Citrus Sinensis ID: 040234

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------
Protein Sequence
MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSDKYGNMHSPQREYSIVVPGSEIPEWFEYQNNEGSSITISTPPKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHPIYVHQGDKLTKQLIPFGI
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHccccEEEEccccccHHcccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccEEEEEcccccHHHHHHHHccccccccccEEEEEcccccccccccccEEEEcccccHHHHHHHHcHHccccccccHHHHHHHHHHHccccccHHHHHHHHcccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHcccccccccccccccccccEEEEEcccccccccccccccccEEEEEccccccccccEEEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccEEEEEEEcccccEEEEEEEEEEEcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccEEccHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHccccccccccEEEEEEccHHHHHHccccEEEEEEcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHEEEEcccccccccccccccccccccEEEEEEcccccHHHHHccccccccEEEEccccccccccEEEEEEEEEEEccccccccccccccccccccccEEccccccccccEEEEEEEEEEEccEEEEEEcccccEEEEEEcccccEEEEEccEEEEEEccHHHHHHHcccccc
Coil and Loop (DISEMBL)
MGGLGKTTLARVVYDLIShefdgssflaDVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVViddaahpdhlrrlvgepdwfgpgsriIITTRNEhllklhpvkkvyKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVglqnmppsdkygnmhspqreysivvpgseipewfeyqnnegssitistppktyknsklvGYVVCCvfrvpkyslpyyhplwpqypvhelsinrkgttsgLCSIYLRKQFGQAMSDHLFLYYQnreriskvtfdspsglvlkrcgvhpiyvhqgdkltkqlipfgi
Flexible Loop (DISEMBL)
MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVViddaahpdhlrrlvgepdwfgpGSRIIITtrnehllklhpVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSDKYGNMHSPQREYSIVVPGSEIPEWFEYQNNEGSSITISTPPKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHpiyvhqgdkltkqlipfgi
Low Complexity Region (SEG)
MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVIslqkqllsdllkladnnIRNVYDGINMlrvrlrrkkvlvvIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSDKYGNMHSPQREYSIVVPGSEIPEWFEYQNNEGSSITISTPPKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHPIYVHQGDKLTKQLIPFGI
Disordered region (IsUnstruct)
******TTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQ*****************YSIVVPGSEIPEWFEYQNN****ITIST*PKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHPIYVHQGDKLTKQLI****
Disordered Region (DISOPRED)
MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSDKYGNMHSPQREYSIVVPGSEIPEWFEYQNNEGSSITISTPPKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHPIYVHQGDKLTKQLIPFGI
Disordered Region (DISEMBL)
MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSDKYGNMHSPQREYSIVVPGSEIPEWFEYQNNEGSSITISTPPKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHPIYVHQGDKLTKQLIPFGI
Disordered Region (DISPRO)
**GLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSDKYGNMHSPQREYSIVVPGSEIPEWFEYQNNEGSSITISTPPKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHPIYVHQGDKLTKQLIPFGI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSDKYGNMHSPQREYSIVVPGSEIPEWFEYQNNEGSSITISTPPKTYKNSKLVGYVVCCVFRVPKYSLPYYHPLWPQYPVHELSINRKGTTSGLCSIYLRKQFGQAMSDHLFLYYQNRERISKVTFDSPSGLVLKRCGVHPIYVHQGDKLTKQLIPFGI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	377	2.2.26 [Sep-21-2011]
Q40392	1144	TMV resistance protein N	N/A	no	0.413	0.136	0.437	4e-27
O23530	1301	Protein SUPPRESSOR OF npr	no	no	0.419	0.121	0.331	6e-20
O82500	1095	Putative disease resistan	no	no	0.405	0.139	0.339	7e-20
Q9FL92	1372	Probable WRKY transcripti	no	no	0.445	0.122	0.323	4e-19
Q9FH83	1288	Probable WRKY transcripti	no	no	0.336	0.098	0.372	8e-17
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.413	0.096	0.329	7e-14
Q9SZ67	1895	Probable WRKY transcripti	no	no	0.464	0.092	0.289	3e-13
Q9XIF0	906	Putative disease resistan	no	no	0.419	0.174	0.297	9e-08
Q9FG91	848	Probable disease resistan	no	no	0.450	0.200	0.262	5e-05
Q8W3K0	1138	Probable disease resistan	no	no	0.400	0.132	0.253	0.0002

>sp|Q40392|TMVRN_NICGU TMV resistance protein N OS=Nicotiana glutinosa GN=N PE=1 SV=1

 Score =  122 bits (307), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 74/169 (43%), Positives = 108/169 (63%), Gaps = 13/169 (7%)

Query: 1   MGGLGKTTLARVVYDLI------SHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKL 54
           MGG+GKTT+AR ++D +      S++FDG+ FL D++E  +K G + SLQ  LLS+LL+ 
Sbjct: 217 MGGVGKTTIARAIFDTLLGRMDSSYQFDGACFLKDIKE--NKRG-MHSLQNALLSELLR- 272

Query: 55  ADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDH-LRRLVGEPDWFGPGSRIIITTRN 113
              N  N  DG + +  RLR KKVL+V+DD  + DH L  L G+ DWFG GSRIIITTR+
Sbjct: 273 EKANYNNEEDGKHQMASRLRSKKVLIVLDDIDNKDHYLEYLAGDLDWFGNGSRIIITTRD 332

Query: 114 EHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVV 162
           +HL++ + +  +Y++ AL   E+ +L    AF    P E + +L+  VV
Sbjct: 333 KHLIEKNDI--IYEVTALPDHESIQLFKQHAFGKEVPNENFEKLSLEVV 379

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.
Nicotiana glutinosa (taxid: 35889)

>sp|O23530|SNC1_ARATH Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1 OS=Arabidopsis thaliana GN=SNC1 PE=1 SV=3

 Score = 98.6 bits (244), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 94/163 (57%), Gaps = 5/163 (3%)

Query: 3   GLGKTTLARVVYDLISHEFDGSSFLA-DVREKCDKEGSVISLQKQLLSDLLKLADNNIRN 61
           G+GK+T+ R +Y  +S +F   +F+        D  G  +  +K+LLS++L   D  I +
Sbjct: 215 GIGKSTIGRALYSKLSIQFHHRAFITYKSTSGSDVSGMKLRWEKELLSEILGQKDIKIEH 274

Query: 62  VYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHP 121
                 ++  RL+++KVL+++DD    + L+ LVG+ +WFG GSRII+ T++  LLK H 
Sbjct: 275 ----FGVVEQRLKQQKVLILLDDVDSLEFLKTLVGKAEWFGSGSRIIVITQDRQLLKAHE 330

Query: 122 VKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRI 164
           +  +Y++E  +   A  +LC  AF    P +++ ELA  V ++
Sbjct: 331 IDLIYEVEFPSEHLALTMLCRSAFGKDSPPDDFKELAFEVAKL 373

Disease resistance protein of the TIR-NB-LRR-type. Part of the RPP5 locus that contains a cluster of several paralogous disease resistance (R) genes. 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. Regulated by RNA silencing. Expression regulated by MOS1 at chromatin level. Negatively regulated at the transcript level by BON1.

Arabidopsis thaliana (taxid: 3702)

>sp|O82500|Y4117_ARATH Putative disease resistance protein At4g11170 OS=Arabidopsis thaliana GN=At4g11170 PE=2 SV=1

 Score = 98.6 bits (244), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 55/162 (33%), Positives = 89/162 (54%), Gaps = 9/162 (5%)

Query: 2   GGLGKTTLARVVYDLISHEFDGSSFLADVREK-----CDKEGSVISLQKQLLSDLLKLAD 56
            G+GKTT+AR +Y+     F+ S F+ +VRE       D  G  + LQ++ LS LL   D
Sbjct: 214 AGVGKTTIARALYNQYHENFNLSIFMENVRESYGEAGLDDYGLKLHLQQRFLSKLLDQKD 273

Query: 57  NNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHL 116
             +R+    +  +  RL+ +KVL+++DD  + + L+ L  E  WFG  SRI++TT+N+ L
Sbjct: 274 LRVRH----LGAIEERLKSQKVLIILDDVDNIEQLKALAKENQWFGNKSRIVVTTQNKQL 329

Query: 117 LKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELA 158
           L  H +  +Y++   +  EA  + C  AF    P ++   LA
Sbjct: 330 LVSHDINHMYQVAYPSKQEALTIFCQHAFKQSSPSDDLKHLA 371

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FL92|WRK16_ARATH Probable WRKY transcription factor 16 OS=Arabidopsis thaliana GN=WRKY16 PE=2 SV=1

 Score = 95.9 bits (237), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 56/173 (32%), Positives = 93/173 (53%), Gaps = 5/173 (2%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           M G+GKTTLA+ V+D +S EFD   F+ D  +   ++G    L++Q L +     +    
Sbjct: 171 MPGIGKTTLAKAVFDQMSGEFDAHCFIEDYTKAIQEKGVYCLLEEQFLKE-----NAGAS 225

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
                +++LR RL  K+VLVV+DD   P  +   +G  DWFGP S IIIT++++ + +L 
Sbjct: 226 GTVTKLSLLRDRLNNKRVLVVLDDVRSPLVVESFLGGFDWFGPKSLIIITSKDKSVFRLC 285

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLN 173
            V ++Y+++ L   EA +L  L A       +   E++  V++  +     LN
Sbjct: 286 RVNQIYEVQGLNEKEALQLFSLCASIDDMAEQNLHEVSMKVIKYANGHPLALN 338

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element. May also act as a disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FH83|WRK52_ARATH Probable WRKY transcription factor 52 OS=Arabidopsis thaliana GN=WRKY52 PE=2 SV=3

 Score = 88.6 bits (218), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 57/153 (37%), Positives = 85/153 (55%), Gaps = 26/153 (16%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLL----SDLLKLAD 56
           M G+GKTTLA+ V+D +S  FD S F+ D  +   ++G    L++QLL    + ++KL+ 
Sbjct: 180 MPGIGKTTLAKAVFDQMSSAFDASCFIEDYDKSIHEKGLYCLLEEQLLPGNDATIMKLSS 239

Query: 57  NNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEP-----DWFGPGSRIIITT 111
                       LR RL  K+VLVV+DD  +      LVGE      DW GPGS IIIT+
Sbjct: 240 ------------LRDRLNSKRVLVVLDDVRNA-----LVGESFLEGFDWLGPGSLIIITS 282

Query: 112 RNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKA 144
           R++ +  L  + ++Y+++ L   EA +L  L A
Sbjct: 283 RDKQVFCLCGINQIYEVQGLNEKEARQLFLLSA 315

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element. Acts also as a disease resistance protein conferring resistance to Ralstonia solanacearum.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKN7|DAR4_ARATH Protein DA1-related 4 OS=Arabidopsis thaliana GN=DAR4 PE=1 SV=2

 Score = 78.6 bits (192), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 55/167 (32%), Positives = 92/167 (55%), Gaps = 11/167 (6%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           M G+GKTTLA+ V++ +S ++D S F+ +  E   KEG +  L K+ +  +LK  + +I 
Sbjct: 197 MPGIGKTTLAKAVFNHMSTDYDASCFIENFDEAFHKEG-LHRLLKERIGKILK-DEFDIE 254

Query: 61  NVYDGINML-RVRLRRKKVLVVIDDA----AHPDHLRRLVGEPDWFGPGSRIIITTRNEH 115
           + Y     L R +L  K++LVV+DD     A    L+RL    DWFG GS IIIT+ ++ 
Sbjct: 255 SSYIMRPTLHRDKLYDKRILVVLDDVRDSLAAESFLKRL----DWFGSGSLIIITSVDKQ 310

Query: 116 LLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVV 162
           +     + ++Y ++ L   EA +L     F  ++P +   +L+  V+
Sbjct: 311 VFAFCQINQIYTVQGLNVHEALQLFSQSVFGINEPEQNDRKLSMKVI 357

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZ67|WRK19_ARATH Probable WRKY transcription factor 19 OS=Arabidopsis thaliana GN=WRKY19 PE=2 SV=1

 Score = 76.6 bits (187), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 96/176 (54%), Gaps = 1/176 (0%)

Query: 3    GLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNV 62
            G+GKTT+A  ++  IS +++    L D+ ++ + +G   ++++  LS++L++  + IR  
Sbjct: 847  GIGKTTIAEEIFRKISVQYETCVVLKDLHKEVEVKGH-DAVRENFLSEVLEVEPHVIRIS 905

Query: 63   YDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPV 122
                + LR RL+RK++LV++DD      +   +G  ++FGPGSRII+T+RN  +  L  +
Sbjct: 906  DIKTSFLRSRLQRKRILVILDDVNDYRDVDTFLGTLNYFGPGSRIIMTSRNRRVFVLCKI 965

Query: 123  KKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSV 178
              VY+++ L   ++  LL           E Y  L+  +V+  +     L  L S+
Sbjct: 966  DHVYEVKPLDIPKSLLLLDRGTCQIVLSPEVYKTLSLELVKFSNGNPQVLQFLSSI 1021

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element. May act also as a disease resistance protein with a serine/threonine-protein kinase activity.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XIF0|DRL13_ARATH Putative disease resistance protein At1g59780 OS=Arabidopsis thaliana GN=At1g59780 PE=2 SV=1

 Score = 58.5 bits (140), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 91/178 (51%), Gaps = 20/178 (11%)

Query: 1   MGGLGKTTLARVVYD--LISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLL-KLADN 57
           +GGLGKTTLAR ++D   +   FDG +++   +E   K+     + K +L +L  K  D+
Sbjct: 188 LGGLGKTTLARQIFDHDKVKSHFDGLAWVCVSQEFTRKD-----VWKTILGNLSPKYKDS 242

Query: 58  NIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLL 117
           ++    D    L   L  KK L+V DD    +   R+         G ++++T+RN+   
Sbjct: 243 DLPE-DDIQKKLFQLLETKKALIVFDDLWKREDWYRIAPMFPERKAGWKVLLTSRND--- 298

Query: 118 KLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPL------EEYVELAESVVRICHCQK 169
            +HP    +K E LT+DE ++LL   AF   K +      +E V++A+ + +  HC++
Sbjct: 299 AIHPHCVTFKPELLTHDECWKLLQRIAFSKQKTITGYIIDKEMVKMAKEMTK--HCKR 354

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FG91|DRL32_ARATH Probable disease resistance protein At5g43730 OS=Arabidopsis thaliana GN=At5g43730 PE=2 SV=1

 Score = 49.3 bits (116), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 81/179 (45%), Gaps = 9/179 (5%)

Query: 1   MGGLGKTTLARVVYDL---ISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN 57
           MGG+GKTTL   + +    +  EFD   ++        K+  +  +Q Q+L  L    + 
Sbjct: 180 MGGIGKTTLLESLNNKFVELESEFDVVIWVV-----VSKDFQLEGIQDQILGRLRPDKEW 234

Query: 58  NIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLL 117
                    +++   L+RKK ++++DD      L ++   P     GS+I+ TTR++ + 
Sbjct: 235 ERETESKKASLINNNLKRKKFVLLLDDLWSEVDLIKIGVPPPSRENGSKIVFTTRSKEVC 294

Query: 118 KLHPVKKVYKLEALTYDEAFRLLCLKAFD-THKPLEEYVELAESVVRICHCQKSTLNAL 175
           K     K  K++ L+ DEA+ L  L   D   +  ++   LA  V   CH     LN +
Sbjct: 295 KHMKADKQIKVDCLSPDEAWELFRLTVGDIILRSHQDIPALARIVAAKCHGLPLALNVI 353

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W3K0|DRL9_ARATH Probable disease resistance protein At1g58602 OS=Arabidopsis thaliana GN=At1g58602 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 48/189 (25%), Positives = 89/189 (47%), Gaps = 38/189 (20%)

Query: 1   MGGLGKTTLARVVY--DLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNN 58
           MGGLGKTTLAR V+  D+++ +FD  ++++       ++ ++ ++ + +L DL    +  
Sbjct: 190 MGGLGKTTLARQVFNHDMVTKKFDKLAWVS-----VSQDFTLKNVWQNILGDLKPKEEET 244

Query: 59  IRNVYDGINMLRVRLRRK--------KVLVVIDDAAHPDHLRRLVGEPDW------FGP- 103
                  + M    L+R+        K L+V+DD         +  + DW      F P 
Sbjct: 245 KEEEKKILEMTEYTLQRELYQLLEMSKSLIVLDD---------IWKKEDWEVIKPIFPPT 295

Query: 104 -GSRIIITTRNEHLLKLHPVKKV-YKLEALTYDEAFRLLCLKAFDTHKPL-----EEYVE 156
            G ++++T+RNE ++     K   +K E L  D++++L    AF  +        EE  +
Sbjct: 296 KGWKLLLTSRNESIVAPTNTKYFNFKPECLKTDDSWKLFQRIAFPINDASEFEIDEEMEK 355

Query: 157 LAESVVRIC 165
           L E ++  C
Sbjct: 356 LGEKMIEHC 364

Potential 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	377
22947641	171	putative citrus disease resistance prote	0.429	0.947	0.598	4e-47
22947648	172	putative citrus disease resistance prote	0.432	0.947	0.588	2e-46
62361219	175	resistance protein PLTR [Arachis hypogae	0.432	0.931	0.490	1e-37
255547494	1082	TMV resistance protein N, putative [Rici	0.480	0.167	0.469	3e-37
222066084	174	NBS-LLR resistance protein [Gossypium ar	0.429	0.931	0.554	8e-37
222066088	174	NBS-LLR resistance protein [Gossypium ar	0.429	0.931	0.554	9e-37
399920191	1320	TIR-NBS-LRR [Rosa rugosa]	0.432	0.123	0.512	1e-36
222066074	171	NBS-LLR resistance protein [Gossypium ar	0.429	0.947	0.554	1e-36
332002068	173	NBS-LRR-like protein [Malus baccata]	0.456	0.994	0.480	2e-36
22324566	176	PR-protein [Capsicum annuum]	0.429	0.920	0.460	4e-36

>gi|22947641|gb|AAN08166.1| putative citrus disease resistance protein Pt6 [Citrus maxima x Citrus trifoliata]

 Score =  195 bits (495), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 97/162 (59%), Positives = 123/162 (75%)

Query: 2   GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRN 61
           GG+GKTTLARVVYDLISHEF+GSSFLADVREK + +GSVIS Q+QLL ++LK   ++I N
Sbjct: 1   GGVGKTTLARVVYDLISHEFEGSSFLADVREKFENKGSVISFQRQLLFEILKFEKDSIWN 60

Query: 62  VYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHP 121
           V DGIN+L  RL+ KKVL+VIDD      L  L G+ +WFG GSRII+T+R+EHLLK H 
Sbjct: 61  VGDGINILGSRLQHKKVLLVIDDVVDIKQLEYLAGKREWFGSGSRIIVTSRDEHLLKTHG 120

Query: 122 VKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVR 163
           + ++YK   L Y +A +L  +KAF   KPLEE V+L+E V+R
Sbjct: 121 MDEIYKPNELNYHDALQLFNMKAFKIQKPLEECVQLSEGVLR 162

Source: Citrus maxima x Citrus trifoliata

Species: Citrus maxima x Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22947648|gb|AAN08167.1| putative citrus disease resistance protein Pt12 [Citrus maxima x Citrus trifoliata]

 Score =  192 bits (489), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/163 (58%), Positives = 123/163 (75%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           +GG+GKTTLARVVYDLISHEF+GSSFLADVREK + +GSVIS Q+QLL ++LK   ++I 
Sbjct: 1   IGGVGKTTLARVVYDLISHEFEGSSFLADVREKFENKGSVISFQRQLLFEILKFEKDSIW 60

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           NV DGIN+L  RL+ K VL+VIDD      L  L G+ +WFG GSRII+T+R+EHLLK H
Sbjct: 61  NVGDGINILGSRLQHKMVLLVIDDVVDIKQLAYLAGKREWFGSGSRIIVTSRDEHLLKTH 120

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVR 163
            + ++YK   L Y +A +L  +KAF   KPLEE V+L+E V+R
Sbjct: 121 GMDEIYKPNELNYHDALQLFNMKAFKIQKPLEECVQLSEGVLR 163

Source: Citrus maxima x Citrus trifoliata

Species: Citrus maxima x Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62361219|gb|AAX81288.1| resistance protein PLTR [Arachis hypogaea]

 Score =  164 bits (414), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 81/165 (49%), Positives = 109/165 (66%), Gaps = 2/165 (1%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGG+GKTT+AR+VY+ I  EF+ S F A VRE C+K G ++  QK+L+  +   + +N  
Sbjct: 2   MGGVGKTTIARIVYEAIQSEFEVSYFHASVRETCEKNG-IVQAQKELVGHI-NGSSSNFN 59

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           N YDG  +++  L RKKVL+V+DD      L+ L  E DWFG GSRIIITTR+ HLLK+H
Sbjct: 60  NEYDGRRIIQASLYRKKVLLVLDDINEEKQLKNLAEEQDWFGSGSRIIITTRDMHLLKIH 119

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRIC 165
              K+Y +E L   EAF L  LKAF   KP EEY++L++  V+ C
Sbjct: 120 DANKIYSVEGLGESEAFDLFGLKAFKQRKPAEEYLDLSKQAVQYC 164

Source: Arachis hypogaea

Species: Arachis hypogaea

Genus: Arachis

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547494|ref|XP_002514804.1| TMV resistance protein N, putative [Ricinus communis] gi|223545855|gb|EEF47358.1| TMV resistance protein N, putative [Ricinus communis]

 Score =  162 bits (409), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 86/183 (46%), Positives = 119/183 (65%), Gaps = 2/183 (1%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGG+GKTT+AR VY  +S EF+GS FLA+VRE   +E + +SLQ+QLLS+ L      + 
Sbjct: 219 MGGIGKTTIARAVYAELSSEFEGSCFLANVREV--EEKNSLSLQEQLLSETLMERKITVW 276

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           +++ G N ++ RL  KKVL+++DD  H + L+ L G  DWFG GSRIIITTR+EHLL  H
Sbjct: 277 DIHAGRNEIKNRLSHKKVLIILDDVNHLEQLKSLAGMSDWFGNGSRIIITTRDEHLLLCH 336

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSY 180
            V+++Y++  L +DEA RL  LKAF    P ++YVEL+   V   +     L+ L S  Y
Sbjct: 337 GVERIYRVGGLNHDEALRLFSLKAFKNDYPADDYVELSNHFVNYANGLPLALDVLGSCLY 396

Query: 181 TVS 183
             S
Sbjct: 397 GRS 399

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222066084|emb|CAX28550.1| NBS-LLR resistance protein [Gossypium arboreum]

 Score =  160 bits (405), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 91/164 (55%), Positives = 115/164 (70%), Gaps = 2/164 (1%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGG+GKTTLARVVY  IS  F+G SFLADVRE  +K G ++SLQKQLLS +L     N  
Sbjct: 2   MGGVGKTTLARVVYTQISPHFEGKSFLADVREVSNKWG-LVSLQKQLLSLILLDECFNFF 60

