|+|||||...+...
T Consensus        11 ~k~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          11 KKTGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34445889999999999999998654

>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=94.25  E-value=0.0093  Score=49.90  Aligned_cols=25  Identities=20%  Similarity=0.236  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+.--.
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCc
Confidence            3589999999999999999997654

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=94.24  E-value=0.028  Score=50.59  Aligned_cols=29  Identities=21%  Similarity=0.000  Sum_probs=25.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ++.+.+.++||+|+|||++|..+++....
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~~~  180 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELCGG  180 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            45568999999999999999999988764

>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=94.23  E-value=0.0075  Score=50.90  Aligned_cols=26  Identities=23%  Similarity=0.314  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+.|+|-|+.|+||||+++.+.+...
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            46899999999999999999987654

>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=94.22  E-value=0.014  Score=50.66  Aligned_cols=26  Identities=27%  Similarity=0.363  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||++.+.....
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCCc
Confidence            46799999999999999999986543

>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=94.21  E-value=0.028  Score=46.84  Aligned_cols=37  Identities=30%  Similarity=0.353  Sum_probs=28.8

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          173 NMIGVY-GMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       173 ~vi~I~-G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      ++|+|+ |-||+||||+|..+.......  -..++.+...
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~la~~--g~~VlliD~D   39 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVALAQL--GHDVTIVDAD   39 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHHHHT--TCCEEEEECC
T ss_pred             EEEEEECCCCCChHHHHHHHHHHHHHhC--CCCEEEEeCC
Confidence            678777 899999999999998887653  3356777664

>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=94.17  E-value=0.012  Score=46.94  Aligned_cols=21  Identities=24%  Similarity=0.411  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||+..+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            679999999999999998765

>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=94.17  E-value=0.026  Score=52.22  Aligned_cols=28  Identities=25%  Similarity=0.382  Sum_probs=24.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~  199 (426)
                      ++.|.++||.|+|||.||+.+.....+.
T Consensus        49 ksNILliGPTGvGKTlLAr~LAk~l~VP   76 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARRLAKLANAP   76 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTCC
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            3568999999999999999999877654

>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=94.15  E-value=0.012  Score=46.51  Aligned_cols=21  Identities=24%  Similarity=0.426  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |+|+|.+|+|||||+..+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999998764

>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=94.08  E-value=0.013  Score=46.24  Aligned_cols=21  Identities=33%  Similarity=0.324  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999999865

>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=94.07  E-value=0.022  Score=45.25  Aligned_cols=33  Identities=18%  Similarity=0.345  Sum_probs=24.3

Q ss_pred             HHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          162 GILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       162 ~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+..++.+... -|.|+|.+|+|||||...+...
T Consensus         6 ~~~~~~~~k~~-kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           6 RIWRLFNHQEH-KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHTTSCE-EEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHhCCCeE-EEEEECCCCCCHHHHHHHHhcC
Confidence            44544444444 4779999999999999998764

>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=94.06  E-value=0.014  Score=45.97  Aligned_cols=21  Identities=24%  Similarity=0.561  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988764

>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=94.03  E-value=0.016  Score=47.65  Aligned_cols=46  Identities=13%  Similarity=0.030  Sum_probs=30.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCc----cceEEEEEecCCcCHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKENNL----FEKVISSRVSQTPQIK  217 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~  217 (426)
                      -.++.|.|++|+|||+|+.++.........    +....++.........
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPE   72 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHH
Confidence            358999999999999999999876543222    2234455544444433

>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=94.02  E-value=0.056  Score=45.44  Aligned_cols=46  Identities=20%  Similarity=0.112  Sum_probs=34.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh----cCccceEEEEEecCCcCHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAKE----NNLFEKVISSRVSQTPQIK  217 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~~----~~~f~~~~wv~v~~~~~~~  217 (426)
                      -.++.|.|++|+|||++|.++......    ...+..+.|+.....++..
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            458999999999999999999865432    2234567788777666643

>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=93.99  E-value=0.027  Score=50.71  Aligned_cols=26  Identities=23%  Similarity=0.324  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+..+...||.|+|||.||+.+....
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcceeeeCCCCccHHHHHHHHHhhc
Confidence            45668899999999999999998764