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           NVY+G  ++  +L RKKVL+V+DD  +  HL+ LVG  DWFG GSRII+TTR+EHLL+ +
Sbjct: 61  NVYEGNAVISHKLSRKKVLIVLDDVDNIQHLKCLVGRRDWFGLGSRIIVTTRDEHLLRSY 120

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHK-PLEEYVELAESVVR 163
            V  VYK   L   +A RL  LKAFD    P E+++EL++ VVR
Sbjct: 121 RVDDVYKPTTLNLKDALRLFNLKAFDDDTIPTEDFIELSKHVVR 164

Source: Gossypium arboreum

Species: Gossypium arboreum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222066088|emb|CAX28552.1| NBS-LLR resistance protein [Gossypium arboreum] gi|222066094|emb|CAX28555.1| NBS-LLR resistance protein [Gossypium arboreum]

 Score =  160 bits (405), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 91/164 (55%), Positives = 115/164 (70%), Gaps = 2/164 (1%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGG+GKTTLARVVY  IS  F+G SFLADVRE  +K G ++SLQKQLLS +L     N  
Sbjct: 2   MGGVGKTTLARVVYTQISPHFEGKSFLADVREVSNKWG-LVSLQKQLLSLILLDECFNFF 60

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           NVY+G  ++  +L RKKVL+V+DD  +  HL+ LVG  DWFG GSRII+TTR+EHLL+ +
Sbjct: 61  NVYEGNAVISHKLSRKKVLIVLDDVDNIQHLKCLVGRRDWFGLGSRIIVTTRDEHLLRSY 120

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHK-PLEEYVELAESVVR 163
            V  VYK   L   +A RL  LKAFD    P E+++EL++ VVR
Sbjct: 121 RVDDVYKPTTLNLKDALRLFNLKAFDDDTIPTEDFIELSKHVVR 164

Source: Gossypium arboreum

Species: Gossypium arboreum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|399920191|gb|AFP55538.1| TIR-NBS-LRR [Rosa rugosa]

 Score =  160 bits (404), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 84/164 (51%), Positives = 111/164 (67%), Gaps = 1/164 (0%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGGLGKTTLAR+VY+ ISH+F+   FLA+VRE     G ++ LQKQ+LS +LK  +  + 
Sbjct: 225 MGGLGKTTLARLVYEKISHQFEVCVFLANVREVSATHG-LVYLQKQILSHILKEENAQVW 283

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           NVY GI M++     K VL+V+DD    + L  L GE DWFG  SRIIITTR+ H+L  H
Sbjct: 284 NVYSGITMIKRCFCNKAVLLVLDDVDQSEQLEHLAGEKDWFGLRSRIIITTRDRHVLVTH 343

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRI 164
            ++K Y+L+ L  DEA +L   KAF  H+P E+Y E ++SVVRI
Sbjct: 344 DIEKPYELKGLEEDEALQLFSWKAFRKHEPEEDYAEQSKSVVRI 387

Source: Rosa rugosa

Species: Rosa rugosa

Genus: Rosa

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222066074|emb|CAX28545.1| NBS-LLR resistance protein [Gossypium arboreum]

 Score =  160 bits (404), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 91/164 (55%), Positives = 115/164 (70%), Gaps = 2/164 (1%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGG+GKTTLARVVY  IS  F+G SFLADVRE  +K G ++SLQKQLLS +L     N  
Sbjct: 2   MGGVGKTTLARVVYTQISPHFEGKSFLADVREVSNKWG-LVSLQKQLLSLILLDECFNFF 60

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           NVY+G  ++  +L RKKVL+V+DD  +  HL+ LVG  DWFG GSRII+TTR+EHLL+ +
Sbjct: 61  NVYEGNAVISHKLSRKKVLIVLDDVDNIQHLKCLVGRRDWFGLGSRIIVTTRDEHLLRSY 120

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHK-PLEEYVELAESVVR 163
            V  VYK   L   +A RL  LKAFD    P E+++EL++ VVR
Sbjct: 121 RVDDVYKPTTLNLKDALRLFNLKAFDDDTIPTEDFIELSKHVVR 164

Source: Gossypium arboreum

Species: Gossypium arboreum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|332002068|gb|AED99177.1| NBS-LRR-like protein [Malus baccata]

 Score =  159 bits (403), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 87/181 (48%), Positives = 118/181 (65%), Gaps = 9/181 (4%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGG+GKTTLAR+VYD+ISH+F+GSSFLA+VRE C K+G +  LQKQLLSD+L   D  + 
Sbjct: 2   MGGVGKTTLARLVYDIISHDFEGSSFLANVREVCSKDG-IAHLQKQLLSDILGDNDIQVW 60

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           N Y GI  +  R   KKVL+++DD    D L +LV + +WFG GSRI+ITTRNE LL  H
Sbjct: 61  NAYSGITRIS-RCLFKKVLLILDDVDQSDQLEKLVKQKEWFGFGSRIVITTRNERLLVEH 119

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSY 180
            ++K Y+++ L  DEA  L   KAF          EL E  +++  C  S  ++L + ++
Sbjct: 120 GIEKAYEVKPLNQDEALFLFSRKAFKDD-------ELEEDFLKLSKCFISYASSLTNTTH 172

Query: 181 T 181
           T
Sbjct: 173 T 173

Source: Malus baccata

Species: Malus baccata

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22324566|gb|AAM95614.1|AF525138_1 PR-protein [Capsicum annuum]

 Score =  158 bits (400), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/163 (46%), Positives = 114/163 (69%), Gaps = 1/163 (0%)

Query: 1   MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR 60
           MGG+GKTTLARV+Y+ I  EF G+ FL +VR++  K G  + LQ+ LLS++L   D  I 
Sbjct: 2   MGGVGKTTLARVIYENIRSEFKGACFLHEVRDRLSKHGLEL-LQEMLLSEILVEKDRRIN 60

Query: 61  NVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
           N ++G N+ ++RLR KK+L+V+DD  H D L  L GE +WFGPG R+IITT+N+HL+  +
Sbjct: 61  NSFEGANVQKLRLRYKKILLVLDDVGHTDQLDALAGESEWFGPGCRVIITTKNKHLIIKY 120

Query: 121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVR 163
            V+K+Y++ +L  DE+ +L    AF  ++P EE+ +L+  V++
Sbjct: 121 EVEKIYRMSSLNEDESLQLFKQHAFRKNQPTEEFADLSAQVIK 163

Source: Capsicum annuum

Species: Capsicum annuum

Genus: Capsicum

Family: Solanaceae

Order: Solanales

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	377
UNIPROTKB|Q40392	1144	N "TMV resistance protein N" [	0.413	0.136	0.337	9.1e-19
TAIR|locus:2175991	1294	AT5G17680 [Arabidopsis thalian	0.275	0.080	0.390	2.2e-16
TAIR|locus:2205824	1384	AT1G27170 [Arabidopsis thalian	0.432	0.117	0.286	2e-15
TAIR|locus:2160487	1085	AT5G41550 [Arabidopsis thalian	0.222	0.077	0.369	8.8e-14
TAIR|locus:2156579	1190	AT5G48770 [Arabidopsis thalian	0.416	0.131	0.289	1.2e-13
TAIR|locus:2195468	1017	AT1G63880 [Arabidopsis thalian	0.222	0.082	0.380	1.4e-13
TAIR|locus:2164486	1104	AT5G40910 [Arabidopsis thalian	0.222	0.076	0.357	2.1e-13
TAIR|locus:2094498	1981	AT3G25510 [Arabidopsis thalian	0.220	0.041	0.421	2.3e-13
TAIR|locus:2175075	1068	AT5G41750 [Arabidopsis thalian	0.222	0.078	0.369	4.8e-13
TAIR|locus:2146228	1245	AT5G18350 [Arabidopsis thalian	0.220	0.066	0.373	5.3e-13

UNIPROTKB|Q40392 N "TMV resistance protein N" [Nicotiana glutinosa (taxid:35889)]

 Score = 223 (83.6 bits), Expect = 9.1e-19, Sum P(2) = 9.1e-19
 Identities = 57/169 (33%), Positives = 87/169 (51%)

Query:     1 MGGLGKTTLARVVYDLI------SHEFDGSSFLADVREKCDKEGSVIXXXXXXXXXXXXX 54
             MGG+GKTT+AR ++D +      S++FDG+ FL D++E  +K G  +             
Sbjct:   217 MGGVGKTTIARAIFDTLLGRMDSSYQFDGACFLKDIKE--NKRG--MHSLQNALLSELLR 272

Query:    55 XXXXIRNVYDGINMXXXXXXXXXXXXXIDDAAHPDH-LRRLVGEPDWFGPGSRIIITTRN 113
                   N  DG +              +DD  + DH L  L G+ DWFG GSRIIITTR+
Sbjct:   273 EKANYNNEEDGKHQMASRLRSKKVLIVLDDIDNKDHYLEYLAGDLDWFGNGSRIIITTRD 332

Query:   114 EHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVV 162
             +HL++ + +  +Y++ AL   E+ +L    AF    P E + +L+  VV
Sbjct:   333 KHLIEKNDI--IYEVTALPDHESIQLFKQHAFGKEVPNENFEKLSLEVV 379

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2175991 AT5G17680 [Arabidopsis thaliana (taxid:3702)]

 Score = 166 (63.5 bits), Expect = 2.2e-16, Sum P(3) = 2.2e-16
 Identities = 41/105 (39%), Positives = 52/105 (49%)

Query:    82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLC 141
             +DD    + L  LV E  WFGPGSRII+TTR+ HLL  H +  VYK++ L   EA +L C
Sbjct:   294 LDDVDRSEQLNELVKETGWFGPGSRIIVTTRDRHLLLSHGINLVYKVKCLPKKEALQLFC 353

Query:   142 LKAFDTHKPLEE-YVELAESVVRICHCQKSTLNALMSVSYTVSHL 185
               AF     L   + EL+   V         L  L S  Y  S +
Sbjct:   354 NYAFREEIILPHGFEELSVQAVNYASGLPLALRVLGSFLYRRSQI 398

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2205824 AT1G27170 [Arabidopsis thaliana (taxid:3702)]

 Score = 214 (80.4 bits), Expect = 2.0e-15, Sum P(2) = 2.0e-15
 Identities = 47/164 (28%), Positives = 81/164 (49%)

Query:     1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVIXXXXXXXXXXXXXXXXXIR 60
             MGG+GKTTLA+  Y+ I   F+  +F++D+RE+   E  ++                 I 
Sbjct:   219 MGGIGKTTLAKAFYNKIVGNFEQRAFISDIRERSSAENGLVTLQKTLIKELFRLVPE-IE 277

Query:    61 NVYDGINMXXXXXXXXXXXXXIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
             +V  G+               +DD  H D +  LVGE  W+G G+ I+ITTR+  +L   
Sbjct:   278 DVSIGLEKIKANVHEKKIIVVLDDVDHIDQVHALVGETRWYGQGTLIVITTRDSEILSKL 337

Query:   121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRI 164
              V + Y+++ LT  +A +L    +    +P +  + L++ +V+I
Sbjct:   338 SVNQQYEVKCLTEPQALKLFSYHSLRKEEPTKNLLALSKKIVQI 381

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0009507 "chloroplast" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2160487 AT5G41550 [Arabidopsis thaliana (taxid:3702)]

 Score = 158 (60.7 bits), Expect = 8.8e-14, Sum P(3) = 8.8e-14
 Identities = 31/84 (36%), Positives = 48/84 (57%)

Query:    82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLC 141
             +DD    + L  L  E  WFG GSRII+ T ++ +LK H +  +Y ++  + +EA  +LC
Sbjct:   298 LDDVDDLEQLEVLAKELSWFGSGSRIIVATEDKKILKEHGINDIYHVDFPSMEEALEILC 357

Query:   142 LKAFDTHKPLEEYVELAESVVRIC 165
             L AF      + + ELA+ VV +C
Sbjct:   358 LSAFKQSSVPDGFEELAKKVVHLC 381

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2156579 AT5G48770 [Arabidopsis thaliana (taxid:3702)]

 Score = 185 (70.2 bits), Expect = 1.2e-13, Sum P(2) = 1.2e-13
 Identities = 46/159 (28%), Positives = 76/159 (47%)

Query:     1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVIXXXXXXXXXXXXXXXXXIR 60
             MGG+GKTT+A+ +Y+ ++ +F   SF+ DV + C K+  +                  + 
Sbjct:   216 MGGIGKTTIAKYLYEQLASQFPAHSFIEDVGQIC-KKVDLKCIQQQLLCDILSTKRVALM 274

Query:    61 NVYDGINMXXXXXXXXXXXXXIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH 120
             ++ +G N+             +D     + L  L  E  WFGPGSRIIITTR+  LL   
Sbjct:   275 SIQNGANLIRSRLGTLKVLFVLDGVDKVEQLHALAKEASWFGPGSRIIITTRDRRLLDSC 334

Query:   121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKP-LEEYVELA 158
              V   Y+++ L  +++ +++   AF    P L+ Y   A
Sbjct:   335 RVTNKYEVKCLQNEDSLKIVKNIAFAGGVPTLDGYERFA 373

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2195468 AT1G63880 [Arabidopsis thaliana (taxid:3702)]

 Score = 170 (64.9 bits), Expect = 1.4e-13, Sum P(4) = 1.4e-13
 Identities = 32/84 (38%), Positives = 48/84 (57%)

Query:    82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLC 141
             +DD      L  L  E  WFGPGSRI++TT N+ LL+ H +   Y +   + ++A ++LC
Sbjct:   297 LDDVNKLKQLEALANETTWFGPGSRIVVTTENKELLQQHGINNTYHVGFPSDEDALKILC 356

Query:   142 LKAFDTHKPLEEYVELAESVVRIC 165
               AF    P   + EL+ESV ++C
Sbjct:   357 SYAFKQTSPRHGFEELSESVTKLC 380

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

GO:0050832 "defense response to fungus" evidence=IMP

TAIR|locus:2164486 AT5G40910 [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 2.1e-13, Sum P(3) = 2.1e-13
 Identities = 30/84 (35%), Positives = 49/84 (58%)

Query:    82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLC 141
             +DD    + L  L  E  WFG GSRII++  +  +LK H +  +Y ++  + +EA  +LC
Sbjct:   289 LDDVDDLEQLEVLAKESSWFGHGSRIIVSLNDRKILKAHGINDIYDVDFPSEEEALEILC 348

Query:   142 LKAFDTHKPLEEYVELAESVVRIC 165
             L AF  + P + + E+A+ VV +C
Sbjct:   349 LSAFKQNSPQDGFEEVAKRVVELC 372

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2094498 AT3G25510 [Arabidopsis thaliana (taxid:3702)]

 Score = 175 (66.7 bits), Expect = 2.3e-13, Sum P(3) = 2.3e-13
 Identities = 35/83 (42%), Positives = 46/83 (55%)

Query:    82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLC 141
             +DD      L  L  E  WFGPGSRIIITT N  LL  H +  +YK+E  + DEAF++ C
Sbjct:   313 LDDVDQLGQLDALAKETRWFGPGSRIIITTENLRLLMAHRINHIYKVEFSSTDEAFQIFC 372

Query:   142 LKAFDTHKPLEEYVELAESVVRI 164
             + AF    P   + EL+  V  +
Sbjct:   373 MHAFGQKHPYNGFYELSREVTEL 395

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2175075 AT5G41750 [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 4.8e-13, Sum P(3) = 4.8e-13
 Identities = 31/84 (36%), Positives = 50/84 (59%)

Query:    82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLC 141
             +DD    + L  L  +P WFG GSRII+TT ++++LK H ++ +Y ++  + +EA  +LC
Sbjct:   295 LDDVDDLEQLEVLAEDPSWFGSGSRIIVTTEDKNILKAHRIQDIYHVDFPSEEEALEILC 354

Query:   142 LKAFDTHKPLEEYVELAESVVRIC 165
             L AF      + + ELA  V  +C
Sbjct:   355 LSAFKQSSIPDGFEELANKVAELC 378

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2146228 AT5G18350 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 5.3e-13, Sum P(3) = 5.3e-13
 Identities = 31/83 (37%), Positives = 49/83 (59%)

Query:    82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLC 141
             +DD  H + L  +  E  WFG GSRIIITT++  LLK H +  +Y++     D+A ++ C
Sbjct:   316 LDDVDHLEQLDAMAKETGWFGYGSRIIITTQDRKLLKAHNIDYIYEVGLPRKDDALQIFC 375

Query:   142 LKAFDTHKPLEEYVELAESVVRI 164
             L AF  + P +++  LA  V ++
Sbjct:   376 LSAFGQNFPHDDFQYLACEVTQL 398

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.I.3722.1 tir-nbs-lrr resistance protein (524 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	377
PLN03210	1153	PLN03210, PLN03210, Resistant to P	1e-23
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-19

>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P

 Score =  102 bits (255), Expect = 1e-23
 Identities = 53/169 (31%), Positives = 86/169 (50%), Gaps = 14/169 (8%)

Query: 3   GLGKTTLARVVYDLISHEFDGSSFLADV----------REKCDKEGSVISLQKQLLSDLL 52
           G+GKTT+AR ++  +S +F  S F+                 D     + LQ+  LS++L
Sbjct: 217 GIGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEIL 276

Query: 53  KLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTR 112
              D  I      +  +  RL+ +KVL+ IDD    D L  L G+  WFG GSRII+ T+
Sbjct: 277 DKKDIKI----YHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITK 332

Query: 113 NEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESV 161
           ++H L+ H +  +Y++   + + A  + C  AF  + P + ++ELA  V
Sbjct: 333 DKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEV 381

syringae 6; Provisional. Length = 1153

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

 Score = 87.0 bits (216), Expect = 2e-19
 Identities = 47/174 (27%), Positives = 83/174 (47%), Gaps = 18/174 (10%)

Query: 1   MGGLGKTTLARVVY--DLISHEFDGSSFLADVREKCDKEGSVIS-LQKQLLSDLLK---- 53
           MGG+GKTTLA+ +Y  D +   FD  +++         +      LQK +L +L      
Sbjct: 27  MGGVGKTTLAKQIYNDDSVGGHFDSVAWV------VVSKTYTEFRLQKDILQELGLDDSD 80

Query: 54  LADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRN 113
             + N     +    ++  L RK+ L+V+DD    +   ++         GSR+I+TTR+
Sbjct: 81  WVEKNES---ELAVKIKEALLRKRFLLVLDDVWEKNDWDKIGVPFPDGENGSRVIVTTRS 137

Query: 114 EHLLK-LHPVKKVYKLEALTYDEAFRLLCLKAFD-THKPLEEYVELAESVVRIC 165
           E +   +    K +++E+L  +E++ L   K F+    P  E  E+A+ +V  C
Sbjct: 138 ESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPELEEVAKEIVEKC 191