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.92  E-value=0.014  Score=46.11  Aligned_cols=21  Identities=33%  Similarity=0.575  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||...+.++
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998765

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=93.84  E-value=0.015  Score=47.93  Aligned_cols=19  Identities=26%  Similarity=0.457  Sum_probs=17.7

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEV  192 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v  192 (426)
                      +|+|+|+.|+||||+++.+
T Consensus         5 iIgitG~igSGKStv~~~l   23 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHH
Confidence            8999999999999999866

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.83  E-value=0.017  Score=47.29  Aligned_cols=23  Identities=26%  Similarity=0.265  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +.|+|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            57899999999999999999764

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.82  E-value=0.015  Score=45.72  Aligned_cols=21  Identities=24%  Similarity=0.379  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||+..+.+.
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998764

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.82  E-value=0.015  Score=46.15  Aligned_cols=21  Identities=38%  Similarity=0.607  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||.+.+.+.
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>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=93.81  E-value=0.016  Score=47.71  Aligned_cols=21  Identities=33%  Similarity=0.458  Sum_probs=18.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVG  193 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~  193 (426)
                      -+|+|+|..|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            479999999999999998763

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.79  E-value=0.016  Score=46.01  Aligned_cols=21  Identities=24%  Similarity=0.398  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||...+.+.
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=93.78  E-value=0.015  Score=45.90  Aligned_cols=21  Identities=33%  Similarity=0.499  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||+..+.+.
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            689999999999999998764

>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=93.78  E-value=0.011  Score=49.97  Aligned_cols=25  Identities=28%  Similarity=0.457  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -.+++|.|+.|+|||||.+.+..-.
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            3589999999999999999997643

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.74  E-value=0.016  Score=45.80  Aligned_cols=22  Identities=18%  Similarity=0.432  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.|+|.+|+|||||...+.+..
T Consensus         7 i~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999987643

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.72  E-value=0.015  Score=46.17  Aligned_cols=21  Identities=38%  Similarity=0.814  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||...+...
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999988764

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.71  E-value=0.016  Score=45.86  Aligned_cols=22  Identities=27%  Similarity=0.622  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.++|.+|+|||+|...+.+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999998753

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.69  E-value=0.017  Score=45.87  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.|+|.+|+|||||+..+.+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6899999999999999988543

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=93.67  E-value=0.017  Score=45.53  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||...+...
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            679999999999999998654

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.66  E-value=0.017  Score=46.06  Aligned_cols=22  Identities=32%  Similarity=0.495  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999998764

>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=93.65  E-value=0.016  Score=48.87  Aligned_cols=26  Identities=23%  Similarity=0.417  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|.|+.|.|||||.+.+.--.+
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl~~   57 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            35899999999999999999976543

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.61  E-value=0.019  Score=45.25  Aligned_cols=21  Identities=29%  Similarity=0.442  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999998764

>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=93.61  E-value=0.017  Score=45.92  Aligned_cols=21  Identities=29%  Similarity=0.518  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |+|+|.+|+|||||...+.+.
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999998754

>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=93.56  E-value=0.018  Score=45.47  Aligned_cols=23  Identities=22%  Similarity=0.407  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|+|+|..|+|||||...+.+.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            34788999999999999998754

>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=93.54  E-value=0.018  Score=48.61  Aligned_cols=26  Identities=31%  Similarity=0.471  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      -.+++|+|+.|+|||||.+.+..-..
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~~~   53 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTLIK   53 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            35899999999999999999976543

>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=93.54  E-value=0.018  Score=45.54  Aligned_cols=21  Identities=29%  Similarity=0.551  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            679999999999999998654

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.52  E-value=0.018  Score=45.67  Aligned_cols=21  Identities=33%  Similarity=0.540  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||...+.+.
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998764

>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=93.48  E-value=0.019  Score=45.37  Aligned_cols=22  Identities=32%  Similarity=0.558  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.|+|..|+|||+|...+....
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6799999999999999987653

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.48  E-value=0.019  Score=45.48  Aligned_cols=22  Identities=23%  Similarity=0.448  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .|+|.|.+|+|||||...+...
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            5899999999999999998753

>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=93.45  E-value=0.021  Score=44.37  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|+++|.+|+|||||...+...
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999998764

>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=93.42  E-value=0.019  Score=45.24  Aligned_cols=21  Identities=33%  Similarity=0.620  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||...+.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998865

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.42  E-value=0.018  Score=46.38  Aligned_cols=21  Identities=29%  Similarity=0.434  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||+..+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            679999999999999998754

>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=93.41  E-value=0.02  Score=45.68  Aligned_cols=21  Identities=29%  Similarity=0.589  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|..|+|||||+..+.+.
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>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=93.38  E-value=0.02  Score=45.72  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.|+|.+|+|||+|...+.+..
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6788999999999999887653

>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=93.37  E-value=0.019  Score=48.92  Aligned_cols=25  Identities=28%  Similarity=0.412  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .+++|.|+.|+|||||++.+.--.+
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHCCCc
Confidence            5899999999999999999986543

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.36  E-value=0.023  Score=46.56  Aligned_cols=23  Identities=22%  Similarity=0.190  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +.|+|+|.+|+|||||...+...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999998764

>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=93.36  E-value=0.02  Score=45.51  Aligned_cols=21  Identities=29%  Similarity=0.423  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||+..+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998754

>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=93.30  E-value=0.059  Score=44.84  Aligned_cols=37  Identities=27%  Similarity=0.419  Sum_probs=28.2

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHhhhcCccceEEEEEec
Q 044858          173 NMIGVY-GMGGIGKTTLVKEVGRQAKENNLFEKVISSRVS  211 (426)
Q Consensus       173 ~vi~I~-G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~  211 (426)
                      ++|+|+ +-||+||||+|..+.......  -..++-+...
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~--g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDR--GRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHT--TCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhC--CCCEEEEeCC
Confidence            588888 789999999999998887653  2346666654

>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=93.28  E-value=0.021  Score=45.15  Aligned_cols=22  Identities=18%  Similarity=0.370  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |+|+|..|+|||+|...+.+..
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999987653

>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=93.25  E-value=0.025  Score=45.54  Aligned_cols=22  Identities=32%  Similarity=0.462  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |.++|.+|+|||+|.+++....
T Consensus         5 ivllG~~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKIIH   26 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            6799999999999999986554

>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=93.18  E-value=0.022  Score=45.72  Aligned_cols=22  Identities=32%  Similarity=0.369  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999998764

>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=93.14  E-value=0.025  Score=44.73  Aligned_cols=21  Identities=29%  Similarity=0.445  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |+|+|.+|+|||+|+..+.+.
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>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=93.13  E-value=0.025  Score=45.11  Aligned_cols=24  Identities=21%  Similarity=0.391  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+.|+|+|.+|+|||||...+...
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999999865

>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=93.11  E-value=0.027  Score=47.39  Aligned_cols=24  Identities=21%  Similarity=0.171  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .+|+|+|..|+||||+|+.+.+..
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            579999999999999999987653

>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=93.09  E-value=0.023  Score=45.16  Aligned_cols=22  Identities=36%  Similarity=0.578  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|.++|.+|+|||||...+...
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999988653

>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=93.08  E-value=0.025  Score=45.90  Aligned_cols=21  Identities=24%  Similarity=0.477  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |+|+|.+|+|||||+..+.+.
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            779999999999999998864

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.99  E-value=0.024  Score=45.60  Aligned_cols=21  Identities=33%  Similarity=0.457  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||+|...+.+.
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            789999999999999998764

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.97  E-value=0.016  Score=49.39  Aligned_cols=24  Identities=33%  Similarity=0.468  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -..++|+|+.|+|||||++.+..-
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~gl   67 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPRF   67 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhc
Confidence            357999999999999999988643

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.93  E-value=0.027  Score=44.79  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ...|+|+|.+|+|||||...+.+.
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

>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=92.92  E-value=0.046  Score=45.31  Aligned_cols=33  Identities=18%  Similarity=0.498  Sum_probs=24.9