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	377
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.97
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.95
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.08
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.96
COG3903	414	Predicted ATPase [General function prediction only	98.93
PF05729	166	NACHT: NACHT domain	98.92
PRK04841	903	transcriptional regulator MalT; Provisional	98.83
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.67
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.59
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.58
PRK06893	229	DNA replication initiation factor; Validated	98.58
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.49
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.4
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.32
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.3
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.24
PRK13342	413	recombination factor protein RarA; Reviewed	98.24
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.23
PF13173	128	AAA_14: AAA domain	98.19
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.17
PRK08727	233	hypothetical protein; Validated	98.17
PRK09087	226	hypothetical protein; Validated	98.17
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.1
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.08
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.01
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.0
PRK05642	234	DNA replication initiation factor; Validated	97.99
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.95
PLN03025	319	replication factor C subunit; Provisional	97.95
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.94
PRK12402	337	replication factor C small subunit 2; Reviewed	97.93
PRK08084	235	DNA replication initiation factor; Provisional	97.93
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.92
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.91
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.91
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.9
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.88
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.86
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.86
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.86
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.85
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.84
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.84
PRK12422	445	chromosomal replication initiation protein; Provis	97.79
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.78
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.77
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.77
PRK13341	725	recombination factor protein RarA/unknown domain f	97.75
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.73
PRK04195	482	replication factor C large subunit; Provisional	97.71
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.71
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.7
PTZ00112	1164	origin recognition complex 1 protein; Provisional	97.69
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.69
KOG2028	554	consensus ATPase related to the helicase subunit o	97.67
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.67
cd01128	249	rho_factor Transcription termination factor rho is	97.64
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.62
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.62
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.61
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.6
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.59
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.58
PRK09376	416	rho transcription termination factor Rho; Provisio	97.57
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.53
PRK06620	214	hypothetical protein; Validated	97.53
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.52
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.5
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.45
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.45
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.42
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.42
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.41
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.39
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.35
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.33
PRK08116	268	hypothetical protein; Validated	97.33
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.33
PRK04132	846	replication factor C small subunit; Provisional	97.3
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.3
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.28
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.26
PF14516	331	AAA_35: AAA-like domain	97.25
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.23
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.18
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.15
CHL00181	287	cbbX CbbX; Provisional	97.14
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.09
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.09
PF00004	132	AAA: ATPase family associated with various cellula	97.09
TIGR00767	415	rho transcription termination factor Rho. Members	97.07
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.04
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.03
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.03
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.03
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.99
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	96.97
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.96
smart00382	148	AAA ATPases associated with a variety of cellular	96.9
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.9
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.87
COG3899	849	Predicted ATPase [General function prediction only	96.85
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.84
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.82
CHL00176	638	ftsH cell division protein; Validated	96.81
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.8
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.8
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.79
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.77
PHA02544	316	44 clamp loader, small subunit; Provisional	96.73
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.72
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.68
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.66
PRK08181	269	transposase; Validated	96.62
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.54
PRK06921	266	hypothetical protein; Provisional	96.47
PRK12377	248	putative replication protein; Provisional	96.45
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.43
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.37
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	96.36
PRK06526	254	transposase; Provisional	96.34
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.34
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.31
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.24
PRK09183	259	transposase/IS protein; Provisional	96.22
PRK12608	380	transcription termination factor Rho; Provisional	96.2
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.13
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.11
PRK07952	244	DNA replication protein DnaC; Validated	96.1
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.07
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.06
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.06
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.96
PRK10536	262	hypothetical protein; Provisional	95.93
CHL00195	489	ycf46 Ycf46; Provisional	95.93
PRK06835	329	DNA replication protein DnaC; Validated	95.86
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.81
PHA00729	226	NTP-binding motif containing protein	95.8
PRK08939	306	primosomal protein DnaI; Reviewed	95.77
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.76
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	95.67
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.67
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.66
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.63
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	95.59
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.59
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	95.54
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	95.5
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.49
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.43
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	95.42
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.32
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.27
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.23
TIGR02237	209	recomb_radB DNA repair and recombination protein R	95.22
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	95.17
PRK10865	857	protein disaggregation chaperone; Provisional	95.15
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	95.14
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	95.12
PRK04296	190	thymidine kinase; Provisional	95.06
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	95.05
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.05
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.04
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	95.04
PRK08118	167	topology modulation protein; Reviewed	95.04
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.01
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.99
CHL00095	821	clpC Clp protease ATP binding subunit	94.94
PRK07276	290	DNA polymerase III subunit delta'; Validated	94.92
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	94.9
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.88
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	94.86
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	94.85
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	94.75
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.75
PTZ00202	550	tuzin; Provisional	94.67
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	94.66
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.58
PRK09354	349	recA recombinase A; Provisional	94.57
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	94.57
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	94.48
cd01394	218	radB RadB. The archaeal protein radB shares simila	94.46
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	94.46
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	94.46
PRK05541	176	adenylylsulfate kinase; Provisional	94.45
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.42
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	94.42
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	94.41
PRK10865	857	protein disaggregation chaperone; Provisional	94.41
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	94.33
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	94.26
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.15
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	94.1
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	94.08
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	94.05
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	93.99
PRK07261	171	topology modulation protein; Provisional	93.99
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	93.87
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	93.8
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	93.69
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	93.62
PRK06762	166	hypothetical protein; Provisional	93.56
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.55
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	93.52
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.43
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	93.41
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	93.36
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	93.29
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	93.25
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	93.23
PF00154	322	RecA: recA bacterial DNA recombination protein; In	93.22
PRK06067	234	flagellar accessory protein FlaH; Validated	93.17
CHL00095	821	clpC Clp protease ATP binding subunit	93.16
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	93.16
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	93.08
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	93.05
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	92.96
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	92.93
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	92.92
cd03115	173	SRP The signal recognition particle (SRP) mediates	92.9
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	92.88
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	92.86
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	92.71
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	92.71
PRK07132	299	DNA polymerase III subunit delta'; Validated	92.58
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	92.51
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	92.45
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	92.38
PRK08233	182	hypothetical protein; Provisional	92.34
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	92.26
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	92.22
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	92.2
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	92.18
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	92.16
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	92.12
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	92.12
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	92.11
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	92.07
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	92.06
PRK04328	249	hypothetical protein; Provisional	91.99
PRK08533	230	flagellar accessory protein FlaH; Reviewed	91.91
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	91.91
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	91.68
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	91.67
COG2884	223	FtsE Predicted ATPase involved in cell division [C	91.64
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	91.63
PRK04301	317	radA DNA repair and recombination protein RadA; Va	91.47
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	91.35
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	91.31
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	91.29
PRK10867	433	signal recognition particle protein; Provisional	91.21
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	91.16
PF07726	131	AAA_3: ATPase family associated with various cellu	91.13
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	91.05
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	91.04
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	90.96
PRK00771	437	signal recognition particle protein Srp54; Provisi	90.94
KOG1514	767	consensus Origin recognition complex, subunit 1, a	90.93
PRK03839	180	putative kinase; Provisional	90.89
PF07015	231	VirC1: VirC1 protein; InterPro: IPR009744 This fam	90.88
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	90.73
TIGR00959	428	ffh signal recognition particle protein. This mode	90.6
TIGR02236	310	recomb_radA DNA repair and recombination protein R	90.56
KOG1969	877	consensus DNA replication checkpoint protein CHL12	90.56
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	90.53
KOG3022	300	consensus Predicted ATPase, nucleotide-binding [Ce	90.46
cd03216	163	ABC_Carb_Monos_I This family represents the domain	90.37
COG1192	259	Soj ATPases involved in chromosome partitioning [C	90.35
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	90.31
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	90.28
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	90.28
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	90.28
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	90.24
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	90.24
PRK09519	790	recA DNA recombination protein RecA; Reviewed	90.17
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	90.16
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	90.14
PRK10875	615	recD exonuclease V subunit alpha; Provisional	90.04
cd03246	173	ABCC_Protease_Secretion This family represents the	90.02
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	90.01
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	90.01
CHL00060	494	atpB ATP synthase CF1 beta subunit	90.0
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	89.91
PRK00625	173	shikimate kinase; Provisional	89.86
PRK11823	446	DNA repair protein RadA; Provisional	89.76
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	89.72
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	89.65
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	89.64
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	89.58
PTZ00088	229	adenylate kinase 1; Provisional	89.58
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	89.55
PRK05917	290	DNA polymerase III subunit delta'; Validated	89.54
PRK12678	672	transcription termination factor Rho; Provisional	89.52
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	89.52
PRK13947	171	shikimate kinase; Provisional	89.47
PRK14974	336	cell division protein FtsY; Provisional	89.38
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	89.38
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	89.22
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	89.18
PRK05922	434	type III secretion system ATPase; Validated	89.18
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	89.16
PRK00131	175	aroK shikimate kinase; Reviewed	89.16
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	89.16
PF01656	195	CbiA: CobQ/CobB/MinD/ParA nucleotide binding domai	89.11
CHL00206	2281	ycf2 Ycf2; Provisional	88.99
CHL00059	485	atpA ATP synthase CF1 alpha subunit	88.79
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	88.77
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	88.75
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	88.65
cd02034	116	CooC The accessory protein CooC, which contains a	88.62
PHA02518	211	ParA-like protein; Provisional	88.6
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	88.59
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	88.56
PTZ00301	210	uridine kinase; Provisional	88.52
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	88.49
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	88.46
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	88.43
cd02037	169	MRP-like MRP (Multiple Resistance and pH adaptatio	88.43
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	88.38
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	88.37
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	88.36
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	88.36
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	88.34
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	88.33
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	88.16
KOG0736	953	consensus Peroxisome assembly factor 2 containing	88.16
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	88.14
cd02042	104	ParA ParA and ParB of Caulobacter crescentus belon	88.03
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	88.02
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	87.84
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	87.84
cd02036	179	MinD Bacterial cell division requires the formatio	87.79
PTZ00035	337	Rad51 protein; Provisional	87.7
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	87.58
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	87.55
PRK09302	509	circadian clock protein KaiC; Reviewed	87.51
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	87.47
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	87.46
PF13245	76	AAA_19: Part of AAA domain	87.42
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	87.41
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	87.39
TIGR00064	272	ftsY signal recognition particle-docking protein F	87.27
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	87.26
COG1149	284	MinD superfamily P-loop ATPase containing an inser	87.14
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	87.13
PRK06936	439	type III secretion system ATPase; Provisional	87.13
PRK06217	183	hypothetical protein; Validated	86.99
PRK13233	275	nifH nitrogenase reductase; Reviewed	86.95
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	86.9
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	86.85
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	86.7
COG1157	441	FliI Flagellar biosynthesis/type III secretory pat	86.69
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	86.66
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	86.64
TIGR00962	501	atpA proton translocating ATP synthase, F1 alpha s	86.62
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	86.6
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	86.54
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	86.49
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	86.38
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	86.35
cd03111	106	CpaE_like This protein family consists of proteins	86.34
PF01202	158	SKI: Shikimate kinase; InterPro: IPR000623 Shikima	86.23
PRK06696	223	uridine kinase; Validated	86.14
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	86.1
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	86.07
PRK08149	428	ATP synthase SpaL; Validated	86.04
PRK13849	231	putative crown gall tumor protein VirC1; Provision	86.03
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	86.03
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	86.02
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	86.01
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	86.0
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	85.97
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	85.94
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	85.9
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	85.87
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	85.86
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	85.81
PTZ00185	574	ATPase alpha subunit; Provisional	85.8
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	85.78
PRK13343	502	F0F1 ATP synthase subunit alpha; Provisional	85.77
PRK14526	211	adenylate kinase; Provisional	85.74
PRK13975	196	thymidylate kinase; Provisional	85.73
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	85.68
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	85.59
PRK06547	172	hypothetical protein; Provisional	85.57
PRK13231	264	nitrogenase reductase-like protein; Reviewed	85.57
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	85.55
TIGR01281	268	DPOR_bchL light-independent protochlorophyllide re	85.54
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	85.54
PF08303	168	tRNA_lig_kinase: tRNA ligase kinase domain; InterP	85.47
PRK13946	184	shikimate kinase; Provisional	85.46
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	85.42
PRK13949	169	shikimate kinase; Provisional	85.42
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	85.31
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	85.29
PRK00889	175	adenylylsulfate kinase; Provisional	85.23
PRK13948	182	shikimate kinase; Provisional	85.17
PRK10037	250	cell division protein; Provisional	85.13
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	85.07
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	85.04
TIGR01969	251	minD_arch cell division ATPase MinD, archaeal. Thi	85.03
PRK11545	163	gntK gluconate kinase 1; Provisional	85.03
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	85.02
PRK05973	237	replicative DNA helicase; Provisional	84.93
PRK04040	188	adenylate kinase; Provisional	84.82
smart00487	201	DEXDc DEAD-like helicases superfamily.	84.79
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	84.78
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	84.76
PRK03846	198	adenylylsulfate kinase; Provisional	84.75
PRK13833	323	conjugal transfer protein TrbB; Provisional	84.73
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	84.71
cd02040	270	NifH NifH gene encodes component II (iron protein)	84.66
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	84.65
PRK03731	171	aroL shikimate kinase II; Reviewed	84.63
PRK07667	193	uridine kinase; Provisional	84.61
PRK05480	209	uridine/cytidine kinase; Provisional	84.61
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	84.59
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	84.51
PRK05595	444	replicative DNA helicase; Provisional	84.49
PF02223	186	Thymidylate_kin: Thymidylate kinase; InterPro: IPR	84.48
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	84.44
TIGR00665	434	DnaB replicative DNA helicase. This model describe	84.36
cd02032	267	Bchl_like This family of proteins contains bchL an	84.34
TIGR00235	207	udk uridine kinase. Model contains a number of lon	84.34
PRK07594	433	type III secretion system ATPase SsaN; Validated	84.22
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	84.13
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	84.12
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	84.03
PRK13230	279	nitrogenase reductase-like protein; Reviewed	83.81
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	83.81
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	83.77
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	83.75
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	83.74
PRK11608	326	pspF phage shock protein operon transcriptional ac	83.51
PRK13764	602	ATPase; Provisional	83.46
cd03110	179	Fer4_NifH_child This protein family's function is	83.46
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	83.42
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	83.42
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	83.41
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	83.4
PRK05057	172	aroK shikimate kinase I; Reviewed	83.4
KOG2383	467	consensus Predicted ATPase [General function predi	83.39
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	83.31
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	83.25
PRK13185	270	chlL protochlorophyllide reductase iron-sulfur ATP	83.24
PRK10646	153	ADP-binding protein; Provisional	83.23
COG0125	208	Tmk Thymidylate kinase [Nucleotide transport and m	83.18
TIGR03371	246	cellulose_yhjQ cellulose synthase operon protein Y	83.03
PF04548	212	AIG1: AIG1 family; InterPro: IPR006703 This entry	83.01
COG3265	161	GntK Gluconate kinase [Carbohydrate transport and	82.91
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	82.86
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	82.85
COG0055	468	AtpD F0F1-type ATP synthase, beta subunit [Energy	82.83
PRK09099	441	type III secretion system ATPase; Provisional	82.78
COG1485	367	Predicted ATPase [General function prediction only	82.78
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	82.72
PRK14532	188	adenylate kinase; Provisional	82.71
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	82.67
TIGR02533	486	type_II_gspE general secretory pathway protein E.	82.65
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	82.65
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	82.54
PRK04196	460	V-type ATP synthase subunit B; Provisional	82.38
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	82.37
PRK09165	497	replicative DNA helicase; Provisional	82.35
COG3910	233	Predicted ATPase [General function prediction only	82.27
TIGR01287	275	nifH nitrogenase iron protein. This model describe	82.26
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	82.22
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	82.22
PRK05022	509	anaerobic nitric oxide reductase transcription reg	82.2
PRK14529	223	adenylate kinase; Provisional	82.14
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	82.13
TIGR01968	261	minD_bact septum site-determining protein MinD. Th	82.09
PRK13235	274	nifH nitrogenase reductase; Reviewed	82.07
PRK13232	273	nifH nitrogenase reductase; Reviewed	81.99
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	81.94
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	81.9
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	81.86
PRK12339	197	2-phosphoglycerate kinase; Provisional	81.85
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	81.83
PRK06761	282	hypothetical protein; Provisional	81.72
COG0488	530	Uup ATPase components of ABC transporters with dup	81.68
cd02117	212	NifH_like This family contains the NifH (iron prot	81.46
PRK14530	215	adenylate kinase; Provisional	81.28
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	81.19
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	81.13
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	80.93
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	80.87
COG0802	149	Predicted ATPase or kinase [General function predi	80.81
TIGR03018	207	pepcterm_TyrKin exopolysaccharide/PEPCTERM locus t	80.7
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	80.63
PRK04182	180	cytidylate kinase; Provisional	80.6
PRK15453	290	phosphoribulokinase; Provisional	80.45
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	80.44
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	80.43
PRK08506	472	replicative DNA helicase; Provisional	80.39
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	80.23
PRK06820	440	type III secretion system ATPase; Validated	80.14
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	80.11
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	80.11

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=3.8e-33  Score=287.31  Aligned_cols=214  Identities=23%  Similarity=0.235  Sum_probs=184.4

Q ss_pred             CCCCcHHHHHHHHHc--h-hccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-cCccchhhhHHHHHHHhcCc
Q 040234            1 MGGLGKTTLARVVYD--L-ISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-NNIRNVYDGINMLRVRLRRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~--~-~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~~~~~~~~l~~~l~~k   76 (377)
                      |||+||||||+++++  . ++.+|+..+|++ ||+.+    +...++.+|+..++.... ....+.++.+..+.+.|.++
T Consensus       187 MGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~-VSk~f----~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~k  261 (889)
T KOG4658|consen  187 MGGVGKTTLARQIFNKFDEVGNHFDGVIWVV-VSKEF----TTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGK  261 (889)
T ss_pred             CCcccHHHHHHHHhcccchhcccCceEEEEE-Ecccc----cHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccC
Confidence            899999999999999  3 889999999999 99988    999999999999876322 22234478889999999999


Q ss_pred             eEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCC-CCCchhH
Q 040234           77 KVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDT-HKPLEEY  154 (377)
Q Consensus        77 ~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~-~~~~~~~  154 (377)
                      |+||||||||+..+|+.+..++|....||+|++|||++.|+.. +++...++++.|+++|||+||.+.++.. ...++..
T Consensus       262 rfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i  341 (889)
T KOG4658|consen  262 RFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDI  341 (889)
T ss_pred             ceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhccccccccccH
Confidence            9999999999999999999999988889999999999999998 7778899999999999999999999876 4455668


Q ss_pred             HHHHHHHHHHhCCCCchhhHHHHHhhhhchh-HHHHHHHHHhhccC-----chhHHHHHHHHHhhcccCCCCC
Q 040234          155 VELAESVVRICHCQKSTLNALMSVSYTVSHL-LLTLCLKLMQYMLC-----PFILFVYLLFFSVGLQNMPPSD  221 (377)
Q Consensus       155 ~~~~~~I~~~c~G~~lplal~~~~~~l~~~~-~~~~~~~L~~~~~~-----~~~~~~~~~~l~~Sy~~L~~~~  221 (377)
                      +++|++++++|+|  ||||+.++|+.+..+. ..+|....+.....     +.....+..++.+||+.||+.-
T Consensus       342 ~~lak~v~~kC~G--LPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~l  412 (889)
T KOG4658|consen  342 EELAKEVAEKCGG--LPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILKLSYDNLPEEL  412 (889)
T ss_pred             HHHHHHHHHHhCC--hHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhhccHhhhhHHH
Confidence            9999999999999  9999999999998765 44677775544222     2335689999999999999544

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

Probab=99.97  E-value=3.4e-32  Score=251.65  Aligned_cols=229  Identities=27%  Similarity=0.338  Sum_probs=167.1

Q ss_pred             CCCCcHHHHHHHHHch--hccccccceEEecchhhcccccCHHHHHHHHHHHHhhcccc--CccchhhhHHHHHHHhcCc
Q 040234            1 MGGLGKTTLARVVYDL--ISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN--NIRNVYDGINMLRVRLRRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~--~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~~l~~~l~~k   76 (377)
                      |||+||||||.+++++  ++++|+..+|+. +++..    +...++..++.++......  ...+.++..+.+++.|.++
T Consensus        27 ~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~-~~~~~----~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~~  101 (287)
T PF00931_consen   27 MGGIGKTTLARQVARDLRIKNRFDGVIWVS-LSKNP----SLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELLKDK  101 (287)
T ss_dssp             STTSSHHHHHHHHHCHHHHCCCCTEEEEEE-EES-S----CCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHHCCT
T ss_pred             CCcCCcceeeeecccccccccccccccccc-ccccc----ccccccccccccccccccccccccccccccccchhhhccc
Confidence            7999999999999997  899998888887 66554    6688899999998766332  4567778899999999999


Q ss_pred             eEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhCCC-CCeeecCCCChhhhHHHHHHHhcCCC-CCchhH
Q 040234           77 KVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPV-KKVYKLEALTYDEAFRLLCLKAFDTH-KPLEEY  154 (377)
Q Consensus        77 ~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~-~~~~~l~~L~~~ea~~L~~~~~~~~~-~~~~~~  154 (377)
                      ++||||||||+...|+.+...++....+++||||||+..++..... ...+++++|++++|++||.+.++... ...+..
T Consensus       102 ~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~  181 (287)
T PF00931_consen  102 RCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSEEEALELFKKRAGRKESESPEDL  181 (287)
T ss_dssp             SEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS----TTS
T ss_pred             cceeeeeeeccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            9999999999999998888877776779999999999988776543 67899999999999999999997655 234445


Q ss_pred             HHHHHHHHHHhCCCCchhhHHHHHhhhhch-hHHHHHHHHHhhccCc----hhHHHHHHHHHhhcccCCCCCcccCCCCC
Q 040234          155 VELAESVVRICHCQKSTLNALMSVSYTVSH-LLLTLCLKLMQYMLCP----FILFVYLLFFSVGLQNMPPSDKYGNMHSP  229 (377)
Q Consensus       155 ~~~~~~I~~~c~G~~lplal~~~~~~l~~~-~~~~~~~~L~~~~~~~----~~~~~~~~~l~~Sy~~L~~~~~~~~~~~~  229 (377)
                      ++.+++|++.|+|  +|||+.++|+++..+ ...+|...+.+.....    .....+..++.+||+.|++..        
T Consensus       182 ~~~~~~i~~~c~g--lPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~~~l~~s~~~L~~~~--------  251 (287)
T PF00931_consen  182 EDLAKEIVEKCGG--LPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVFSALELSYDSLPDEL--------  251 (287)
T ss_dssp             CTHHHHHHHHTTT---HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHHHHHHHHHHSSHTCC--------
T ss_pred             ccccccccccccc--cccccccccccccccccccccccccccccccccccccccccccccceechhcCCccH--------
Confidence            6789999999999  999999999998543 2334444443322221    134689999999999999976        


Q ss_pred             CCceEE--EecCC-CCCc
Q 040234          230 QREYSI--VVPGS-EIPE  244 (377)
Q Consensus       230 ~~~~~~--~~pg~-~iP~  244 (377)
                      +..|..  +||.. .||.
T Consensus       252 ~~~f~~L~~f~~~~~i~~  269 (287)
T PF00931_consen  252 RRCFLYLSIFPEGVPIPR  269 (287)
T ss_dssp             HHHHHHGGGSGTTS-EEH
T ss_pred             HHHHhhCcCCCCCceECH
Confidence            555544  56544 5553

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

>PLN03210 Resistant to P

Probab=99.95  E-value=2.4e-27  Score=255.41  Aligned_cols=212  Identities=27%  Similarity=0.419  Sum_probs=170.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecc--hhh---cc-----cccCHHHHHHHHHHHHhhccccCccchhhhHHHHH
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADV--REK---CD-----KEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLR   70 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~--~~~---~~-----~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~   70 (377)
                      |||+||||||+++|+++..+|+..+|+...  +..   ..     .......++.+++.++.........    ....++
T Consensus       215 ~gGiGKTTLA~~l~~~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~----~~~~~~  290 (1153)
T PLN03210        215 SSGIGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIY----HLGAME  290 (1153)
T ss_pred             CCCCchHHHHHHHHHHHhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccC----CHHHHH
Confidence            799999999999999999999988887531  111   00     0001234555666665443222111    135678


Q ss_pred             HHhcCceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhCCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           71 VRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        71 ~~l~~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +.++++|+||||||||+.++|+.+.....+.++|++||||||++.++......++|+++.|++++|++||.++||+...+
T Consensus       291 ~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~  370 (1153)
T PLN03210        291 ERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSP  370 (1153)
T ss_pred             HHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCC
Confidence            88999999999999999999999988777778899999999999998877777899999999999999999999987666


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHHhhhhchhHHHHHHHHHhhccCchhHHHHHHHHHhhcccCCCC
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPS  220 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~~~~~~~~~~L~~~~~~~~~~~~~~~~l~~Sy~~L~~~  220 (377)
                      .+...+++++|+++|||  +|||++++|++++.+...+|...+.+.....  ...+.+++.+||+.|++.
T Consensus       371 ~~~~~~l~~~iv~~c~G--LPLAl~vlgs~L~~k~~~~W~~~l~~L~~~~--~~~I~~~L~~SYd~L~~~  436 (1153)
T PLN03210        371 PDGFMELASEVALRAGN--LPLGLNVLGSYLRGRDKEDWMDMLPRLRNGL--DGKIEKTLRVSYDGLNNK  436 (1153)
T ss_pred             cHHHHHHHHHHHHHhCC--CcHHHHHHHHHHcCCCHHHHHHHHHHHHhCc--cHHHHHHHHHhhhccCcc
Confidence            67788999999999999  9999999999999988888888887776533  246889999999999864

syringae 6; Provisional

>PLN03210 Resistant to P

Probab=99.08  E-value=5.7e-10  Score=121.32  Aligned_cols=49  Identities=20%  Similarity=0.494  Sum_probs=43.8

Q ss_pred             EEEecCCCCCcccccccCCCceEE-EeCCCCCcCCCCeeeEEEEEEEecCCC
Q 040234          234 SIVVPGSEIPEWFEYQNNEGSSIT-ISTPPKTYKNSKLVGYVVCCVFRVPKY  284 (377)
Q Consensus       234 ~~~~pg~~iP~w~~~~~~~g~s~~-~~l~~~~~~~~~~~Gf~~c~v~~~~~~  284 (377)
                      .+.+||.++|.||.|++ .|++++ +.||++|+ ...++||++|+|+++.+.
T Consensus       957 ~~~l~g~evp~~f~hr~-~g~sl~~i~l~~~~~-~~~~~~f~~c~v~~~~~~ 1006 (1153)
T PLN03210        957 QLILSGEEVPSYFTHRT-TGASLTNIPLLHISP-CQPFFRFRACAVVDSESF 1006 (1153)
T ss_pred             EEECCCccCchhccCCc-ccceeeeeccCCccc-CCCccceEEEEEEecCcc
Confidence            35899999999999998 799998 99999998 578999999999987653

syringae 6; Provisional

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

Probab=98.96  E-value=3.1e-08  Score=90.63  Aligned_cols=170  Identities=15%  Similarity=0.062  Sum_probs=99.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHH-----hcC
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVR-----LRR   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~-----l~~   75 (377)
                      .+|+|||||++.+++.....-...+++.  ....    +..+++..++..++....  ..+.......+...     ..+
T Consensus        51 ~~G~GKTtl~~~l~~~l~~~~~~~~~~~--~~~~----~~~~~l~~i~~~lG~~~~--~~~~~~~~~~l~~~l~~~~~~~  122 (269)
T TIGR03015        51 EVGAGKTTLIRNLLKRLDQERVVAAKLV--NTRV----DAEDLLRMVAADFGLETE--GRDKAALLRELEDFLIEQFAAG  122 (269)
T ss_pred             CCCCCHHHHHHHHHHhcCCCCeEEeeee--CCCC----CHHHHHHHHHHHcCCCCC--CCCHHHHHHHHHHHHHHHHhCC
Confidence            4799999999999987653211112222  1111    556777777777643311  11212222333322     256


Q ss_pred             ceEEEEEeCCCCh--hhhhHhh---CCCCCCCCCCeEEEEecchhHHhhC----------CCCCeeecCCCChhhhHHHH
Q 040234           76 KKVLVVIDDAAHP--DHLRRLV---GEPDWFGPGSRIIITTRNEHLLKLH----------PVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        76 k~~LLVLDdv~~~--~~~~~l~---~~l~~~~~gs~IIvTTR~~~v~~~~----------~~~~~~~l~~L~~~ea~~L~  140 (377)
                      ++.+||+||++..  ..++.+.   ...........|++|.... .....          .....+++++|+.+|..+++
T Consensus       123 ~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~~~l  201 (269)
T TIGR03015       123 KRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPLDREETREYI  201 (269)
T ss_pred             CCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCCCHHHHHHHH
Confidence            7899999999874  3344433   2211112223455665432 11111          12346789999999999999


Q ss_pred             HHHhcCCC--CCchhHHHHHHHHHHHhCCCCchhhHHHHHhhh
Q 040234          141 CLKAFDTH--KPLEEYVELAESVVRICHCQKSTLNALMSVSYT  181 (377)
Q Consensus       141 ~~~~~~~~--~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l  181 (377)
                      ..++....  ....-.++..+.|++.++|  .|..+..++..+
T Consensus       202 ~~~l~~~g~~~~~~~~~~~~~~i~~~s~G--~p~~i~~l~~~~  242 (269)
T TIGR03015       202 EHRLERAGNRDAPVFSEGAFDAIHRFSRG--IPRLINILCDRL  242 (269)
T ss_pred             HHHHHHcCCCCCCCcCHHHHHHHHHHcCC--cccHHHHHHHHH
Confidence            87764322  1122345789999999999  999998777754

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.