Q ss_pred             HHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          160 LKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       160 ~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      ++.|..++.+   +..+++|.+|+|||||...+..+
T Consensus        86 ~~~L~~~l~~---kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          86 IEELKEYLKG---KISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             HHHHHHHHSS---SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HhhHHHHhcC---CeEEEECCCCCCHHHHHHhhcch
Confidence            3455555543   46789999999999999988654

>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=92.86  E-value=0.027  Score=44.66  Aligned_cols=22  Identities=27%  Similarity=0.376  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|.++|.+|+|||||...+.+.
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3679999999999999998754

>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=92.86  E-value=0.021  Score=47.95  Aligned_cols=22  Identities=27%  Similarity=0.555  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .+++|.|+.|.|||||.+.+..
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5799999999999999999875

>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=92.84  E-value=0.03  Score=43.99  Aligned_cols=21  Identities=29%  Similarity=0.422  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||...+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            678999999999999988654

>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=92.84  E-value=0.029  Score=45.02  Aligned_cols=21  Identities=29%  Similarity=0.551  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999998764

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.80  E-value=0.027  Score=44.71  Aligned_cols=21  Identities=29%  Similarity=0.572  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||+..+.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999888764

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=92.79  E-value=0.028  Score=44.43  Aligned_cols=22  Identities=27%  Similarity=0.462  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999998754

>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=92.75  E-value=1.1  Score=36.94  Aligned_cols=44  Identities=18%  Similarity=0.171  Sum_probs=35.9

Q ss_pred             chHHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          155 SRKSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       155 gR~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      ......+++.+.+..+.+....|+|..|+|||.++-......-.
T Consensus        59 ~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~  102 (233)
T d2eyqa3          59 DQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD  102 (233)
T ss_dssp             HHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH
Confidence            45667778888888888888999999999999999887766543

>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=92.75  E-value=0.038  Score=45.43  Aligned_cols=27  Identities=26%  Similarity=0.180  Sum_probs=23.6

Q ss_pred             cEEEEEcCC-CCcHHHHHHHHHHHhhhc
Q 044858          173 NMIGVYGMG-GIGKTTLVKEVGRQAKEN  199 (426)
Q Consensus       173 ~vi~I~G~~-GiGKTtLa~~v~~~~~~~  199 (426)
                      +.+.|+|-+ |+||||++..+......+
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~   29 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAA   29 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHC
Confidence            458899998 999999999999888765

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.58  E-value=0.032  Score=44.29  Aligned_cols=21  Identities=29%  Similarity=0.450  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||+..+...
T Consensus         6 v~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999988643

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.58  E-value=0.033  Score=44.52  Aligned_cols=21  Identities=33%  Similarity=0.422  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|..|+|||+|+..+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988775

>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=92.56  E-value=0.031  Score=44.21  Aligned_cols=21  Identities=33%  Similarity=0.558  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|..|+|||||+..+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578899999999999998864

>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=92.52  E-value=0.035  Score=44.85  Aligned_cols=21  Identities=29%  Similarity=0.482  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||+|...+...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999998654

>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=92.51  E-value=0.031  Score=45.18  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |+++|.+|+|||+|+..+.+..
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999887643

>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=92.50  E-value=0.03  Score=45.35  Aligned_cols=18  Identities=39%  Similarity=0.656  Sum_probs=17.0

Q ss_pred             EEEEcCCCCcHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEV  192 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v  192 (426)
                      |.|+|.+|+|||||...+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            679999999999999998

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.49  E-value=0.032  Score=44.45  Aligned_cols=21  Identities=29%  Similarity=0.528  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.++|.+|+|||||...+.+.
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>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=92.35  E-value=0.02  Score=45.47  Aligned_cols=21  Identities=43%  Similarity=0.518  Sum_probs=17.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||...+.+.
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987654

>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=92.29  E-value=0.026  Score=45.07  Aligned_cols=21  Identities=29%  Similarity=0.604  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |+|+|.+|+|||||...+.+.
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999998643

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.25  E-value=0.032  Score=44.54  Aligned_cols=22  Identities=27%  Similarity=0.395  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998754