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.93  E-value=9e-10  Score=102.46  Aligned_cols=207  Identities=16%  Similarity=0.100  Sum_probs=143.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|||||||++.++.. ++..|+.++|+++..+..    +...+...+...++-..    .+-+.....+...+.++|.++
T Consensus        22 ~ggvgkttl~~~~a~-~~~~~~~~v~~vdl~pit----D~~~v~~~~ag~~gl~~----~~g~~~~~~~~~~~~~rr~ll   92 (414)
T COG3903          22 AGGVGKTTLALQAAH-AASEYADGVAFVDLAPIT----DPALVFPTLAGALGLHV----QPGDSAVDTLVRRIGDRRALL   92 (414)
T ss_pred             cCccceehhhhhhHh-HhhhcccceeeeeccccC----chhHhHHHHHhhccccc----ccchHHHHHHHHHHhhhhHHH
Confidence            489999999999999 999999999999887775    55555555554443332    122345567778889999999


Q ss_pred             EEeCCCCh-hhhhHhhCCCCCCCCCCeEEEEecchhHHhhCCCCCeeecCCCChh-hhHHHHHHHhcCCCC---CchhHH
Q 040234           81 VIDDAAHP-DHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYD-EAFRLLCLKAFDTHK---PLEEYV  155 (377)
Q Consensus        81 VLDdv~~~-~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~~~l~~L~~~-ea~~L~~~~~~~~~~---~~~~~~  155 (377)
                      |+||..+. ++...+...+..+++.-.|+.|+|+...   ..+.....+++|+.. ++.++|...+.....   -.....
T Consensus        93 vldncehl~~~~a~~i~all~~~~~~~~~atsre~~l---~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~~~~~  169 (414)
T COG3903          93 VLDNCEHLLDACAALIVALLGACPRLAILATSREAIL---VAGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWLTDDNA  169 (414)
T ss_pred             HhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhc---ccccccccCCccccCCchhHHHHHHHHHhccceeecCCch
Confidence            99999873 3444444444444677789999997743   334566788888876 788998777643322   123335


Q ss_pred             HHHHHHHHHhCCCCchhhHHHHHhhhhchhHHHHHHHHH----hhccC----chhHHHHHHHHHhhcccCCCCC
Q 040234          156 ELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLM----QYMLC----PFILFVYLLFFSVGLQNMPPSD  221 (377)
Q Consensus       156 ~~~~~I~~~c~G~~lplal~~~~~~l~~~~~~~~~~~L~----~~~~~----~~~~~~~~~~l~~Sy~~L~~~~  221 (377)
                      ..+.+|+++..|  .|+++..+++..++-.......-|+    .....    ....+..++++++||.-|...+
T Consensus       170 a~v~~icr~ldg--~~laielaaarv~sl~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtgwe  241 (414)
T COG3903         170 AAVAEICRRLDG--IPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTGWE  241 (414)
T ss_pred             HHHHHHHHHhhc--chHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhhHH
Confidence            678999999999  9999999999876644333222211    11111    1223467889999999988776

>PF05729 NACHT: NACHT domain

Probab=98.92  E-value=6.5e-09  Score=87.49  Aligned_cols=135  Identities=23%  Similarity=0.324  Sum_probs=77.8

Q ss_pred             CCCCcHHHHHHHHHchhcccc------ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHH-h
Q 040234            1 MGGLGKTTLARVVYDLISHEF------DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVR-L   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f------~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~-l   73 (377)
                      .+|+||||+++.++.+.....      ...+|+. .+...... ....+...+..+...    .......   .+... .
T Consensus         8 ~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~-~~~~l~~~l~~~~~~----~~~~~~~---~~~~~~~   78 (166)
T PF05729_consen    8 EPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFS-LRDISDSN-NSRSLADLLFDQLPE----SIAPIEE---LLQELLE   78 (166)
T ss_pred             CCCCChHHHHHHHHHHHHhcCcccccceEEEEEe-ehhhhhcc-ccchHHHHHHHhhcc----chhhhHH---HHHHHHH
Confidence            379999999999998554443      2333433 44443211 111233333333211    1111111   22222 2


Q ss_pred             cCceEEEEEeCCCChhh---------hhHhhC-CCCC-CCCCCeEEEEecchhH---HhhCCCCCeeecCCCChhhhHHH
Q 040234           74 RRKKVLVVIDDAAHPDH---------LRRLVG-EPDW-FGPGSRIIITTRNEHL---LKLHPVKKVYKLEALTYDEAFRL  139 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~~~---------~~~l~~-~l~~-~~~gs~IIvTTR~~~v---~~~~~~~~~~~l~~L~~~ea~~L  139 (377)
                      ..+++|||||++++...         +..++. .+.. ..++.++|||+|....   .........+++++|++++..++
T Consensus        79 ~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  158 (166)
T PF05729_consen   79 KNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQY  158 (166)
T ss_pred             cCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHH
Confidence            56899999999976321         222221 1111 2568999999998765   33345556899999999999999


Q ss_pred             HHHHh
Q 040234          140 LCLKA  144 (377)
Q Consensus       140 ~~~~~  144 (377)
                      +.++.
T Consensus       159 ~~~~f  163 (166)
T PF05729_consen  159 LRKYF  163 (166)
T ss_pred             HHHHh
Confidence            97765

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.83  E-value=6e-08  Score=103.74  Aligned_cols=164  Identities=13%  Similarity=0.095  Sum_probs=101.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccC---c---------cchhhhHHH
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNN---I---------RNVYDGINM   68 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~---~---------~~~~~~~~~   68 (377)
                      ++|.|||||+.++.++.    +.++|+. +.....   +.......++..+.......   .         .+.......
T Consensus        40 paG~GKTtl~~~~~~~~----~~~~w~~-l~~~d~---~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (903)
T PRK04841         40 PAGYGKTTLISQWAAGK----NNLGWYS-LDESDN---QPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQ  111 (903)
T ss_pred             CCCCCHHHHHHHHHHhC----CCeEEEe-cCcccC---CHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHH
Confidence            58999999999988632    3578886 543321   55566667776664221110   0         111122223


Q ss_pred             HHHHhc--CceEEEEEeCCCChh------hhhHhhCCCCCCCCCCeEEEEecchhHHh--hC-CCCCeeecC----CCCh
Q 040234           69 LRVRLR--RKKVLVVIDDAAHPD------HLRRLVGEPDWFGPGSRIIITTRNEHLLK--LH-PVKKVYKLE----ALTY  133 (377)
Q Consensus        69 l~~~l~--~k~~LLVLDdv~~~~------~~~~l~~~l~~~~~gs~IIvTTR~~~v~~--~~-~~~~~~~l~----~L~~  133 (377)
                      +...+.  +++++|||||+...+      .+..+....   .++.++|||||...-..  .. ......+++    +|+.
T Consensus       112 ~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~---~~~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~  188 (903)
T PRK04841        112 LFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQ---PENLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQLAFDH  188 (903)
T ss_pred             HHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhC---CCCeEEEEEeCCCCCCchHhHHhcCcceecCHHhCCCCH
Confidence            333333  679999999986532      333444332   45668889999842111  11 112344555    8999


Q ss_pred             hhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhh
Q 040234          134 DEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTV  182 (377)
Q Consensus       134 ~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~  182 (377)
                      +|+.++|....+...     ..+.+.+|.+.++|  .|+++..++..+.
T Consensus       189 ~e~~~ll~~~~~~~~-----~~~~~~~l~~~t~G--wp~~l~l~~~~~~  230 (903)
T PRK04841        189 QEAQQFFDQRLSSPI-----EAAESSRLCDDVEG--WATALQLIALSAR  230 (903)
T ss_pred             HHHHHHHHhccCCCC-----CHHHHHHHHHHhCC--hHHHHHHHHHHHh
Confidence            999999987764321     14567899999999  9999988776543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.67  E-value=4.5e-07  Score=87.71  Aligned_cols=169  Identities=15%  Similarity=0.101  Sum_probs=97.2

Q ss_pred             CCCCcHHHHHHHHHchhccccc--cceEEecchhhcccccCHHHHHHHHHHHHhhccc-cCccchhhhHHHHHHHhc--C
Q 040234            1 MGGLGKTTLARVVYDLISHEFD--GSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-NNIRNVYDGINMLRVRLR--R   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~--~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~~~~~~~~l~~~l~--~   75 (377)
                      .+|+|||++++.+++++....+  ..+++. .....    +...++..++.++.+... ....+.++..+.+.+.+.  +
T Consensus        63 ~~GtGKT~l~~~v~~~l~~~~~~~~~v~in-~~~~~----~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~  137 (394)
T PRK00411         63 PPGTGKTTTVKKVFEELEEIAVKVVYVYIN-CQIDR----TRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERD  137 (394)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEEEE-CCcCC----CHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcC
Confidence            4799999999999997765542  223333 33332    666888888888765211 122244556666666665  4


Q ss_pred             ceEEEEEeCCCChh------hhhHhhCCCCCCCCCCe--EEEEecchhHHhhC-------CCCCeeecCCCChhhhHHHH
Q 040234           76 KKVLVVIDDAAHPD------HLRRLVGEPDWFGPGSR--IIITTRNEHLLKLH-------PVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        76 k~~LLVLDdv~~~~------~~~~l~~~l~~~~~gs~--IIvTTR~~~v~~~~-------~~~~~~~l~~L~~~ea~~L~  140 (377)
                      ++.+||||+++...      .+..+...... .++++  +|.++....+....       -....+.+++++.++..+++
T Consensus       138 ~~~viviDE~d~l~~~~~~~~l~~l~~~~~~-~~~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il  216 (394)
T PRK00411        138 RVLIVALDDINYLFEKEGNDVLYSLLRAHEE-YPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDIL  216 (394)
T ss_pred             CEEEEEECCHhHhhccCCchHHHHHHHhhhc-cCCCeEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHH
Confidence            57899999997632      34444332221 12333  56666554332221       11346789999999999999


Q ss_pred             HHHhcCC---CCCch-hHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          141 CLKAFDT---HKPLE-EYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       141 ~~~~~~~---~~~~~-~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      ..++...   ....+ ..+.+++......|.  .+.|+.++
T Consensus       217 ~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd--~r~a~~ll  255 (394)
T PRK00411        217 KDRVEEGFYPGVVDDEVLDLIADLTAREHGD--ARVAIDLL  255 (394)
T ss_pred             HHHHHhhcccCCCCHhHHHHHHHHHHHhcCc--HHHHHHHH
Confidence            8876322   11122 222223333333455  77776554

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

Probab=98.59  E-value=1.6e-06  Score=80.79  Aligned_cols=190  Identities=19%  Similarity=0.239  Sum_probs=110.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+||||||+.++.....+|...   ..+..      +++++... ++..                 -+....+++.+|
T Consensus        56 PPG~GKTTlA~liA~~~~~~f~~~---sAv~~------gvkdlr~i-~e~a-----------------~~~~~~gr~tiL  108 (436)
T COG2256          56 PPGTGKTTLARLIAGTTNAAFEAL---SAVTS------GVKDLREI-IEEA-----------------RKNRLLGRRTIL  108 (436)
T ss_pred             CCCCCHHHHHHHHHHhhCCceEEe---ccccc------cHHHHHHH-HHHH-----------------HHHHhcCCceEE
Confidence            489999999999999777776431   11111      33333222 2211                 012235889999


Q ss_pred             EEeCCC--ChhhhhHhhCCCCCCCCCCeEEE--EecchhHH---hhCCCCCeeecCCCChhhhHHHHHHHhcCCCCCc--
Q 040234           81 VIDDAA--HPDHLRRLVGEPDWFGPGSRIII--TTRNEHLL---KLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPL--  151 (377)
Q Consensus        81 VLDdv~--~~~~~~~l~~~l~~~~~gs~IIv--TTR~~~v~---~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~--  151 (377)
                      .+|.|-  +..|-+.|++.+   ..|.-|+|  ||.++...   ...+...++.+++|+.++-.+++.+.+.......  
T Consensus       109 flDEIHRfnK~QQD~lLp~v---E~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~  185 (436)
T COG2256         109 FLDEIHRFNKAQQDALLPHV---ENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGG  185 (436)
T ss_pred             EEehhhhcChhhhhhhhhhh---cCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCc
Confidence            999995  456677777765   45665665  67776431   1124578999999999999999988553222211  


Q ss_pred             ---hhHHHHHHHHHHHhCCCCchhhHHHH---Hhhhhch---hHHHHHHHH----HhhccCchhHHHHHHHHHhhcccCC
Q 040234          152 ---EEYVELAESVVRICHCQKSTLNALMS---VSYTVSH---LLLTLCLKL----MQYMLCPFILFVYLLFFSVGLQNMP  218 (377)
Q Consensus       152 ---~~~~~~~~~I~~~c~G~~lplal~~~---~~~l~~~---~~~~~~~~L----~~~~~~~~~~~~~~~~l~~Sy~~L~  218 (377)
                         .-.+++.+-|++.++| +.-.++..+   .......   ........+    ..+....+..+.+..++..|.+.-+
T Consensus       186 ~~~~i~~~a~~~l~~~s~G-D~R~aLN~LE~~~~~~~~~~~~~~~~l~~~l~~~~~~~Dk~gD~hYdliSA~hKSvRGSD  264 (436)
T COG2256         186 QIIVLDEEALDYLVRLSNG-DARRALNLLELAALSAEPDEVLILELLEEILQRRSARFDKDGDAHYDLISALHKSVRGSD  264 (436)
T ss_pred             ccccCCHHHHHHHHHhcCc-hHHHHHHHHHHHHHhcCCCcccCHHHHHHHHhhhhhccCCCcchHHHHHHHHHHhhccCC
Confidence               1234567788888888 233333222   1111111   112222222    2233444556778888888887766


Q ss_pred             CCC
Q 040234          219 PSD  221 (377)
Q Consensus       219 ~~~  221 (377)
                      +++
T Consensus       265 ~dA  267 (436)
T COG2256         265 PDA  267 (436)
T ss_pred             cCH
Confidence            654

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.58  E-value=5.7e-07  Score=79.95  Aligned_cols=170  Identities=19%  Similarity=0.135  Sum_probs=80.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHH------HHHHHHHHhhcccc---------Cccchhhh
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISL------QKQLLSDLLKLADN---------NIRNVYDG   65 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~------~~~i~~~l~~~~~~---------~~~~~~~~   65 (377)
                      ..|+|||+|++++.+..++.-...+|+.........  ....+      ...+...+......         ........
T Consensus        28 ~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (234)
T PF01637_consen   28 PRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNES--SLRSFIEETSLADELSEALGISIPSITLEKISKDLSEDSFSA  105 (234)
T ss_dssp             STTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHH--HHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-GG-G--
T ss_pred             CCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhh--HHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcchhhHHHH
Confidence            369999999999999775543344555422221100  11111      11111222111000         01122223


Q ss_pred             HHHHHHHhc--CceEEEEEeCCCChh-----------hhhHhhCCCCCCCCCCeEEEEecchhHHhh--------CCCCC
Q 040234           66 INMLRVRLR--RKKVLVVIDDAAHPD-----------HLRRLVGEPDWFGPGSRIIITTRNEHLLKL--------HPVKK  124 (377)
Q Consensus        66 ~~~l~~~l~--~k~~LLVLDdv~~~~-----------~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~--------~~~~~  124 (377)
                      ...+.+.+.  +++.+||+|++....           .+..+........+. .+|+++....+...        .....
T Consensus       106 l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~v~~~S~~~~~~~~~~~~~~~~~~~~  184 (234)
T PF01637_consen  106 LERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNV-SIVITGSSDSLMEEFLDDKSPLFGRFS  184 (234)
T ss_dssp             HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTE-EEEEEESSHHHHHHTT-TTSTTTT---
T ss_pred             HHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCc-eEEEECCchHHHHHhhcccCccccccc
Confidence            333333343  345999999986544           122233222222333 44455444444332        13345


Q ss_pred             eeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHH
Q 040234          125 VYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALM  176 (377)
Q Consensus       125 ~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~  176 (377)
                      .+.+++|+.+++++++....... ...+...+..++|...+||  .|..|..
T Consensus       185 ~~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~gG--~P~~l~~  233 (234)
T PF01637_consen  185 HIELKPLSKEEAREFLKELFKEL-IKLPFSDEDIEEIYSLTGG--NPRYLQE  233 (234)
T ss_dssp             EEEE----HHHHHHHHHHHHHCC-------HHHHHHHHHHHTT---HHHHHH
T ss_pred             eEEEeeCCHHHHHHHHHHHHHHh-hcccCCHHHHHHHHHHhCC--CHHHHhc
Confidence            59999999999999999876433 1112235677999999999  9988753

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

>PRK06893 DNA replication initiation factor; Validated

Probab=98.58  E-value=4.9e-07  Score=80.59  Aligned_cols=144  Identities=13%  Similarity=0.161  Sum_probs=86.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++...+.....|+. +...       ......                      +.+.+. +.-+|
T Consensus        47 ~~G~GKThL~~ai~~~~~~~~~~~~y~~-~~~~-------~~~~~~----------------------~~~~~~-~~dlL   95 (229)
T PRK06893         47 GKSSGKSHLLKAVSNHYLLNQRTAIYIP-LSKS-------QYFSPA----------------------VLENLE-QQDLV   95 (229)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCeEEee-HHHh-------hhhhHH----------------------HHhhcc-cCCEE
Confidence            3799999999999997655544555654 2110       000001                      111112 23489


Q ss_pred             EEeCCCCh---hhhh-HhhCCCCCC-CCCCeEEE-Eecc---------hhHHhhCCCCCeeecCCCChhhhHHHHHHHhc
Q 040234           81 VIDDAAHP---DHLR-RLVGEPDWF-GPGSRIII-TTRN---------EHLLKLHPVKKVYKLEALTYDEAFRLLCLKAF  145 (377)
Q Consensus        81 VLDdv~~~---~~~~-~l~~~l~~~-~~gs~IIv-TTR~---------~~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~  145 (377)
                      +|||++..   .+|+ .+...+... ..+..+|| |++.         +.+..++.....+++++++.++.++++.+.+.
T Consensus        96 ilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~  175 (229)
T PRK06893         96 CLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAY  175 (229)
T ss_pred             EEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHH
Confidence            99999862   3333 222212111 23555544 5543         35555556667899999999999999998886


Q ss_pred             CCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          146 DTHKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       146 ~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ...-.  -.++...-|++.++|  -.-++..+-.
T Consensus       176 ~~~l~--l~~~v~~~L~~~~~~--d~r~l~~~l~  205 (229)
T PRK06893        176 QRGIE--LSDEVANFLLKRLDR--DMHTLFDALD  205 (229)
T ss_pred             HcCCC--CCHHHHHHHHHhccC--CHHHHHHHHH
Confidence            43322  225678899999998  6665554444

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.49  E-value=5.4e-06  Score=79.31  Aligned_cols=166  Identities=11%  Similarity=0.057  Sum_probs=93.0

Q ss_pred             CCCCcHHHHHHHHHchhccccc------cceEEecchhhcccccCHHHHHHHHHHHHhh--cc-ccCccchhhhHHHHHH
Q 040234            1 MGGLGKTTLARVVYDLISHEFD------GSSFLADVREKCDKEGSVISLQKQLLSDLLK--LA-DNNIRNVYDGINMLRV   71 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~------~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~--~~-~~~~~~~~~~~~~l~~   71 (377)
                      ++|+|||++++.+++++.+..+      ..+++. .....    +...++..++.++..  .. +....+..+..+.+.+
T Consensus        48 ~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in-~~~~~----~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  122 (365)
T TIGR02928        48 KTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVN-CQILD----TLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYK  122 (365)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEE-CCCCC----CHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHH
Confidence            4799999999999986643322      123444 33332    566788888888742  11 1111223344455555