>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=92.15  E-value=0.038  Score=43.03  Aligned_cols=21  Identities=19%  Similarity=0.411  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |+|+|.+|+|||||...+...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999998744

>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=92.14  E-value=0.14  Score=44.96  Aligned_cols=24  Identities=33%  Similarity=0.326  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      .|.|+|+.|+||||+.+.+.....
T Consensus       168 nili~G~tgSGKTT~l~al~~~i~  191 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFIP  191 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGSC
T ss_pred             CEEEEeeccccchHHHHHHhhhcc
Confidence            478999999999999999987654

>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=92.09  E-value=0.038  Score=44.04  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      -|.++|.+|+|||||...+.+..
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999887653

>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=92.05  E-value=0.029  Score=44.98  Aligned_cols=21  Identities=33%  Similarity=0.618  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      -|+|+|.+++|||||...+..
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999864

>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=91.90  E-value=0.045  Score=43.47  Aligned_cols=23  Identities=22%  Similarity=0.293  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|.|.|.+|+||||+|..+..+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45789999999999999988764

>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=91.73  E-value=0.031  Score=44.73  Aligned_cols=23  Identities=30%  Similarity=0.413  Sum_probs=19.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      --|.++|.+|+|||||...+...
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34679999999999999987543

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=91.56  E-value=0.096  Score=46.84  Aligned_cols=62  Identities=16%  Similarity=0.045  Sum_probs=35.7

Q ss_pred             HHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CccceEEEEEecCCcCHHHHHHHH
Q 044858          159 TLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAKEN-NLFEKVISSRVSQTPQIKEIQREI  223 (426)
Q Consensus       159 ~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~~~~il~~i  223 (426)
                      ....+...+.   .++..|.|++|+||||++..+....... ..-...+.+..+.......+...+
T Consensus       153 Q~~A~~~al~---~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         153 QKVAAAVALT---RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             HHHHHHHHHT---BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHc---CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            3444444443   3689999999999999987765543321 112235666665444344444333

>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=91.46  E-value=0.05  Score=43.24  Aligned_cols=23  Identities=22%  Similarity=0.267  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|.|.|++|+||||||..+..+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45789999999999999998754

>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=91.33  E-value=0.057  Score=44.75  Aligned_cols=22  Identities=32%  Similarity=0.454  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|.+.|.+|+|||||.+++...
T Consensus         8 KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999987543

>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=91.31  E-value=0.03  Score=44.41  Aligned_cols=21  Identities=24%  Similarity=0.438  Sum_probs=8.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~  195 (426)
                      |.|+|.+|+|||||...+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999877653

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=91.31  E-value=0.052  Score=43.38  Aligned_cols=22  Identities=23%  Similarity=0.459  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      -|+|+|..|+|||||...+...
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4789999999999999988754

>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=91.19  E-value=0.06  Score=42.46  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .-|.|.|.+|+||||+|..+...
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45789999999999999887765

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=91.16  E-value=0.038  Score=44.00  Aligned_cols=24  Identities=13%  Similarity=0.169  Sum_probs=20.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      +..-|+|+|.+++|||||...+..
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhC
Confidence            456799999999999999988754

>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=90.86  E-value=0.11  Score=43.97  Aligned_cols=37  Identities=32%  Similarity=0.429  Sum_probs=26.6

Q ss_pred             HHHHHHHHhcc--CCccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          159 TLKGILDALSN--RNFNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       159 ~~~~l~~~l~~--~~~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+.++...+.+  ...-.|+|+|..|+|||||...+...
T Consensus        17 ~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          17 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            34444544442  23446889999999999999999865

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=90.61  E-value=0.066  Score=45.92  Aligned_cols=26  Identities=23%  Similarity=0.217  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      +.+.|+|+|..|.|||||+..+....
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            46789999999999999999987554

>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=89.59  E-value=0.12  Score=42.91  Aligned_cols=25  Identities=32%  Similarity=0.412  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      .++|+|.|..++|||||+..+....
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHhhc
Confidence            4679999999999999999887653