Q ss_pred             Hhc--CceEEEEEeCCCChh-----hhhHhhCCC-CCCC--CCCeEEEEecchhHHhhC------C-CCCeeecCCCChh
Q 040234           72 RLR--RKKVLVVIDDAAHPD-----HLRRLVGEP-DWFG--PGSRIIITTRNEHLLKLH------P-VKKVYKLEALTYD  134 (377)
Q Consensus        72 ~l~--~k~~LLVLDdv~~~~-----~~~~l~~~l-~~~~--~gs~IIvTTR~~~v~~~~------~-~~~~~~l~~L~~~  134 (377)
                      .+.  +++.+||||+++...     .+..+.... ....  ....+|.+|........+      . ....+.+++++.+
T Consensus       123 ~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~  202 (365)
T TIGR02928       123 ELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAE  202 (365)
T ss_pred             HHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHH
Confidence            553  568899999998751     123332220 0111  223455555443322111      1 1256889999999


Q ss_pred             hhHHHHHHHhcC---CCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          135 EAFRLLCLKAFD---THKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       135 ea~~L~~~~~~~---~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      +..+++..++..   ...-.++..+.+.+++...+|  .+-.
T Consensus       203 e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~G--d~R~  242 (365)
T TIGR02928       203 ELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHG--DARK  242 (365)
T ss_pred             HHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcC--CHHH
Confidence            999999988741   111233334455667777777  6543

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.40  E-value=1.1e-06  Score=81.91  Aligned_cols=160  Identities=19%  Similarity=0.085  Sum_probs=91.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccc----hhhhHHHHHHHhcCc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRN----VYDGINMLRVRLRRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~----~~~~~~~l~~~l~~k   76 (377)
                      ++|+|||+||+.++++....+.    +.......    .. ..+...+..+....-.-.++    .....+.+...+.+.
T Consensus        38 p~G~GKT~la~~ia~~~~~~~~----~~~~~~~~----~~-~~l~~~l~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~  108 (305)
T TIGR00635        38 PPGLGKTTLAHIIANEMGVNLK----ITSGPALE----KP-GDLAAILTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDF  108 (305)
T ss_pred             CCCCCHHHHHHHHHHHhCCCEE----Eeccchhc----Cc-hhHHHHHHhcccCCEEEEehHhhhCHHHHHHhhHHHhhh
Confidence            4799999999999997654321    11111111    11 12222233322111000000    112345566777777


Q ss_pred             eEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhC--CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhH
Q 040234           77 KVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH--PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEY  154 (377)
Q Consensus        77 ~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~--~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~  154 (377)
                      +..+|+|+..+..++....      .+.+-|.+||+...+....  .....+++++++.++..+++.+.+.....  .-.
T Consensus       109 ~~~~v~~~~~~~~~~~~~~------~~~~li~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~--~~~  180 (305)
T TIGR00635       109 RLDIVIGKGPSARSVRLDL------PPFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNV--EIE  180 (305)
T ss_pred             heeeeeccCccccceeecC------CCeEEEEecCCccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCC--CcC
Confidence            7778888776665554322      2244566677765443321  12456789999999999999988754322  222


Q ss_pred             HHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          155 VELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       155 ~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ++.+..|++.|+|  .|-.+..+..
T Consensus       181 ~~al~~ia~~~~G--~pR~~~~ll~  203 (305)
T TIGR00635       181 PEAALEIARRSRG--TPRIANRLLR  203 (305)
T ss_pred             HHHHHHHHHHhCC--CcchHHHHHH
Confidence            5677899999999  9966544443

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.32  E-value=5.7e-06  Score=77.97  Aligned_cols=160  Identities=19%  Similarity=0.059  Sum_probs=89.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccch----hhhHHHHHHHhcCc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNV----YDGINMLRVRLRRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~----~~~~~~l~~~l~~k   76 (377)
                      ++|+|||+||+.++++....+.    +.... ..    .....+..++..+....-.-.++.    ....+.+...+.+.
T Consensus        59 ppG~GKT~la~~ia~~l~~~~~----~~~~~-~~----~~~~~l~~~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~  129 (328)
T PRK00080         59 PPGLGKTTLANIIANEMGVNIR----ITSGP-AL----EKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDF  129 (328)
T ss_pred             CCCccHHHHHHHHHHHhCCCeE----EEecc-cc----cChHHHHHHHHhcccCCEEEEecHhhcchHHHHHHHHHHHhc
Confidence            4799999999999997654321    11111 11    111222333333221110000010    12334455666666


Q ss_pred             eEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhC--CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhH
Q 040234           77 KVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH--PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEY  154 (377)
Q Consensus        77 ~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~--~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~  154 (377)
                      +..+|+|+..+...+....      .+.+-|..|+|...+...+  .....++++++++++..+++.+.+......  -.
T Consensus       130 ~~~~~l~~~~~~~~~~~~l------~~~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~--~~  201 (328)
T PRK00080        130 RLDIMIGKGPAARSIRLDL------PPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVE--ID  201 (328)
T ss_pred             ceeeeeccCccccceeecC------CCceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCC--cC
Confidence            7777777765544333211      1234566677754432221  123568999999999999999887543322  23


Q ss_pred             HHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          155 VELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       155 ~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ++.+..|++.|+|  .|-.+..+..
T Consensus       202 ~~~~~~ia~~~~G--~pR~a~~~l~  224 (328)
T PRK00080        202 EEGALEIARRSRG--TPRIANRLLR  224 (328)
T ss_pred             HHHHHHHHHHcCC--CchHHHHHHH
Confidence            5678999999999  9965544443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.30  E-value=7e-06  Score=72.95  Aligned_cols=144  Identities=18%  Similarity=0.164  Sum_probs=82.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++..+.....+++. +....       .-...+                      ...+.. .-+|
T Consensus        46 ~~G~GKT~la~~~~~~~~~~~~~~~~i~-~~~~~-------~~~~~~----------------------~~~~~~-~~lL   94 (226)
T TIGR03420        46 ESGSGKSHLLQAACAAAEERGKSAIYLP-LAELA-------QADPEV----------------------LEGLEQ-ADLV   94 (226)
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCcEEEEe-HHHHH-------HhHHHH----------------------Hhhccc-CCEE
Confidence            3799999999999986654433334443 32221       000011                      111122 2389


Q ss_pred             EEeCCCChh---h-hhHhhCCCCC-CCCCCeEEEEecchh---------HHhhCCCCCeeecCCCChhhhHHHHHHHhcC
Q 040234           81 VIDDAAHPD---H-LRRLVGEPDW-FGPGSRIIITTRNEH---------LLKLHPVKKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        81 VLDdv~~~~---~-~~~l~~~l~~-~~~gs~IIvTTR~~~---------v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      ||||++...   . .+.+...+.. ...+..+|+||+...         +.........+++.++++++...++...+..
T Consensus        95 vIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~  174 (226)
T TIGR03420        95 CLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAAR  174 (226)
T ss_pred             EEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHHH
Confidence            999997532   2 2223222111 023347888887532         2222333467899999999999998876532


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ...  +-.++..+.|++.++|  .+..+..+..
T Consensus       175 ~~~--~~~~~~l~~L~~~~~g--n~r~L~~~l~  203 (226)
T TIGR03420       175 RGL--QLPDEVADYLLRHGSR--DMGSLMALLD  203 (226)
T ss_pred             cCC--CCCHHHHHHHHHhccC--CHHHHHHHHH
Confidence            211  1224667888889999  8888775544

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.24  E-value=1.2e-05  Score=81.49  Aligned_cols=167  Identities=16%  Similarity=0.139  Sum_probs=104.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCc------------cchhhhHHH
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNI------------RNVYDGINM   68 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~------------~~~~~~~~~   68 (377)
                      ++|.|||||+.+++... ..=..+.|+. +.+...   ++.+....++.++....+...            .+.......
T Consensus        45 PAGfGKttl~aq~~~~~-~~~~~v~Wls-lde~dn---dp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~  119 (894)
T COG2909          45 PAGFGKTTLLAQWRELA-ADGAAVAWLS-LDESDN---DPARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSS  119 (894)
T ss_pred             CCCCcHHHHHHHHHHhc-CcccceeEee-cCCccC---CHHHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHH
Confidence            58999999999998833 3335678887 443321   778888888888753322111            122233444


Q ss_pred             HHHHhc--CceEEEEEeCC---CCh---hhhhHhhCCCCCCCCCCeEEEEecchhH---HhhCCCCCeeecC----CCCh
Q 040234           69 LRVRLR--RKKVLVVIDDA---AHP---DHLRRLVGEPDWFGPGSRIIITTRNEHL---LKLHPVKKVYKLE----ALTY  133 (377)
Q Consensus        69 l~~~l~--~k~~LLVLDdv---~~~---~~~~~l~~~l~~~~~gs~IIvTTR~~~v---~~~~~~~~~~~l~----~L~~  133 (377)
                      +...+.  .++.+|||||.   .++   +.++.++...   .++-.+|||||++.-   +...-....++++    .++.
T Consensus       120 L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~---P~~l~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~  196 (894)
T COG2909         120 LLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHA---PENLTLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDT  196 (894)
T ss_pred             HHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhC---CCCeEEEEEeccCCCCcccceeehhhHHhcChHhhcCCh
Confidence            444444  36899999995   343   3355555443   457789999998632   1111112333333    4889


Q ss_pred             hhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhh
Q 040234          134 DEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTV  182 (377)
Q Consensus       134 ~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~  182 (377)
                      +|+.++|....+..-     ....++.|.+..+|  -+-|+..++-.+.
T Consensus       197 eE~~~fl~~~~~l~L-----d~~~~~~L~~~teG--W~~al~L~aLa~~  238 (894)
T COG2909         197 EEAAAFLNDRGSLPL-----DAADLKALYDRTEG--WAAALQLIALALR  238 (894)
T ss_pred             HHHHHHHHHcCCCCC-----ChHHHHHHHhhccc--HHHHHHHHHHHcc
Confidence            999999987663322     24457788888888  8888776665544

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.24  E-value=1.2e-05  Score=78.13  Aligned_cols=145  Identities=23%  Similarity=0.303  Sum_probs=82.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+||||||+.+++.....|.   .+.   ....   .... ++.++.....                 ....+++.+|
T Consensus        44 ppGtGKTtLA~~ia~~~~~~~~---~l~---a~~~---~~~~-ir~ii~~~~~-----------------~~~~g~~~vL   96 (413)
T PRK13342         44 PPGTGKTTLARIIAGATDAPFE---ALS---AVTS---GVKD-LREVIEEARQ-----------------RRSAGRRTIL   96 (413)
T ss_pred             CCCCCHHHHHHHHHHHhCCCEE---EEe---cccc---cHHH-HHHHHHHHHH-----------------hhhcCCceEE
Confidence            4799999999999987654432   111   1110   2111 1222221100                 0114577899


Q ss_pred             EEeCCCC--hhhhhHhhCCCCCCCCCCeEEE--Eecchh--HH-hhCCCCCeeecCCCChhhhHHHHHHHhcCCCCCc-h
Q 040234           81 VIDDAAH--PDHLRRLVGEPDWFGPGSRIII--TTRNEH--LL-KLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPL-E  152 (377)
Q Consensus        81 VLDdv~~--~~~~~~l~~~l~~~~~gs~IIv--TTR~~~--v~-~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~-~  152 (377)
                      +||+++.  ..+.+.|+..+.   .+..+++  ||.+..  +. ...+....+.+.+++.++..+++.+.+....... .
T Consensus        97 ~IDEi~~l~~~~q~~LL~~le---~~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~  173 (413)
T PRK13342         97 FIDEIHRFNKAQQDALLPHVE---DGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVE  173 (413)
T ss_pred             EEechhhhCHHHHHHHHHHhh---cCcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCCCC
Confidence            9999986  345556655543   2444444  344432  11 1113346789999999999999988653211111 2


Q ss_pred             hHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          153 EYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       153 ~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      ...+..+.|++.++|  .+..+...
T Consensus       174 i~~~al~~l~~~s~G--d~R~aln~  196 (413)
T PRK13342        174 LDDEALDALARLANG--DARRALNL  196 (413)
T ss_pred             CCHHHHHHHHHhCCC--CHHHHHHH
Confidence            235667889999999  87665433

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

Probab=98.23  E-value=4.1e-06  Score=67.56  Aligned_cols=104  Identities=20%  Similarity=0.255  Sum_probs=68.9

Q ss_pred             CCCcHHHHHHHHHchhccc-----cccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCc
Q 040234            2 GGLGKTTLARVVYDLISHE-----FDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRK   76 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-----f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k   76 (377)
                      +|+|||+++.+++++....     -...+|+. +....    +...+...++.++...... ..+..+..+.+.+.+...
T Consensus        13 ~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~----~~~~~~~~i~~~l~~~~~~-~~~~~~l~~~~~~~l~~~   86 (131)
T PF13401_consen   13 PGSGKTTLIKRLARQLNAEAEIKNHPDVIYVN-CPSSR----TPRDFAQEILEALGLPLKS-RQTSDELRSLLIDALDRR   86 (131)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEE-HHHHS----SHHHHHHHHHHHHT-SSSS-TS-HHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHhHHhhhccCCCcEEEEE-eCCCC----CHHHHHHHHHHHhCccccc-cCCHHHHHHHHHHHHHhc
Confidence            7999999999999965443     23344555 55554    7889999999998665332 345566667777777665


Q ss_pred             e-EEEEEeCCCCh---hhhhHhhCCCCCCCCCCeEEEEecc
Q 040234           77 K-VLVVIDDAAHP---DHLRRLVGEPDWFGPGSRIIITTRN  113 (377)
Q Consensus        77 ~-~LLVLDdv~~~---~~~~~l~~~l~~~~~gs~IIvTTR~  113 (377)
                      + .+||||+++..   +.++.+.....  ..+.++|+..+.
T Consensus        87 ~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   87 RVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             TEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             CCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            4 59999999765   23444433222  556677777664

>PF13173 AAA_14: AAA domain

Probab=98.19  E-value=2.9e-06  Score=68.41  Aligned_cols=110  Identities=18%  Similarity=0.183  Sum_probs=68.0

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      -|+|||||+++++++.. .-...+++. .....       . .. ..            ..+ ..+.+.+....++.+|+
T Consensus        11 R~vGKTtll~~~~~~~~-~~~~~~yi~-~~~~~-------~-~~-~~------------~~~-~~~~~~~~~~~~~~~i~   66 (128)
T PF13173_consen   11 RGVGKTTLLKQLAKDLL-PPENILYIN-FDDPR-------D-RR-LA------------DPD-LLEYFLELIKPGKKYIF   66 (128)
T ss_pred             CCCCHHHHHHHHHHHhc-ccccceeec-cCCHH-------H-HH-Hh------------hhh-hHHHHHHhhccCCcEEE
Confidence            58999999999998665 222344443 33221       1 00 00            000 22334444444778999


Q ss_pred             EeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhh-----C-CCCCeeecCCCChhh
Q 040234           82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKL-----H-PVKKVYKLEALTYDE  135 (377)
Q Consensus        82 LDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~-----~-~~~~~~~l~~L~~~e  135 (377)
                      ||++.....|......+.+..+..+|++|+........     . +....+++.||+-.|
T Consensus        67 iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E  126 (128)
T PF13173_consen   67 IDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFRE  126 (128)
T ss_pred             EehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHH
Confidence            99998877777666665554567899999987765432     1 224567899998776

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.17  E-value=2.9e-05  Score=76.04  Aligned_cols=159  Identities=14%  Similarity=0.131  Sum_probs=96.2

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+|||+|++.+++.+....+ ..+.+.          +..++...+...+....        ...+.+++.++. .-+|
T Consensus       150 ~G~GKTHLl~Ai~~~l~~~~~~~~v~yv----------~~~~f~~~~~~~l~~~~--------~~~~~~~~~~~~-~dvL  210 (450)
T PRK14087        150 SGMGKTHLLKAAKNYIESNFSDLKVSYM----------SGDEFARKAVDILQKTH--------KEIEQFKNEICQ-NDVL  210 (450)
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCCeEEEE----------EHHHHHHHHHHHHHHhh--------hHHHHHHHHhcc-CCEE
Confidence            699999999999997654433 223232          44456666666553210        123344444443 3488


Q ss_pred             EEeCCCCh---hh-hhHhhCCCCCC-CCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcC
Q 040234           81 VIDDAAHP---DH-LRRLVGEPDWF-GPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        81 VLDdv~~~---~~-~~~l~~~l~~~-~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      ||||+...   +. .+.|...+... ..+..||+|+...         .+..++...-+.++++++.++-.+++.+++-.
T Consensus       211 iIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~  290 (450)
T PRK14087        211 IIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKN  290 (450)
T ss_pred             EEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHHh
Confidence            89999542   11 12222211111 2345788887642         33334455677889999999999999988743


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhh
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLNALMSVSYT  181 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l  181 (377)
                      ......-.++++.-|++.++|  .+-.+..+...+
T Consensus       291 ~gl~~~l~~evl~~Ia~~~~g--d~R~L~gaL~~l  323 (450)
T PRK14087        291 QNIKQEVTEEAINFISNYYSD--DVRKIKGSVSRL  323 (450)
T ss_pred             cCCCCCCCHHHHHHHHHccCC--CHHHHHHHHHHH
Confidence            221112336788999999999  888877665543

>PRK08727 hypothetical protein; Validated

Probab=98.17  E-value=1.8e-05  Score=70.80  Aligned_cols=133  Identities=18%  Similarity=0.106  Sum_probs=78.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||.|++.+++...+.....+++. ..+          ....+.+.                  + +.+ .+.-+||
T Consensus        50 ~G~GKThL~~a~~~~~~~~~~~~~y~~-~~~----------~~~~~~~~------------------~-~~l-~~~dlLi   98 (233)
T PRK08727         50 AGTGKTHLALALCAAAEQAGRSSAYLP-LQA----------AAGRLRDA------------------L-EAL-EGRSLVA   98 (233)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCcEEEEe-HHH----------hhhhHHHH------------------H-HHH-hcCCEEE
Confidence            699999999999987655544445544 211          11111110                  0 111 1234899


Q ss_pred             EeCCCCh---hhhh-HhhCCCCCC-CCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcCC
Q 040234           82 IDDAAHP---DHLR-RLVGEPDWF-GPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDT  147 (377)
Q Consensus        82 LDdv~~~---~~~~-~l~~~l~~~-~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~  147 (377)
                      |||+...   ..+. .+...+... ..+..||+||+..         .+..++.....+++++++.++-.+++.+++...
T Consensus        99 IDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~  178 (233)
T PRK08727         99 LDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRR  178 (233)
T ss_pred             EeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHHHHc
Confidence            9998642   1221 222211110 2356799999852         233333445689999999999999999877432


Q ss_pred             CCCchhHHHHHHHHHHHhCC
Q 040234          148 HKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       148 ~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .  ..-.++...-|++.++|
T Consensus       179 ~--l~l~~e~~~~La~~~~r  196 (233)
T PRK08727        179 G--LALDEAAIDWLLTHGER  196 (233)
T ss_pred             C--CCCCHHHHHHHHHhCCC
Confidence            2  12225678889999988

>PRK09087 hypothetical protein; Validated

Probab=98.17  E-value=2.4e-05  Score=69.52  Aligned_cols=95  Identities=16%  Similarity=0.080  Sum_probs=62.3

Q ss_pred             EEEEeCCCC----hhhhhHhhCCCCCCCCCCeEEEEecc---------hhHHhhCCCCCeeecCCCChhhhHHHHHHHhc
Q 040234           79 LVVIDDAAH----PDHLRRLVGEPDWFGPGSRIIITTRN---------EHLLKLHPVKKVYKLEALTYDEAFRLLCLKAF  145 (377)
Q Consensus        79 LLVLDdv~~----~~~~~~l~~~l~~~~~gs~IIvTTR~---------~~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~  145 (377)
                      +|+|||+..    .+.+-.+...+.  ..|..+|+|++.         +.+..++....++++++++.++-.+++.+++.
T Consensus        90 ~l~iDDi~~~~~~~~~lf~l~n~~~--~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~  167 (226)
T PRK09087         90 PVLIEDIDAGGFDETGLFHLINSVR--QAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFA  167 (226)
T ss_pred             eEEEECCCCCCCCHHHHHHHHHHHH--hCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHH
Confidence            788899954    223333322222  336679998873         33444456678899999999999999998884


Q ss_pred             CCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          146 DTHKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       146 ~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ...-  .-.+++..-|++.+.|  ..-++..+..
T Consensus       168 ~~~~--~l~~ev~~~La~~~~r--~~~~l~~~l~  197 (226)
T PRK09087        168 DRQL--YVDPHVVYYLVSRMER--SLFAAQTIVD  197 (226)
T ss_pred             HcCC--CCCHHHHHHHHHHhhh--hHHHHHHHHH
Confidence            4321  1225678888888888  6666654333

>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=98.10  E-value=3.3e-05  Score=68.29  Aligned_cols=150  Identities=20%  Similarity=0.200  Sum_probs=88.8

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+|||.|.+.++++..+..+ .++.+.          +..+....+...+..          ...+.++..++.- =+|
T Consensus        43 ~G~GKTHLL~Ai~~~~~~~~~~~~v~y~----------~~~~f~~~~~~~~~~----------~~~~~~~~~~~~~-DlL  101 (219)
T PF00308_consen   43 SGLGKTHLLQAIANEAQKQHPGKRVVYL----------SAEEFIREFADALRD----------GEIEEFKDRLRSA-DLL  101 (219)
T ss_dssp             TTSSHHHHHHHHHHHHHHHCTTS-EEEE----------EHHHHHHHHHHHHHT----------TSHHHHHHHHCTS-SEE
T ss_pred             CCCCHHHHHHHHHHHHHhccccccceee----------cHHHHHHHHHHHHHc----------ccchhhhhhhhcC-CEE
Confidence            699999999999997766554 334333          344555555554422          1224455555543 478


Q ss_pred             EEeCCCCh---hhhh----HhhCCCCCCCCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           81 VIDDAAHP---DHLR----RLVGEPDWFGPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        81 VLDdv~~~---~~~~----~l~~~l~~~~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      +|||+...   ..|+    .+...+.  ..|.+||+|++..         ++..++...-++++++++.++-.+++.+++
T Consensus       102 ~iDDi~~l~~~~~~q~~lf~l~n~~~--~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a  179 (219)
T PF00308_consen  102 IIDDIQFLAGKQRTQEELFHLFNRLI--ESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKA  179 (219)
T ss_dssp             EEETGGGGTTHHHHHHHHHHHHHHHH--HTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHHH
T ss_pred             EEecchhhcCchHHHHHHHHHHHHHH--hhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHH
Confidence            89999652   2121    2222211  3466899999643         333444566789999999999999999888


Q ss_pred             cCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          145 FDTHKPLEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      ....-.  -.++++.-|++.+.+  ..-.+..+-
T Consensus       180 ~~~~~~--l~~~v~~~l~~~~~~--~~r~L~~~l  209 (219)
T PF00308_consen  180 KERGIE--LPEEVIEYLARRFRR--DVRELEGAL  209 (219)
T ss_dssp             HHTT----S-HHHHHHHHHHTTS--SHHHHHHHH
T ss_pred             HHhCCC--CcHHHHHHHHHhhcC--CHHHHHHHH
Confidence            543322  235778888888888  665555443

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.08  E-value=5.5e-05  Score=65.27  Aligned_cols=88  Identities=19%  Similarity=0.152  Sum_probs=60.0

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +.+-++|+||++..  +..+.|+..+....+.+.+|++|++. .+...+ .....+++.+++.++..+.+.+. +    .
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~-g----i  169 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQ-G----I  169 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHc-C----C
Confidence            45668999999763  34556665555445566777776653 232222 23568999999999999988776 1    1


Q ss_pred             chhHHHHHHHHHHHhCCCCchh
Q 040234          151 LEEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpl  172 (377)
                      .   ++.+..|++.+||  .|.
T Consensus       170 ~---~~~~~~i~~~~~g--~~r  186 (188)
T TIGR00678       170 S---EEAAELLLALAGG--SPG  186 (188)
T ss_pred             C---HHHHHHHHHHcCC--Ccc
Confidence            1   4678899999999  764

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.01  E-value=0.0001  Score=70.33  Aligned_cols=96  Identities=15%  Similarity=0.116  Sum_probs=62.7

Q ss_pred             CceEEEEEeCCCChh--hhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHPD--HLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~~--~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++...  .++.++..+.......++|++|.+ ..+...+ +....+++.+++.++..+.+...+......
T Consensus       118 ~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~  197 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESID  197 (363)
T ss_pred             CCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            345699999998743  466666655543456666666654 3333322 335689999999999999888766432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        -.++.++.|++.++|  .|-.+
T Consensus       198 --i~~~al~~ia~~s~G--~~R~a  217 (363)
T PRK14961        198 --TDEYALKLIAYHAHG--SMRDA  217 (363)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHH
Confidence              124567889999999  77643

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.00  E-value=9.7e-05  Score=72.25  Aligned_cols=151  Identities=19%  Similarity=0.177  Sum_probs=88.4

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      +|+|||+||+.+++.+.+..+ ..+.+.          +..+++..+...+...      +    .+.+++.+..+.-+|
T Consensus       139 ~G~GKTHLl~ai~~~l~~~~~~~~v~yi----------~~~~f~~~~~~~~~~~------~----~~~f~~~~~~~~dvL  198 (440)
T PRK14088        139 VGLGKTHLLQSIGNYVVQNEPDLRVMYI----------TSEKFLNDLVDSMKEG------K----LNEFREKYRKKVDVL  198 (440)
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCCeEEEE----------EHHHHHHHHHHHHhcc------c----HHHHHHHHHhcCCEE
Confidence            799999999999998766554 334443          3334455555544211      1    123344444445689


Q ss_pred             EEeCCCCh---h----hhhHhhCCCCCCCCCCeEEEEec-chh--------HHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           81 VIDDAAHP---D----HLRRLVGEPDWFGPGSRIIITTR-NEH--------LLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        81 VLDdv~~~---~----~~~~l~~~l~~~~~gs~IIvTTR-~~~--------v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      +|||+...   .    .+-.+...+.  ..+..||+||. .+.        +..++....++++++.+.+.-.+++.+.+
T Consensus       199 lIDDi~~l~~~~~~q~elf~~~n~l~--~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~  276 (440)
T PRK14088        199 LIDDVQFLIGKTGVQTELFHTFNELH--DSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKML  276 (440)
T ss_pred             EEechhhhcCcHHHHHHHHHHHHHHH--HcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHH
Confidence            99999742   1    1212211111  23456888875 221        22223445678999999999999998887


Q ss_pred             cCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          145 FDTHKPLEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      ....-..  .++++.-|++.+.|  .--.+..+-
T Consensus       277 ~~~~~~l--~~ev~~~Ia~~~~~--~~R~L~g~l  306 (440)
T PRK14088        277 EIEHGEL--PEEVLNFVAENVDD--NLRRLRGAI  306 (440)
T ss_pred             HhcCCCC--CHHHHHHHHhcccc--CHHHHHHHH
Confidence            4322222  24677888888887  655544333

>PRK05642 DNA replication initiation factor; Validated

Probab=97.99  E-value=6.6e-05  Score=67.12  Aligned_cols=143  Identities=16%  Similarity=0.188  Sum_probs=82.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||.|++.++++..+.-..++|+. .          .++...                   ...+.+.+.+-. +||
T Consensus        54 ~G~GKTHLl~a~~~~~~~~~~~v~y~~-~----------~~~~~~-------------------~~~~~~~~~~~d-~Li  102 (234)
T PRK05642         54 DGVGRSHLLQAACLRFEQRGEPAVYLP-L----------AELLDR-------------------GPELLDNLEQYE-LVC  102 (234)
T ss_pred             CCCCHHHHHHHHHHHHHhCCCcEEEee-H----------HHHHhh-------------------hHHHHHhhhhCC-EEE
Confidence            699999999999986654423344443 2          222111                   011222222222 688


Q ss_pred             EeCCCCh---hhhhH-hhCCCCCC-CCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcCC
Q 040234           82 IDDAAHP---DHLRR-LVGEPDWF-GPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDT  147 (377)
Q Consensus        82 LDdv~~~---~~~~~-l~~~l~~~-~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~  147 (377)
                      +||+...   ..|+. +...+... ..|..+|+||+..         .+..++....++++++++.++-.+++..++...
T Consensus       103 iDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~~~  182 (234)
T PRK05642        103 LDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRASRR  182 (234)
T ss_pred             EechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHc
Confidence            9999532   23322 22222111 3466789988753         222223345778999999999999998666432


Q ss_pred             CCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          148 HKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       148 ~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      .-.  -.+++..-|++.+.|  ..-.+..+-.
T Consensus       183 ~~~--l~~ev~~~L~~~~~~--d~r~l~~~l~  210 (234)
T PRK05642        183 GLH--LTDEVGHFILTRGTR--SMSALFDLLE  210 (234)
T ss_pred             CCC--CCHHHHHHHHHhcCC--CHHHHHHHHH
Confidence            211  225788899999999  6555543333

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.95  E-value=7.2e-05  Score=74.15  Aligned_cols=96  Identities=15%  Similarity=0.093  Sum_probs=62.3

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEec-chhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTR-NEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR-~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|||+++..  +.++.|+..+..-.....+|++|. ...+...+ .....+++.+++.++..+.+.+.+-.....
T Consensus       115 ~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi~  194 (504)
T PRK14963        115 GGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGRE  194 (504)
T ss_pred             CCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            45668999999763  456666666554344555555554 33333222 335689999999999999998877433211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        ..++.+..|++.++|  .+--+
T Consensus       195 --i~~~Al~~ia~~s~G--dlR~a  214 (504)
T PRK14963        195 --AEPEALQLVARLADG--AMRDA  214 (504)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHH
Confidence              124677888888988  66544

>PLN03025 replication factor C subunit; Provisional

Probab=97.95  E-value=0.00012  Score=68.71  Aligned_cols=97  Identities=11%  Similarity=0.138  Sum_probs=58.1

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|||+++..  ...+.|...+..-...+++|+++... .+...+ .....+++++++.++..+.+...+-...-.
T Consensus        98 ~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~  177 (319)
T PLN03025         98 GRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVP  177 (319)
T ss_pred             CCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCC
Confidence            34669999999873  23333333222223456677666432 222211 224578999999999999988877432221


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                      -  .++....|++.++| ++..++
T Consensus       178 i--~~~~l~~i~~~~~g-DlR~al  198 (319)
T PLN03025        178 Y--VPEGLEAIIFTADG-DMRQAL  198 (319)
T ss_pred             C--CHHHHHHHHHHcCC-CHHHHH
Confidence            1  24567889999998 344444

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.94  E-value=0.0002  Score=70.84  Aligned_cols=95  Identities=18%  Similarity=0.190  Sum_probs=63.3

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEE-EEecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRII-ITTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~II-vTTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++.  ...++.|+..+..-.+.+.+| +||+.+.+...+ .....+++.+++.++..+.+...+......
T Consensus       127 ~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~  206 (507)
T PRK06645        127 GKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLK  206 (507)
T ss_pred             CCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCC
Confidence            4567899999987  345777766555434555555 455555554433 345679999999999999998887433221


Q ss_pred             chhHHHHHHHHHHHhCCCCchhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                        ...+.+..|++.++|  .+--
T Consensus       207 --ie~eAL~~Ia~~s~G--slR~  225 (507)
T PRK06645        207 --TDIEALRIIAYKSEG--SARD  225 (507)
T ss_pred             --CCHHHHHHHHHHcCC--CHHH
Confidence              124566778888888  6543

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.93  E-value=0.00012  Score=69.07  Aligned_cols=95  Identities=19%  Similarity=0.054  Sum_probs=57.8

Q ss_pred             ceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           76 KKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        76 k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      .+-+|||||++..  +....+...+......+++|+||... .+...+ .....+++.+++.++..+++.+.+...... 
T Consensus       125 ~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~-  203 (337)
T PRK12402        125 DYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVD-  203 (337)
T ss_pred             CCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCC-
Confidence            3458999999753  22333333222223456787777543 222222 234678899999999999998876432221 


Q ss_pred             hhHHHHHHHHHHHhCCCCchhhH
Q 040234          152 EEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lplal  174 (377)
                       -..+.++.|++.++|  .+-.+
T Consensus       204 -~~~~al~~l~~~~~g--dlr~l  223 (337)
T PRK12402        204 -YDDDGLELIAYYAGG--DLRKA  223 (337)
T ss_pred             -CCHHHHHHHHHHcCC--CHHHH
Confidence             225678888999988  55444

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.93  E-value=0.00013  Score=65.32  Aligned_cols=141  Identities=16%  Similarity=0.194  Sum_probs=81.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      +.|+|||+|++.+++.....-....++. +....       ....                  +..+.+    .. .-+|
T Consensus        53 p~G~GKThLl~a~~~~~~~~~~~v~y~~-~~~~~-------~~~~------------------~~~~~~----~~-~dll  101 (235)
T PRK08084         53 REGAGRSHLLHAACAELSQRGRAVGYVP-LDKRA-------WFVP------------------EVLEGM----EQ-LSLV  101 (235)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCeEEEEE-HHHHh-------hhhH------------------HHHHHh----hh-CCEE
Confidence            4799999999999986654422333433 22110       0000                  111111    11 1389


Q ss_pred             EEeCCCCh---hhhh----HhhCCCCCCCCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           81 VIDDAAHP---DHLR----RLVGEPDWFGPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        81 VLDdv~~~---~~~~----~l~~~l~~~~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      +|||+...   .+|+    .+...... ..+.++|+||+..         .+..++....++++.+++.++-.+++.+++
T Consensus       102 iiDdi~~~~~~~~~~~~lf~l~n~~~e-~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a  180 (235)
T PRK08084        102 CIDNIECIAGDELWEMAIFDLYNRILE-SGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRA  180 (235)
T ss_pred             EEeChhhhcCCHHHHHHHHHHHHHHHH-cCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHH
Confidence            99999652   2332    12111111 1224799998754         344445556789999999999999998766


Q ss_pred             cCCCCCchhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          145 FDTHKPLEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      ....  ..-.++...-|++.+.|  ..-++..+
T Consensus       181 ~~~~--~~l~~~v~~~L~~~~~~--d~r~l~~~  209 (235)
T PRK08084        181 RLRG--FELPEDVGRFLLKRLDR--EMRTLFMT  209 (235)
T ss_pred             HHcC--CCCCHHHHHHHHHhhcC--CHHHHHHH
Confidence            4322  22235788899999998  55555433

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=0.00014  Score=72.83  Aligned_cols=98  Identities=11%  Similarity=0.038  Sum_probs=64.9

Q ss_pred             cCceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEE-EecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCC
Q 040234           74 RRKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIII-TTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHK  149 (377)
Q Consensus        74 ~~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIv-TTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~  149 (377)
                      .++.-++|||+++.  ...++.|+..+..-..+.++|+ ||....+...+ +....+.+..++.++..+.+.+.+.....
T Consensus       122 ~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi  201 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGI  201 (700)
T ss_pred             cCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCC
Confidence            34566999999986  4567777776654345566555 45444444332 33577899999999999988877643221


Q ss_pred             CchhHHHHHHHHHHHhCCCCchhhHH
Q 040234          150 PLEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       150 ~~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      .  ...+..+.|++.++|  .+....
T Consensus       202 ~--~d~eAL~~IA~~A~G--s~RdAL  223 (700)
T PRK12323        202 A--HEVNALRLLAQAAQG--SMRDAL  223 (700)
T ss_pred             C--CCHHHHHHHHHHcCC--CHHHHH
Confidence            1  124566788999999  876443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.91  E-value=0.00011  Score=74.70  Aligned_cols=99  Identities=8%  Similarity=0.001  Sum_probs=64.4

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|||+++..  ..++.|+..+..-....++|+||++. .+... .+....+.++.++.++..+.|.+......- 
T Consensus       118 gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI-  196 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERI-  196 (830)
T ss_pred             CCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCC-
Confidence            34558999999874  44676766554435577877777664 33222 234678999999999999999887643321 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALM  176 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~  176 (377)
                       ....+..+.|++.++| .+.-++.+
T Consensus       197 -~id~eAL~lIA~~A~G-smRdALsL  220 (830)
T PRK07003        197 -AFEPQALRLLARAAQG-SMRDALSL  220 (830)
T ss_pred             -CCCHHHHHHHHHHcCC-CHHHHHHH
Confidence             1224667788888877 13344443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.91  E-value=0.00013  Score=75.41  Aligned_cols=97  Identities=16%  Similarity=0.095  Sum_probs=63.9

Q ss_pred             cCceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEe-cchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCC
Q 040234           74 RRKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITT-RNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHK  149 (377)
Q Consensus        74 ~~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~  149 (377)
                      .+++-++|||++..  .+..+.|+..+..-....++|++| ....+... ......+++.+|+.++..+.+.+.+.... 
T Consensus       117 ~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~Eg-  195 (944)
T PRK14949        117 RGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQ-  195 (944)
T ss_pred             cCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcC-
Confidence            35667999999976  456677666654434456665554 44444322 23457899999999999999888764321 


Q ss_pred             CchhHHHHHHHHHHHhCCCCchhhH
Q 040234          150 PLEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       150 ~~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                       .....+.+..|++.++|  .+--+
T Consensus       196 -I~~edeAL~lIA~~S~G--d~R~A  217 (944)
T PRK14949        196 -LPFEAEALTLLAKAANG--SMRDA  217 (944)
T ss_pred             -CCCCHHHHHHHHHHcCC--CHHHH
Confidence             12224667888888888  77533

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.90  E-value=0.00017  Score=70.01  Aligned_cols=152  Identities=17%  Similarity=0.170  Sum_probs=87.1

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+|||.|++.+++++.++.+ ..+.+.          +...+...+...+...      .    .+.+++.+++ .-+|
T Consensus       145 ~G~GKThL~~ai~~~l~~~~~~~~v~yi----------~~~~~~~~~~~~~~~~------~----~~~~~~~~~~-~dlL  203 (405)
T TIGR00362       145 VGLGKTHLLHAIGNEILENNPNAKVVYV----------SSEKFTNDFVNALRNN------K----MEEFKEKYRS-VDLL  203 (405)
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCCcEEEE----------EHHHHHHHHHHHHHcC------C----HHHHHHHHHh-CCEE
Confidence            799999999999998766543 223222          2233444444443211      1    2233344433 3488


Q ss_pred             EEeCCCChh---h-hhHhhCCCCCC-CCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcC
Q 040234           81 VIDDAAHPD---H-LRRLVGEPDWF-GPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        81 VLDdv~~~~---~-~~~l~~~l~~~-~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      ||||+....   . .+.+...+... ..+..+|+||...         .+..++.....+++++.+.++-.+++.+++..
T Consensus       204 iiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~  283 (405)
T TIGR00362       204 LIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKAEE  283 (405)
T ss_pred             EEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHH
Confidence            999996421   1 11122111110 2345688887642         12222333457899999999999999988854


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      .....  .+++..-|++.+.|  ..-.+..+-
T Consensus       284 ~~~~l--~~e~l~~ia~~~~~--~~r~l~~~l  311 (405)
T TIGR00362       284 EGLEL--PDEVLEFIAKNIRS--NVRELEGAL  311 (405)
T ss_pred             cCCCC--CHHHHHHHHHhcCC--CHHHHHHHH
Confidence            32222  25677888888888  666554433

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).

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.88  E-value=0.00017  Score=71.87  Aligned_cols=95  Identities=11%  Similarity=0.010  Sum_probs=59.9

Q ss_pred             cCceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEE-EEecchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCC
Q 040234           74 RRKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRII-ITTRNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHK  149 (377)
Q Consensus        74 ~~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~II-vTTR~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~  149 (377)
                      .+++-++|+|+++.  ....+.|+..+..-.....+| +||....+... ......+++.+++.++..+.+.+.+.... 
T Consensus       117 ~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~eg-  195 (546)
T PRK14957        117 QGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKEN-  195 (546)
T ss_pred             cCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcC-
Confidence            34566999999975  345666666555434455555 45554444433 23467899999999999888877553221 


Q ss_pred             CchhHHHHHHHHHHHhCCCCchh
Q 040234          150 PLEEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       150 ~~~~~~~~~~~I~~~c~G~~lpl  172 (377)
                       ....++....|++.++|  .+-
T Consensus       196 -i~~e~~Al~~Ia~~s~G--dlR  215 (546)
T PRK14957        196 -INSDEQSLEYIAYHAKG--SLR  215 (546)
T ss_pred             -CCCCHHHHHHHHHHcCC--CHH
Confidence             11224556778888887  554

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.86  E-value=0.00067  Score=63.50  Aligned_cols=94  Identities=17%  Similarity=0.135  Sum_probs=64.1

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchhH-HhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEHL-LKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~v-~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++.  .+.++.|+..+..-.+++.+|++|.+... ...+ +....+++.++++++....+.+....   .
T Consensus        92 ~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~~---~  168 (313)
T PRK05564         92 GDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYKYND---I  168 (313)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHHhcC---C
Confidence            3455677777654  56688888877765678888888876532 2221 33678999999999998888765421   1


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALM  176 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~  176 (377)
                      .   .+.++.++..++|  .|..+..
T Consensus       169 ~---~~~~~~l~~~~~g--~~~~a~~  189 (313)
T PRK05564        169 K---EEEKKSAIAFSDG--IPGKVEK  189 (313)
T ss_pred             C---HHHHHHHHHHcCC--CHHHHHH
Confidence            1   3446788999999  9976543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.86  E-value=0.00024  Score=71.38  Aligned_cols=95  Identities=12%  Similarity=0.033  Sum_probs=61.6

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|||++...  ...+.|+..+..-..+.++|++|.+. .+... ......+++++|+.++..+.+.+.+..... 
T Consensus       117 gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI-  195 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQI-  195 (702)
T ss_pred             CCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCC-
Confidence            45668999999863  45666665554434566777776653 23211 244678999999999999998877643221 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                       ....+....|++.++|  .+-.
T Consensus       196 -~id~eAL~~IA~~S~G--dLRd  215 (702)
T PRK14960        196 -AADQDAIWQIAESAQG--SLRD  215 (702)
T ss_pred             -CCCHHHHHHHHHHcCC--CHHH
Confidence             1224566778888887  5543

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.86  E-value=0.00018  Score=70.89  Aligned_cols=150  Identities=15%  Similarity=0.154  Sum_probs=88.6

Q ss_pred             CCCcHHHHHHHHHchhcccccc-ceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDG-SSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~-~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+|||+||+.+++++.++++. .+.+.          +...+...+...+...      .    .+.+++.++. .-+|
T Consensus       157 ~G~GKThL~~ai~~~~~~~~~~~~v~yi----------~~~~~~~~~~~~~~~~------~----~~~~~~~~~~-~dlL  215 (450)
T PRK00149        157 VGLGKTHLLHAIGNYILEKNPNAKVVYV----------TSEKFTNDFVNALRNN------T----MEEFKEKYRS-VDVL  215 (450)
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCCeEEEE----------EHHHHHHHHHHHHHcC------c----HHHHHHHHhc-CCEE
Confidence            7999999999999988776643 23222          2334444444443211      1    2333444442 4489


Q ss_pred             EEeCCCCh---h-hhhHhhC---CCCCCCCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           81 VIDDAAHP---D-HLRRLVG---EPDWFGPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        81 VLDdv~~~---~-~~~~l~~---~l~~~~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      ||||+...   + ..+.+..   .+.  ..+..||+||...         .+..++.....+++++.+.++-.+++.+++
T Consensus       216 iiDDi~~l~~~~~~~~~l~~~~n~l~--~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~  293 (450)
T PRK00149        216 LIDDIQFLAGKERTQEEFFHTFNALH--EAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKKA  293 (450)
T ss_pred             EEehhhhhcCCHHHHHHHHHHHHHHH--HCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHHH
Confidence            99999642   1 1112222   111  2344588887643         123334445678999999999999999988


Q ss_pred             cCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          145 FDTHKPLEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      ......  -.+++..-|++.++|  ..-.+..+-
T Consensus       294 ~~~~~~--l~~e~l~~ia~~~~~--~~R~l~~~l  323 (450)
T PRK00149        294 EEEGID--LPDEVLEFIAKNITS--NVRELEGAL  323 (450)
T ss_pred             HHcCCC--CCHHHHHHHHcCcCC--CHHHHHHHH
Confidence            542211  225678888888888  666554333

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.85  E-value=0.00088  Score=63.80  Aligned_cols=96  Identities=15%  Similarity=0.114  Sum_probs=63.7

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++.  .+..+.|+..+..-..++.+|++|.+. .+... .+....+.+.+++.++..+++.+.....   
T Consensus       140 ~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~~---  216 (365)
T PRK07471        140 GGWRVVIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPDL---  216 (365)
T ss_pred             CCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcccC---
Confidence            4567999999976  344555555444324566677777665 33322 2446789999999999999998764211   


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      .   .+....+++.++|  .|+....+.
T Consensus       217 ~---~~~~~~l~~~s~G--sp~~Al~ll  239 (365)
T PRK07471        217 P---DDPRAALAALAEG--SVGRALRLA  239 (365)
T ss_pred             C---HHHHHHHHHHcCC--CHHHHHHHh
Confidence            1   1223688999999  998665544