>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=89.53  E-value=0.033  Score=43.38  Aligned_cols=22  Identities=23%  Similarity=0.428  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 044858          175 IGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       175 i~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      |+++|.+|+|||||...+....
T Consensus         3 I~liG~~n~GKSSLin~l~g~~   24 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNED   24 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7899999999999999997653

>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=89.17  E-value=0.12  Score=44.13  Aligned_cols=24  Identities=29%  Similarity=0.455  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .+.|+|+|..|.|||||+..+...
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHHHH
Confidence            367999999999999999988543

>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=88.82  E-value=0.14  Score=45.10  Aligned_cols=26  Identities=31%  Similarity=0.300  Sum_probs=22.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      -.|.|-|.-|+||||+++.+.+....
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEEEECCccCCHHHHHHHHHHHhcc
Confidence            46889999999999999999987654

>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=88.55  E-value=0.22  Score=43.24  Aligned_cols=18  Identities=22%  Similarity=0.324  Sum_probs=14.2

Q ss_pred             EEEEEcCCCCcHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKE  191 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~  191 (426)
                      .+.|.|.+|+||||.+.+
T Consensus        26 ~~lV~g~aGSGKTt~l~~   43 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTH   43 (318)
T ss_dssp             CEEEEECTTSCHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHH
Confidence            367889999999976543

>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=88.34  E-value=0.25  Score=42.55  Aligned_cols=18  Identities=28%  Similarity=0.285  Sum_probs=14.2

Q ss_pred             cEEEEEcCCCCcHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVK  190 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~  190 (426)
                      ..+.|.|.+|+||||.+.
T Consensus        15 ~~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             SEEEECCCTTSCHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHH
Confidence            346789999999997643

>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=88.32  E-value=0.21  Score=40.14  Aligned_cols=38  Identities=16%  Similarity=0.100  Sum_probs=28.7

Q ss_pred             HHHHHHHhc-cCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          160 LKGILDALS-NRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       160 ~~~l~~~l~-~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      +..+..+|. .++...+.++|+++.|||++|..+.+-..
T Consensus        40 l~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          40 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            445555554 34557899999999999999998877653

>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=87.78  E-value=0.26  Score=44.61  Aligned_cols=40  Identities=20%  Similarity=0.153  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          157 KSTLKGILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       157 ~~~~~~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ...++.+.++ .......|.|.|+.|+||||....+.+...
T Consensus       144 ~~~~~~l~~l-~~~~~GliLvtGpTGSGKSTTl~~~l~~~~  183 (401)
T d1p9ra_         144 AHNHDNFRRL-IKRPHGIILVTGPTGSGKSTTLYAGLQELN  183 (401)
T ss_dssp             HHHHHHHHHH-HTSSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHH-HhhhhceEEEEcCCCCCccHHHHHHhhhhc
Confidence            3444444444 444568999999999999999999887653

>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=86.94  E-value=0.22  Score=42.56  Aligned_cols=34  Identities=21%  Similarity=0.428  Sum_probs=26.9

Q ss_pred             HHHHHhccCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          162 GILDALSNRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       162 ~l~~~l~~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++++.+ ++++.||+|+|+-+.|||+|+..++...
T Consensus        23 ~~l~~~-~~~v~vvsi~G~~~sGKS~llN~l~~~~   56 (277)
T d1f5na2          23 KILSAI-TQPMVVVAIVGLYRTGKSYLMNKLAGKK   56 (277)
T ss_dssp             HHHHTC-CSBEEEEEEEEBTTSSHHHHHHHHTTCS
T ss_pred             HHHHcC-CCCEEEEEEECCCCCCHHHHHHHHcCCC
Confidence            344443 4568899999999999999999998653

>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=86.83  E-value=0.085  Score=43.76  Aligned_cols=23  Identities=22%  Similarity=0.488  Sum_probs=18.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      +...+.|.+|+|||||...+..+
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-
T ss_pred             ceEEEECCCCccHHHHHHhhccH
Confidence            45668899999999999988654

>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=86.17  E-value=0.2  Score=39.68  Aligned_cols=21  Identities=38%  Similarity=0.545  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      .|+|+|..++|||||...+..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            589999999999999999874

>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=85.25  E-value=0.15  Score=44.69  Aligned_cols=25  Identities=24%  Similarity=0.211  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQAK  197 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~~  197 (426)
                      ..|+|-|.-|+||||+++.+.+...
T Consensus         5 lrI~IEG~iGsGKTTl~~~La~~l~   29 (329)
T d1e2ka_           5 LRVYIDGPHGMGKTTTTQLLVALGS   29 (329)
T ss_dssp             EEEEECSCTTSSHHHHHHHHTC---
T ss_pred             eEEEEECCcCCCHHHHHHHHHHHhC
Confidence            3588999999999999999976543

>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=85.20  E-value=0.19  Score=44.15  Aligned_cols=25  Identities=36%  Similarity=0.274  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQAKE  198 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~~~~  198 (426)
                      .|+|-|.-|+||||+++.+.+....
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~   31 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4889999999999999999887653

>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=84.35  E-value=0.37  Score=43.53  Aligned_cols=23  Identities=22%  Similarity=0.388  Sum_probs=20.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 044858          172 FNMIGVYGMGGIGKTTLVKEVGR  194 (426)
Q Consensus       172 ~~vi~I~G~~GiGKTtLa~~v~~  194 (426)
                      +--|+|+|.+|+|||||...+..
T Consensus        56 ~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          56 VLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            44589999999999999999874

>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=84.03  E-value=0.58  Score=34.72  Aligned_cols=51  Identities=12%  Similarity=0.044  Sum_probs=31.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCccceEEEEEecCCcCHHHHHHHHHHHh
Q 044858          171 NFNMIGVYGMGGIGKTTLVKEVGRQAKENNLFEKVISSRVSQTPQIKEIQREIAEKL  227 (426)
Q Consensus       171 ~~~vi~I~G~~GiGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~il~~i~~~l  227 (426)
                      +.++..|+++.|+|||+++-.++...      ...+.+.+....-..+..+.+.+.+
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~~------~~~vli~~P~~~l~~q~~~~~~~~~   57 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH   57 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHTT------TCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHc------CCcEEEEcChHHHHHHHHHHHHHHh
Confidence            35778899999999999887665432      2345555554433444444444443

>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=83.24  E-value=0.11  Score=41.71  Aligned_cols=24  Identities=21%  Similarity=0.210  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          173 NMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       173 ~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++..|+|+.|+||||+...+.--.
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            456689999999999999987554

>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=82.80  E-value=0.39  Score=42.28  Aligned_cols=27  Identities=26%  Similarity=0.293  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          170 RNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       170 ~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ++.+.|+|+|..|.|||||+..+....
T Consensus        15 ~~IRNI~iiGhvd~GKTTL~d~Ll~~~   41 (341)
T d1n0ua2          15 TNVRNMSVIAHVDHGKSTLTDSLVQRA   41 (341)
T ss_dssp             GGEEEEEEECCGGGTHHHHHHHHHHHH
T ss_pred             ccCcEEEEEeCCCCcHHHHHHHHHHHC
Confidence            457889999999999999999886543

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=82.62  E-value=0.73  Score=38.92  Aligned_cols=37  Identities=19%  Similarity=0.229  Sum_probs=27.8

Q ss_pred             HHHHHHHhc--cCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 044858          160 LKGILDALS--NRNFNMIGVYGMGGIGKTTLVKEVGRQA  196 (426)
Q Consensus       160 ~~~l~~~l~--~~~~~vi~I~G~~GiGKTtLa~~v~~~~  196 (426)
                      ...+..+|.  .++...+.++|+|+.|||+++..+.+-.
T Consensus        90 ~~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          90 ASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            344555554  2445688999999999999999988765

>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=82.04  E-value=0.43  Score=38.61  Aligned_cols=22  Identities=32%  Similarity=0.342  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 044858          174 MIGVYGMGGIGKTTLVKEVGRQ  195 (426)
Q Consensus       174 vi~I~G~~GiGKTtLa~~v~~~  195 (426)
                      .|+|.|-.+.|||||+.++...
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~~   26 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTYV   26 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHH
Confidence            4899999999999999998654