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=0.00032  Score=68.98  Aligned_cols=101  Identities=12%  Similarity=-0.008  Sum_probs=61.5

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|++...  ++.+.|+..+....+...+|++|.+ ..+...+ .....+++.+++.++....+.+.+......
T Consensus       116 ~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~  195 (472)
T PRK14962        116 GKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIE  195 (472)
T ss_pred             CCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCCC
Confidence            45669999999753  3455565555432334444444433 3343332 345788999999999999888877432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                        -.++....|++.++| .++.++..+-
T Consensus       196 --i~~eal~~Ia~~s~G-dlR~aln~Le  220 (472)
T PRK14962        196 --IDREALSFIAKRASG-GLRDALTMLE  220 (472)
T ss_pred             --CCHHHHHHHHHHhCC-CHHHHHHHHH
Confidence              124567788887765 2566655443

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.84  E-value=0.00036  Score=67.02  Aligned_cols=94  Identities=16%  Similarity=0.064  Sum_probs=60.8

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  ...+.|+..+..-.++..+|++|.+ ..+...+ +....+.+.+++.++..+.+.+..+.    
T Consensus       116 ~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~~----  191 (394)
T PRK07940        116 GRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDGV----  191 (394)
T ss_pred             CCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcCC----
Confidence            34558888999863  3445555544433456666666555 3444332 34678999999999999888754311    


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      .   .+.+..+++.++|  .|......
T Consensus       192 ~---~~~a~~la~~s~G--~~~~A~~l  213 (394)
T PRK07940        192 D---PETARRAARASQG--HIGRARRL  213 (394)
T ss_pred             C---HHHHHHHHHHcCC--CHHHHHHH
Confidence            1   3557889999999  88755433

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.79  E-value=0.00055  Score=66.96  Aligned_cols=143  Identities=15%  Similarity=0.094  Sum_probs=79.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ..|+|||+|++.+++.+.......+++.           ...+...+...+...          ..+.+++.++. .-+|
T Consensus       149 ~~G~GKTHLl~Ai~~~l~~~~~~v~yi~-----------~~~f~~~~~~~l~~~----------~~~~f~~~~~~-~dvL  206 (445)
T PRK12422        149 PEGSGKTHLMQAAVHALRESGGKILYVR-----------SELFTEHLVSAIRSG----------EMQRFRQFYRN-VDAL  206 (445)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCEEEee-----------HHHHHHHHHHHHhcc----------hHHHHHHHccc-CCEE
Confidence            3799999999999997755422333332           233334444443211          12334444443 3488


Q ss_pred             EEeCCCChh----hhhHhhCCCCCC-CCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcC
Q 040234           81 VIDDAAHPD----HLRRLVGEPDWF-GPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        81 VLDdv~~~~----~~~~l~~~l~~~-~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      +|||+....    ..+.+...+... ..|..||+||...         .+..++.....+++.+++.++-.+++.+++-.
T Consensus       207 iIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~~  286 (445)
T PRK12422        207 FIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAEA  286 (445)
T ss_pred             EEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHHH
Confidence            889985421    111221111100 2345788888542         22333444578899999999999999888744


Q ss_pred             CCCCchhHHHHHHHHHHHhCC
Q 040234          147 THKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ..-..  .+++..-|++...+
T Consensus       287 ~~~~l--~~evl~~la~~~~~  305 (445)
T PRK12422        287 LSIRI--EETALDFLIEALSS  305 (445)
T ss_pred             cCCCC--CHHHHHHHHHhcCC
Confidence            32111  13455556666655

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.78  E-value=0.00016  Score=70.44  Aligned_cols=95  Identities=9%  Similarity=-0.088  Sum_probs=61.5

Q ss_pred             cCceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEE-EEecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCC
Q 040234           74 RRKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRII-ITTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHK  149 (377)
Q Consensus        74 ~~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~II-vTTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~  149 (377)
                      .++.-++|||++..  .+.++.|+..+..-.....+| .||....+...+ +....+.+.+++.++..+.+.+.+.....
T Consensus       119 ~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi  198 (484)
T PRK14956        119 GGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIENV  198 (484)
T ss_pred             cCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcCC
Confidence            34566999999976  456777776665433444544 455444443332 34567999999999999888877643221


Q ss_pred             CchhHHHHHHHHHHHhCCCCchh
Q 040234          150 PLEEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       150 ~~~~~~~~~~~I~~~c~G~~lpl  172 (377)
                        .-.++....|++.++|  .+-
T Consensus       199 --~~e~eAL~~Ia~~S~G--d~R  217 (484)
T PRK14956        199 --QYDQEGLFWIAKKGDG--SVR  217 (484)
T ss_pred             --CCCHHHHHHHHHHcCC--hHH
Confidence              1124567788888888  653

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.77  E-value=0.0014  Score=62.08  Aligned_cols=99  Identities=17%  Similarity=0.140  Sum_probs=62.7

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEe-cchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITT-RNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  ...+.|+..+..-..+..+|++| +...+...+ +....+++.+++.++..+++.+... ... 
T Consensus       140 g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~-~~~-  217 (351)
T PRK09112        140 GNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGS-SQG-  217 (351)
T ss_pred             CCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhc-ccC-
Confidence            45669999999863  34455554443323445545444 433333222 3357899999999999999987431 111 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                        ..++.+..|++.++|  .|.....+..
T Consensus       218 --~~~~~~~~i~~~s~G--~pr~Al~ll~  242 (351)
T PRK09112        218 --SDGEITEALLQRSKG--SVRKALLLLN  242 (351)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHHHHHHh
Confidence              124457789999999  9987655443

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.77  E-value=0.0015  Score=61.29  Aligned_cols=94  Identities=13%  Similarity=0.087  Sum_probs=61.8

Q ss_pred             ceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           76 KKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        76 k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      ++-++|+|+++.  .+..+.|+..+..-..++.+|+||.+. .+...+ +....+.+.+++.+++.+.+.......    
T Consensus       106 ~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~~~----  181 (328)
T PRK05707        106 GRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALPES----  181 (328)
T ss_pred             CCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhcccC----
Confidence            344567899986  445566665554434567777777765 333332 346779999999999999887654111    


Q ss_pred             hhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          152 EEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                        ..+.+..+++.++|  .|+.....
T Consensus       182 --~~~~~~~~l~la~G--sp~~A~~l  203 (328)
T PRK05707        182 --DERERIELLTLAGG--SPLRALQL  203 (328)
T ss_pred             --ChHHHHHHHHHcCC--CHHHHHHH
Confidence              13445678899999  99865544

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

Probab=97.75  E-value=0.00018  Score=74.25  Aligned_cols=90  Identities=19%  Similarity=0.277  Sum_probs=53.5

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEE--Eecchh--HHhh-CCCCCeeecCCCChhhhHHHHHHHhcC-
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIII--TTRNEH--LLKL-HPVKKVYKLEALTYDEAFRLLCLKAFD-  146 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIv--TTR~~~--v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~-  146 (377)
                      +++.+|+||+++.  ..+.+.|++.+.   .+..+++  ||.+..  +... .+....+.+++|+.++...++.+.+.. 
T Consensus       108 ~~~~IL~IDEIh~Ln~~qQdaLL~~lE---~g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~  184 (725)
T PRK13341        108 GKRTILFIDEVHRFNKAQQDALLPWVE---NGTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDK  184 (725)
T ss_pred             CCceEEEEeChhhCCHHHHHHHHHHhc---CceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHH
Confidence            4567999999975  455666665542   3444554  344431  2111 123567899999999999999876631 


Q ss_pred             ----CCCCchhHHHHHHHHHHHhCC
Q 040234          147 ----THKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       147 ----~~~~~~~~~~~~~~I~~~c~G  167 (377)
                          ......-.++..+.|++.++|
T Consensus       185 ~~~~g~~~v~I~deaL~~La~~s~G  209 (725)
T PRK13341        185 ERGYGDRKVDLEPEAEKHLVDVANG  209 (725)
T ss_pred             HhhcCCcccCCCHHHHHHHHHhCCC
Confidence                011111224556667777766

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.73  E-value=0.00067  Score=68.01  Aligned_cols=149  Identities=13%  Similarity=0.134  Sum_probs=87.9

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+|||.|++.+++.....++ ..+.+.          ...++...+...+...          ..+.+++.+.+- =||
T Consensus       323 sGsGKTHLL~AIa~~a~~~~~g~~V~Yi----------taeef~~el~~al~~~----------~~~~f~~~y~~~-DLL  381 (617)
T PRK14086        323 SGLGKTHLLHAIGHYARRLYPGTRVRYV----------SSEEFTNEFINSIRDG----------KGDSFRRRYREM-DIL  381 (617)
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCCeEEEe----------eHHHHHHHHHHHHHhc----------cHHHHHHHhhcC-CEE
Confidence            699999999999997765443 233333          3444444554443211          123344444433 478


Q ss_pred             EEeCCCCh---hh----hhHhhCCCCCCCCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           81 VIDDAAHP---DH----LRRLVGEPDWFGPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        81 VLDdv~~~---~~----~~~l~~~l~~~~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      ||||+...   +.    +-.+...+.  ..+..||+||+..         .+..++...-++++.+.+.+.-.++|.+++
T Consensus       382 lIDDIq~l~gke~tqeeLF~l~N~l~--e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka  459 (617)
T PRK14086        382 LVDDIQFLEDKESTQEEFFHTFNTLH--NANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKA  459 (617)
T ss_pred             EEehhccccCCHHHHHHHHHHHHHHH--hcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHH
Confidence            89998642   21    222222222  2355688888752         334445567788999999999999999887


Q ss_pred             cCCCCCchhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          145 FDTHKPLEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      ....-..  .++++.-|++.+.+  ..-.|..+
T Consensus       460 ~~r~l~l--~~eVi~yLa~r~~r--nvR~Lega  488 (617)
T PRK14086        460 VQEQLNA--PPEVLEFIASRISR--NIRELEGA  488 (617)
T ss_pred             HhcCCCC--CHHHHHHHHHhccC--CHHHHHHH
Confidence            4432222  24667777777776  54444433

>PRK04195 replication factor C large subunit; Provisional

Probab=97.71  E-value=0.0003  Score=69.87  Aligned_cols=146  Identities=11%  Similarity=0.065  Sum_probs=80.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+||||+|+.+++++.  ++. +-+. .+..     .....+..++.......               .....++-+|
T Consensus        47 ppG~GKTtla~ala~el~--~~~-ieln-asd~-----r~~~~i~~~i~~~~~~~---------------sl~~~~~kvI  102 (482)
T PRK04195         47 PPGVGKTSLAHALANDYG--WEV-IELN-ASDQ-----RTADVIERVAGEAATSG---------------SLFGARRKLI  102 (482)
T ss_pred             CCCCCHHHHHHHHHHHcC--CCE-EEEc-cccc-----ccHHHHHHHHHHhhccC---------------cccCCCCeEE
Confidence            479999999999999763  211 1111 2221     11223333332221110               0111356799


Q ss_pred             EEeCCCChh------hhhHhhCCCCCCCCCCeEEEEecchh-HHh-h-CCCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           81 VIDDAAHPD------HLRRLVGEPDWFGPGSRIIITTRNEH-LLK-L-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        81 VLDdv~~~~------~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~-~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      |||+++...      .+..+...+.  ..+..||+|+.+.. ... . ......+++.+++.++....+...+.......
T Consensus       103 iIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i  180 (482)
T PRK04195        103 LLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIEC  180 (482)
T ss_pred             EEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcCCCC
Confidence            999997632      2444443333  23345666664421 111 1 13356789999999999998887764332221


Q ss_pred             hhHHHHHHHHHHHhCCCCchhhHH
Q 040234          152 EEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                        ..++...|++.++| ++-.++.
T Consensus       181 --~~eaL~~Ia~~s~G-DlR~ain  201 (482)
T PRK04195        181 --DDEALKEIAERSGG-DLRSAIN  201 (482)
T ss_pred             --CHHHHHHHHHHcCC-CHHHHHH
Confidence              24678889999988 2333443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.71  E-value=0.00035  Score=62.10  Aligned_cols=100  Identities=14%  Similarity=0.111  Sum_probs=58.0

Q ss_pred             eEEEEEeCCCCh--hhhhHhhCCCCCC-CCCC-eEEEEecchhHH--------hhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           77 KVLVVIDDAAHP--DHLRRLVGEPDWF-GPGS-RIIITTRNEHLL--------KLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        77 ~~LLVLDdv~~~--~~~~~l~~~l~~~-~~gs-~IIvTTR~~~v~--------~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      .-+||+||++..  .....+...+... ..+. .+|+|++.....        ..+.....+++++|++++-..++.+.+
T Consensus        91 ~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~  170 (227)
T PRK08903         91 AELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAA  170 (227)
T ss_pred             CCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHH
Confidence            347899999653  2222222222110 1233 366666643211        122334688999999988777776654


Q ss_pred             cCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhh
Q 040234          145 FDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSY  180 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~  180 (377)
                      ....  ..-.++..+.|++...|  .+..+..+...
T Consensus       171 ~~~~--v~l~~~al~~L~~~~~g--n~~~l~~~l~~  202 (227)
T PRK08903        171 AERG--LQLADEVPDYLLTHFRR--DMPSLMALLDA  202 (227)
T ss_pred             HHcC--CCCCHHHHHHHHHhccC--CHHHHHHHHHH
Confidence            2221  11225678889999999  88888765554

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.70  E-value=0.00062  Score=66.96  Aligned_cols=95  Identities=15%  Similarity=0.095  Sum_probs=62.0

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEe-cchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITT-RNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|+|++..  .+.++.|+..+..-.+..++|++| ..+.+...+ .....+++.+++.++..+.+.+.+......
T Consensus       115 ~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~  194 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIE  194 (491)
T ss_pred             CCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCC
Confidence            4556899999975  344666665554434566666555 444444332 346778999999999999988877443221


Q ss_pred             chhHHHHHHHHHHHhCCCCchhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                        -.++.+..|++.++|  .+..
T Consensus       195 --i~~eAL~lIa~~s~G--slR~  213 (491)
T PRK14964        195 --HDEESLKLIAENSSG--SMRN  213 (491)
T ss_pred             --CCHHHHHHHHHHcCC--CHHH
Confidence              224567788888888  6653

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=97.69  E-value=0.00061  Score=70.17  Aligned_cols=168  Identities=14%  Similarity=0.089  Sum_probs=88.6

Q ss_pred             CCCCcHHHHHHHHHchhccc-----cc--cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh
Q 040234            1 MGGLGKTTLARVVYDLISHE-----FD--GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-----f~--~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l   73 (377)
                      ++|.|||++++.|.+++.+.     .+  ..+++. .....    ....+...|..++.+..........+..+.+...+
T Consensus       789 ~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYIN-Cm~Ls----tp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L  863 (1164)
T PTZ00112        789 MPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEIN-GMNVV----HPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQN  863 (1164)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEe-CCccC----CHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhh
Confidence            47999999999999865432     22  123444 33322    56677888888875443222222233444444443


Q ss_pred             c---CceEEEEEeCCCChh-----hhhHhhCCCCCCCCCCeEEE--Eecch--------hHHhhCCCCCeeecCCCChhh
Q 040234           74 R---RKKVLVVIDDAAHPD-----HLRRLVGEPDWFGPGSRIII--TTRNE--------HLLKLHPVKKVYKLEALTYDE  135 (377)
Q Consensus        74 ~---~k~~LLVLDdv~~~~-----~~~~l~~~l~~~~~gs~IIv--TTR~~--------~v~~~~~~~~~~~l~~L~~~e  135 (377)
                      .   ....+||||+++...     .+-.|.....  ..+++|+|  +|..-        .+...+. ...+...|++.++
T Consensus       864 ~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~--~s~SKLiLIGISNdlDLperLdPRLRSRLg-~eeIvF~PYTaEQ  940 (1164)
T PTZ00112        864 KKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPT--KINSKLVLIAISNTMDLPERLIPRCRSRLA-FGRLVFSPYKGDE  940 (1164)
T ss_pred             hcccccceEEEeehHhhhCccHHHHHHHHHHHhh--ccCCeEEEEEecCchhcchhhhhhhhhccc-cccccCCCCCHHH
Confidence            2   224589999997532     2222222111  23455444  34321        1112222 2346679999999


Q ss_pred             hHHHHHHHhcCCCC--CchhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          136 AFRLLCLKAFDTHK--PLEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       136 a~~L~~~~~~~~~~--~~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      -.+++..++.....  ....++-+|+.++..-|-  .-.||.++-
T Consensus       941 L~dILk~RAe~A~gVLdDdAIELIArkVAq~SGD--ARKALDILR  983 (1164)
T PTZ00112        941 IEKIIKERLENCKEIIDHTAIQLCARKVANVSGD--IRKALQICR  983 (1164)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCH--HHHHHHHHH
Confidence            99999998853221  222333333433333344  666665443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.69  E-value=0.00039  Score=70.47  Aligned_cols=97  Identities=14%  Similarity=0.060  Sum_probs=62.0

Q ss_pred             cCceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEE-EecchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCC
Q 040234           74 RRKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIII-TTRNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHK  149 (377)
Q Consensus        74 ~~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIv-TTR~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~  149 (377)
                      .++.-++|||++..  .+..+.|+..+..-....++|+ ||....+... .+....+.+.+|+.++..+.+.+.......
T Consensus       117 ~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i  196 (647)
T PRK07994        117 RGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQI  196 (647)
T ss_pred             cCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcCC
Confidence            35667999999976  4456666655544344555555 4444444332 233678999999999999998876632211


Q ss_pred             CchhHHHHHHHHHHHhCCCCchhhH
Q 040234          150 PLEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       150 ~~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        ....+....|++.++|  .+-.+
T Consensus       197 --~~e~~aL~~Ia~~s~G--s~R~A  217 (647)
T PRK07994        197 --PFEPRALQLLARAADG--SMRDA  217 (647)
T ss_pred             --CCCHHHHHHHHHHcCC--CHHHH
Confidence              1124566778888888  76643

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

Probab=97.67  E-value=0.00053  Score=63.36  Aligned_cols=141  Identities=19%  Similarity=0.273  Sum_probs=85.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+||||||+.++..-+.+-  ..|+. ++...    .-..-.+.++++...                ...+..||.+|
T Consensus       170 ppG~GKTtlArlia~tsk~~S--yrfve-lSAt~----a~t~dvR~ife~aq~----------------~~~l~krkTil  226 (554)
T KOG2028|consen  170 PPGTGKTTLARLIASTSKKHS--YRFVE-LSATN----AKTNDVRDIFEQAQN----------------EKSLTKRKTIL  226 (554)
T ss_pred             CCCCchHHHHHHHHhhcCCCc--eEEEE-Eeccc----cchHHHHHHHHHHHH----------------HHhhhcceeEE
Confidence            479999999999999666552  23333 33332    122223333333111                12346788999


Q ss_pred             EEeCCCC--hhhhhHhhCCCCCCCCCCeEEE--EecchhH---HhhCCCCCeeecCCCChhhhHHHHHHHhc---CCCC-
Q 040234           81 VIDDAAH--PDHLRRLVGEPDWFGPGSRIII--TTRNEHL---LKLHPVKKVYKLEALTYDEAFRLLCLKAF---DTHK-  149 (377)
Q Consensus        81 VLDdv~~--~~~~~~l~~~l~~~~~gs~IIv--TTR~~~v---~~~~~~~~~~~l~~L~~~ea~~L~~~~~~---~~~~-  149 (377)
                      .+|.|-.  ..|-+.|++..   ..|.-++|  ||.++..   ...+....++.|+.|..++-..+|.+..-   .... 
T Consensus       227 FiDEiHRFNksQQD~fLP~V---E~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~  303 (554)
T KOG2028|consen  227 FIDEIHRFNKSQQDTFLPHV---ENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERP  303 (554)
T ss_pred             EeHHhhhhhhhhhhccccee---ccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhhcccccc
Confidence            9999953  55666666654   45665554  7777654   22235578899999999999999887432   2221 


Q ss_pred             --Cch-----hHHHHHHHHHHHhCC
Q 040234          150 --PLE-----EYVELAESVVRICHC  167 (377)
Q Consensus       150 --~~~-----~~~~~~~~I~~~c~G  167 (377)
                        +.+     -...+.+-++..|.|
T Consensus       304 ~~~l~n~s~~ve~siidyla~lsdG  328 (554)
T KOG2028|consen  304 TDPLPNSSMFVEDSIIDYLAYLSDG  328 (554)
T ss_pred             CCCCCCcchhhhHHHHHHHHHhcCc
Confidence              111     234566677777877

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.67  E-value=0.00054  Score=68.12  Aligned_cols=96  Identities=11%  Similarity=-0.002  Sum_probs=59.0

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|+|+|+.  .+..+.|+..+..-.+.+++|++|.+ +.+...+ .....+++++++.++..+.+...+......
T Consensus       118 ~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~  197 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVE  197 (509)
T ss_pred             CCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCC
Confidence            4556899999986  34566666555443456666655443 3333222 335678899999998888776665332211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        ...+....|++.++|  .+..+
T Consensus       198 --~~~~al~~ia~~s~G--slR~a  217 (509)
T PRK14958        198 --FENAALDLLARAANG--SVRDA  217 (509)
T ss_pred             --CCHHHHHHHHHHcCC--cHHHH
Confidence              123456778888888  66544

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

Probab=97.64  E-value=5e-05  Score=68.28  Aligned_cols=83  Identities=14%  Similarity=0.147  Sum_probs=50.2

Q ss_pred             CCCCcHHHHHHHHHchhc-cccccceEEecchhh-cccccCHHHHHHHHHHHHhhccccCcc-----chhhhHHHHHHH-
Q 040234            1 MGGLGKTTLARVVYDLIS-HEFDGSSFLADVREK-CDKEGSVISLQKQLLSDLLKLADNNIR-----NVYDGINMLRVR-   72 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~-~~f~~~~w~~~~~~~-~~~~~~~~~~~~~i~~~l~~~~~~~~~-----~~~~~~~~l~~~-   72 (377)
                      .+|+|||||++.+++.+. .+|+..+|+..+++. .    ++.++++.+...+.......+.     ......+..... 
T Consensus        24 ~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er~~----ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a~~~~   99 (249)
T cd01128          24 PPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPE----EVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKRLV   99 (249)
T ss_pred             CCCCCHHHHHHHHHhccccccCCeEEEEEEccCCCc----cHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999654 368888898844432 2    7788888873332211111110     001111222222 


Q ss_pred             hcCceEEEEEeCCCC
Q 040234           73 LRRKKVLVVIDDAAH   87 (377)
Q Consensus        73 l~~k~~LLVLDdv~~   87 (377)
                      -.+++.+|++|++..
T Consensus       100 ~~G~~vll~iDei~r  114 (249)
T cd01128         100 EHGKDVVILLDSITR  114 (249)
T ss_pred             HCCCCEEEEEECHHH
Confidence            247899999999965

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.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.62  E-value=0.0014  Score=62.41  Aligned_cols=99  Identities=14%  Similarity=0.074  Sum_probs=63.0

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  ...+.++..+......+.+|++|.+.. +...+ .....+++.++++++..+.+..++-.....
T Consensus       116 ~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~  195 (355)
T TIGR02397       116 GKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIK  195 (355)
T ss_pred             CCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCC
Confidence            34558999998763  445555555543344566666665443 32222 234678899999999999888876432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      .  .++.+..|++.++|  .|..+...
T Consensus       196 i--~~~a~~~l~~~~~g--~~~~a~~~  218 (355)
T TIGR02397       196 I--EDEALELIARAADG--SLRDALSL  218 (355)
T ss_pred             C--CHHHHHHHHHHcCC--ChHHHHHH
Confidence            1  24678889999999  88665443

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.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.62  E-value=0.0005  Score=69.68  Aligned_cols=96  Identities=11%  Similarity=0.005  Sum_probs=59.3

Q ss_pred             CceEEEEEeCCCChh--hhhHhhCCCCCCCCCCeEEEEecch-hHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHPD--HLRRLVGEPDWFGPGSRIIITTRNE-HLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~~--~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|||++....  ..+.|+..+..-....++|++|.+. .+... .+....+.+.+++.++..+.+.+.+..... 
T Consensus       118 gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi-  196 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKI-  196 (709)
T ss_pred             CCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCC-
Confidence            456689999997633  3445554443324456666666543 23221 133456788899999999988877643221 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                       ....+.+..|++.++|  .+.-+
T Consensus       197 -~id~eAL~~Ia~~A~G--slRdA  217 (709)
T PRK08691        197 -AYEPPALQLLGRAAAG--SMRDA  217 (709)
T ss_pred             -CcCHHHHHHHHHHhCC--CHHHH
Confidence             1224567888888888  66443

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.61  E-value=0.0012  Score=66.84  Aligned_cols=96  Identities=9%  Similarity=0.061  Sum_probs=61.5

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEe-cchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITT-RNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|||+|+.  .+.++.|+..+..-....++|++| ..+.+... ......+++++|+.++..+.+.+.+......
T Consensus       123 g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~  202 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVP  202 (618)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCC
Confidence            3455899999986  456777776665434455666554 43444322 2346789999999999999988776432221


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        ...+.+..|++.++|  .+--+
T Consensus       203 --ie~~AL~~La~~s~G--slR~a  222 (618)
T PRK14951        203 --AEPQALRLLARAARG--SMRDA  222 (618)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHH
Confidence              124566778888877  55443

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.60  E-value=0.00073  Score=64.64  Aligned_cols=140  Identities=15%  Similarity=0.187  Sum_probs=74.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||+||+.++++....|-     . +..        ..+....    .+.      ........+...-...+.+|
T Consensus       164 ppGtGKT~lakaia~~l~~~~~-----~-v~~--------~~l~~~~----~g~------~~~~i~~~f~~a~~~~p~il  219 (364)
T TIGR01242       164 PPGTGKTLLAKAVAHETNATFI-----R-VVG--------SELVRKY----IGE------GARLVREIFELAKEKAPSII  219 (364)
T ss_pred             CCCCCHHHHHHHHHHhCCCCEE-----e-cch--------HHHHHHh----hhH------HHHHHHHHHHHHHhcCCcEE
Confidence            4799999999999997765532     1 110        1111110    000      00011111222223456799


Q ss_pred             EEeCCCCh----------------hhhhHhhCCCCC--CCCCCeEEEEecchhH-----HhhCCCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHP----------------DHLRRLVGEPDW--FGPGSRIIITTRNEHL-----LKLHPVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~----------------~~~~~l~~~l~~--~~~gs~IIvTTR~~~v-----~~~~~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++..                ..+..++..+..  ...+..||.||.....     .+.......+.++..+.++..
T Consensus       220 ~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~  299 (364)
T TIGR01242       220 FIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRL  299 (364)
T ss_pred             EhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHH
Confidence            99998652                112233322221  1235678888875432     111122467889999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ++|..+.........   .....+++.+.|
T Consensus       300 ~Il~~~~~~~~l~~~---~~~~~la~~t~g  326 (364)
T TIGR01242       300 EILKIHTRKMKLAED---VDLEAIAKMTEG  326 (364)
T ss_pred             HHHHHHHhcCCCCcc---CCHHHHHHHcCC
Confidence            999887744322211   124567788877

Many proteins may score above the trusted cutoff because an internal

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.59  E-value=0.00066  Score=67.91  Aligned_cols=95  Identities=8%  Similarity=-0.006  Sum_probs=59.6

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecc-hhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRN-EHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  +..+.|+..+..-...+.+|++|.+ +.+... ......+++++++.++..+.+.+.+..... 
T Consensus       118 ~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi-  196 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENI-  196 (527)
T ss_pred             CCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCC-
Confidence            45679999999863  3456666555443445566655543 333222 122567889999999999888776632221 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                       ...++.+..|++.++|  .+--
T Consensus       197 -~~~~~al~~la~~s~G--slr~  216 (527)
T PRK14969        197 -PFDATALQLLARAAAG--SMRD  216 (527)
T ss_pred             -CCCHHHHHHHHHHcCC--CHHH
Confidence             1124566788888888  7753

>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=97.58  E-value=0.00044  Score=56.07  Aligned_cols=96  Identities=19%  Similarity=0.169  Sum_probs=48.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++.....-...+++. ..+..    .. ......... .           ............++.+|
T Consensus        27 ~~G~GKT~l~~~i~~~~~~~~~~v~~~~-~~~~~----~~-~~~~~~~~~-~-----------~~~~~~~~~~~~~~~~l   88 (151)
T cd00009          27 PPGTGKTTLARAIANELFRPGAPFLYLN-ASDLL----EG-LVVAELFGH-F-----------LVRLLFELAEKAKPGVL   88 (151)
T ss_pred             CCCCCHHHHHHHHHHHhhcCCCCeEEEe-hhhhh----hh-hHHHHHhhh-h-----------hHhHHHHhhccCCCeEE
Confidence            3799999999999997643322333333 33321    10 000000000 0           00111122234567899


Q ss_pred             EEeCCCCh-----hhhhHhhCCCCCC---CCCCeEEEEecch
Q 040234           81 VIDDAAHP-----DHLRRLVGEPDWF---GPGSRIIITTRNE  114 (377)
Q Consensus        81 VLDdv~~~-----~~~~~l~~~l~~~---~~gs~IIvTTR~~  114 (377)
                      |+||++..     ..+..+.......   ..+..||+||...
T Consensus        89 ilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~  130 (151)
T cd00009          89 FIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRP  130 (151)
T ss_pred             EEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCcc
Confidence            99999853     2233333333221   3577888888865

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.57  E-value=8.9e-05  Score=70.02  Aligned_cols=84  Identities=14%  Similarity=0.120  Sum_probs=49.4

Q ss_pred             CCCCcHHHHHHHHHchhcc-ccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccch-----hhhHHHHHHH-h
Q 040234            1 MGGLGKTTLARVVYDLISH-EFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNV-----YDGINMLRVR-L   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~-----~~~~~~l~~~-l   73 (377)
                      .+|+||||||+++++.+.. +|+..+|+..+++ ..  ..+.++++.+...+.......+...     ....+.-+.. -
T Consensus       177 ppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgE-R~--~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~~e  253 (416)
T PRK09376        177 PPKAGKTVLLQNIANSITTNHPEVHLIVLLIDE-RP--EEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRLVE  253 (416)
T ss_pred             CCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCC-ch--hHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999996543 7888899985444 21  1666777776532211111111000     0111111111 3


Q ss_pred             cCceEEEEEeCCCC
Q 040234           74 RRKKVLVVIDDAAH   87 (377)
Q Consensus        74 ~~k~~LLVLDdv~~   87 (377)
                      .+++.||++|++..
T Consensus       254 ~G~dVlL~iDsItR  267 (416)
T PRK09376        254 HGKDVVILLDSITR  267 (416)
T ss_pred             cCCCEEEEEEChHH
Confidence            67899999999854

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.53  E-value=0.0018  Score=60.61  Aligned_cols=94  Identities=13%  Similarity=0.157  Sum_probs=57.3

Q ss_pred             eEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCch
Q 040234           77 KVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLE  152 (377)
Q Consensus        77 ~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~  152 (377)
                      +-++++|+++..  +....+...+....+.+.+|+++... .+.... .....+++.++++++....+...+......  
T Consensus       103 ~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~~--  180 (319)
T PRK00440        103 FKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIE--  180 (319)
T ss_pred             ceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCCC--
Confidence            558999998753  23334443333324456777766432 221111 224568999999999999988877433221  


Q ss_pred             hHHHHHHHHHHHhCCCCchhhH
Q 040234          153 EYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       153 ~~~~~~~~I~~~c~G~~lplal  174 (377)
                      -.++.+..+++.++|  .+..+
T Consensus       181 i~~~al~~l~~~~~g--d~r~~  200 (319)
T PRK00440        181 ITDDALEAIYYVSEG--DMRKA  200 (319)
T ss_pred             CCHHHHHHHHHHcCC--CHHHH
Confidence            124578889999999  66553

>PRK06620 hypothetical protein; Validated

Probab=97.53  E-value=0.00065  Score=59.81  Aligned_cols=92  Identities=8%  Similarity=-0.025  Sum_probs=57.5

Q ss_pred             EEEEEeCCCChh--hhhHhhCCCCCCCCCCeEEEEecch-------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcCCC
Q 040234           78 VLVVIDDAAHPD--HLRRLVGEPDWFGPGSRIIITTRNE-------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTH  148 (377)
Q Consensus        78 ~LLVLDdv~~~~--~~~~l~~~l~~~~~gs~IIvTTR~~-------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~  148 (377)
                      -+|++||+...+  .+-.+...+.  ..|..||+|++.+       .+..++....++++++++.++-.+++.+.+....
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 NAFIIEDIENWQEPALLHIFNIIN--EKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS  164 (214)
T ss_pred             CEEEEeccccchHHHHHHHHHHHH--hcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC
Confidence            478899997532  2222222222  3466899998743       2233344456899999999998888887764221


Q ss_pred             CCchhHHHHHHHHHHHhCCCCchhhHH
Q 040234          149 KPLEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       149 ~~~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                        ..-.+++.+-|++.+.|  ---.+.
T Consensus       165 --l~l~~ev~~~L~~~~~~--d~r~l~  187 (214)
T PRK06620        165 --VTISRQIIDFLLVNLPR--EYSKII  187 (214)
T ss_pred             --CCCCHHHHHHHHHHccC--CHHHHH
Confidence              11225788889999988  444443

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

Probab=97.52  E-value=0.0026  Score=60.58  Aligned_cols=165  Identities=15%  Similarity=0.166  Sum_probs=97.3

Q ss_pred             CCCcHHHHHHHHHchhccccccc--eEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhc--Cce
Q 040234            2 GGLGKTTLARVVYDLISHEFDGS--SFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLR--RKK   77 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~--~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~--~k~   77 (377)
                      .|.|||+.++.+.+++++..+..  +++. +....    ...+++..++++++.. +....+..+..+.+.+.+.  ++.
T Consensus        51 ~GTGKT~~~~~v~~~l~~~~~~~~~~yIN-c~~~~----t~~~i~~~i~~~~~~~-p~~g~~~~~~~~~l~~~~~~~~~~  124 (366)
T COG1474          51 TGTGKTATVKFVMEELEESSANVEVVYIN-CLELR----TPYQVLSKILNKLGKV-PLTGDSSLEILKRLYDNLSKKGKT  124 (366)
T ss_pred             CCCCHhHHHHHHHHHHHhhhccCceEEEe-eeeCC----CHHHHHHHHHHHcCCC-CCCCCchHHHHHHHHHHHHhcCCe
Confidence            69999999999999887775544  5555 54444    7789999999988633 2222344455566666664  478


Q ss_pred             EEEEEeCCCChh-----hhhHhhCCCCCCCCCCeE--EEEecchhHH--------hhCCCCCeeecCCCChhhhHHHHHH
Q 040234           78 VLVVIDDAAHPD-----HLRRLVGEPDWFGPGSRI--IITTRNEHLL--------KLHPVKKVYKLEALTYDEAFRLLCL  142 (377)
Q Consensus        78 ~LLVLDdv~~~~-----~~~~l~~~l~~~~~gs~I--IvTTR~~~v~--------~~~~~~~~~~l~~L~~~ea~~L~~~  142 (377)
                      +++|||+++...     .+-.|......  ..++|  |..+-+-...        ..++. ..+..+|-+.++-.+++..
T Consensus       125 ~IvvLDEid~L~~~~~~~LY~L~r~~~~--~~~~v~vi~i~n~~~~~~~ld~rv~s~l~~-~~I~F~pY~a~el~~Il~~  201 (366)
T COG1474         125 VIVILDEVDALVDKDGEVLYSLLRAPGE--NKVKVSIIAVSNDDKFLDYLDPRVKSSLGP-SEIVFPPYTAEELYDILRE  201 (366)
T ss_pred             EEEEEcchhhhccccchHHHHHHhhccc--cceeEEEEEEeccHHHHHHhhhhhhhccCc-ceeeeCCCCHHHHHHHHHH
Confidence            999999997632     22223222111  13433  3344433222        22222 3377899999999999988


Q ss_pred             HhcCC---CCCchhHHHHHHHHHHHhCCCCchhhHHH
Q 040234          143 KAFDT---HKPLEEYVELAESVVRICHCQKSTLNALM  176 (377)
Q Consensus       143 ~~~~~---~~~~~~~~~~~~~I~~~c~G~~lplal~~  176 (377)
                      ++-..   ...++...+.+..++..-+| +.-.|+..
T Consensus       202 R~~~~~~~~~~~~~vl~lia~~~a~~~G-DAR~aidi  237 (366)
T COG1474         202 RVEEGFSAGVIDDDVLKLIAALVAAESG-DARKAIDI  237 (366)
T ss_pred             HHHhhccCCCcCccHHHHHHHHHHHcCc-cHHHHHHH
Confidence            87432   22233333444444444443 15555443

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

Probab=97.50  E-value=0.0011  Score=63.20  Aligned_cols=153  Identities=17%  Similarity=0.130  Sum_probs=90.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||.|++.+.+...+..+....+. +        ........++.++..          ...+.+++..  .-=+|+
T Consensus       122 ~GlGKTHLl~Aign~~~~~~~~a~v~y-~--------~se~f~~~~v~a~~~----------~~~~~Fk~~y--~~dlll  180 (408)
T COG0593         122 VGLGKTHLLQAIGNEALANGPNARVVY-L--------TSEDFTNDFVKALRD----------NEMEKFKEKY--SLDLLL  180 (408)
T ss_pred             CCCCHHHHHHHHHHHHHhhCCCceEEe-c--------cHHHHHHHHHHHHHh----------hhHHHHHHhh--ccCeee
Confidence            599999999999998877776443333 1        333444455554432          2345566665  344889


Q ss_pred             EeCCCCh-------hhhhHhhCCCCCCCCCCeEEEEecc---------hhHHhhCCCCCeeecCCCChhhhHHHHHHHhc
Q 040234           82 IDDAAHP-------DHLRRLVGEPDWFGPGSRIIITTRN---------EHLLKLHPVKKVYKLEALTYDEAFRLLCLKAF  145 (377)
Q Consensus        82 LDdv~~~-------~~~~~l~~~l~~~~~gs~IIvTTR~---------~~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~  145 (377)
                      +||++-.       +.+-.+...+.  ..|..||+|++.         +.+..++..+-++++.+++.+....++.+++.
T Consensus       181 IDDiq~l~gk~~~qeefFh~FN~l~--~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka~  258 (408)
T COG0593         181 IDDIQFLAGKERTQEEFFHTFNALL--ENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAE  258 (408)
T ss_pred             echHhHhcCChhHHHHHHHHHHHHH--hcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHHHH
Confidence            9998641       11212222222  234489999964         34445556678899999999999999998764


Q ss_pred             CCCC--CchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          146 DTHK--PLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       146 ~~~~--~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ...-  +.+...-++..+-+...-  +.-|+..+..
T Consensus       259 ~~~~~i~~ev~~~la~~~~~nvRe--LegaL~~l~~  292 (408)
T COG0593         259 DRGIEIPDEVLEFLAKRLDRNVRE--LEGALNRLDA  292 (408)
T ss_pred             hcCCCCCHHHHHHHHHHhhccHHH--HHHHHHHHHH
Confidence            3322  222233344444444444  4445544444

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.45  E-value=0.0014  Score=66.06  Aligned_cols=91  Identities=9%  Similarity=-0.021  Sum_probs=56.9

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecc-hhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRN-EHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|||+++..  +..+.|+..+..-.....+|++|.+ ..+... ......+++.+++.++..+.+...+......
T Consensus       118 g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~  197 (624)
T PRK14959        118 GRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVD  197 (624)
T ss_pred             CCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCC
Confidence            45669999999763  4556666555432345556655544 444322 2335678999999999998888766432211


Q ss_pred             chhHHHHHHHHHHHhCC
Q 040234          151 LEEYVELAESVVRICHC  167 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G  167 (377)
                        ...+.+..|++..+|
T Consensus       198 --id~eal~lIA~~s~G  212 (624)
T PRK14959        198 --YDPAAVRLIARRAAG  212 (624)
T ss_pred             --CCHHHHHHHHHHcCC
Confidence              124566777777777

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.45  E-value=0.0017  Score=65.11  Aligned_cols=94  Identities=15%  Similarity=0.076  Sum_probs=58.0

Q ss_pred             ceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEe-cchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           76 KKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITT-RNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        76 k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      ++-++|+|+++.  ...++.|+..+..-.....+|++| ....+... ......+++.++++++....+...+......-
T Consensus       119 ~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~I  198 (605)
T PRK05896        119 KYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKIKI  198 (605)
T ss_pred             CcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCC
Confidence            344799999976  344555555443323445555444 44444332 23456889999999999988887764322111


Q ss_pred             hhHHHHHHHHHHHhCCCCchhh
Q 040234          152 EEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lpla  173 (377)
                        ..+.+..|++.++|  .+..
T Consensus       199 --s~eal~~La~lS~G--dlR~  216 (605)
T PRK05896        199 --EDNAIDKIADLADG--SLRD  216 (605)
T ss_pred             --CHHHHHHHHHHcCC--cHHH
Confidence              14567788888988  6653

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=97.42  E-value=0.00051  Score=59.98  Aligned_cols=67  Identities=22%  Similarity=0.052  Sum_probs=42.2

Q ss_pred             EEEEecchhHHhhCCC--CCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          107 IIITTRNEHLLKLHPV--KKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       107 IIvTTR~~~v~~~~~~--~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      |=.|||...+...+..  .-..+++..+.+|-.++..+.+..-.  .+-.++.+.+|++++.|  -|--..-+
T Consensus       153 igATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~--i~i~~~~~~~Ia~rsrG--tPRiAnrl  221 (233)
T PF05496_consen  153 IGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILN--IEIDEDAAEEIARRSRG--TPRIANRL  221 (233)
T ss_dssp             EEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT---EE-HHHHHHHHHCTTT--SHHHHHHH
T ss_pred             eeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhC--CCcCHHHHHHHHHhcCC--ChHHHHHH
Confidence            4468887655444433  23457999999999999988774332  23336789999999999  88755433

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.42  E-value=0.0013  Score=59.88  Aligned_cols=67  Identities=12%  Similarity=0.080  Sum_probs=40.9

Q ss_pred             EEEEEeCCCC----------hhhhhHhhCCCCCCCCCCeEEEEecchhH----------HhhCCCCCeeecCCCChhhhH
Q 040234           78 VLVVIDDAAH----------PDHLRRLVGEPDWFGPGSRIIITTRNEHL----------LKLHPVKKVYKLEALTYDEAF  137 (377)
Q Consensus        78 ~LLVLDdv~~----------~~~~~~l~~~l~~~~~gs~IIvTTR~~~v----------~~~~~~~~~~~l~~L~~~ea~  137 (377)
                      -+|+||++..          .+..+.++..+........+|+++.....          ..+  -...+++++++.++-.
T Consensus       107 ~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sR--f~~~i~f~~~~~~el~  184 (261)
T TIGR02881       107 GVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSR--FPISIDFPDYTVEELM  184 (261)
T ss_pred             CEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhc--cceEEEECCCCHHHHH
Confidence            4889999964          23445555554433333355555543221          111  1346889999999999


Q ss_pred             HHHHHHhcC
Q 040234          138 RLLCLKAFD  146 (377)
Q Consensus       138 ~L~~~~~~~  146 (377)
                      +++.+.+..
T Consensus       185 ~Il~~~~~~  193 (261)
T TIGR02881       185 EIAERMVKE  193 (261)
T ss_pred             HHHHHHHHH
Confidence            999877743

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.41  E-value=0.0032  Score=63.45  Aligned_cols=94  Identities=15%  Similarity=0.032  Sum_probs=59.8

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEE-EEecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRII-ITTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~II-vTTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|++..  .+..+.|+..+..-.....+| +||....+...+ .....+++.+++.++..+.+.+.+......
T Consensus       117 ~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~  196 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGVV  196 (584)
T ss_pred             CCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCC
Confidence            4555899999975  445666666555434455555 455545544332 336789999999999998887766432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchh
Q 040234          151 LEEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpl  172 (377)
                        ...+.+..|++..+|  .+-
T Consensus       197 --i~~~al~~Ia~~s~G--dlR  214 (584)
T PRK14952        197 --VDDAVYPLVIRAGGG--SPR  214 (584)
T ss_pred             --CCHHHHHHHHHHcCC--CHH
Confidence              123556777888888  654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.39  E-value=0.0027  Score=66.51  Aligned_cols=95  Identities=13%  Similarity=0.070  Sum_probs=60.5

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEe-cchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITT-RNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|||+++.  .+..+.|+..+..-...+.+|++| ....+...+ .....+++..++.++..+.+.+..-.... 
T Consensus       119 ~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv-  197 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGV-  197 (824)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCC-
Confidence            4556899999986  345566665555434555655544 444454433 34678999999999999888776532221 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                       ....+....|++.++|  .+..
T Consensus       198 -~id~eal~lLa~~sgG--dlR~  217 (824)
T PRK07764        198 -PVEPGVLPLVIRAGGG--SVRD  217 (824)
T ss_pred             -CCCHHHHHHHHHHcCC--CHHH
Confidence             1124456778888888  6643

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.35  E-value=0.0033  Score=63.67  Aligned_cols=97  Identities=14%  Similarity=0.064  Sum_probs=62.1

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEe-cchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITT-RNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|++...  ...+.|+..+..-.+.+++|++| ....+...+ .....++++.+++++..+.+.+.+......
T Consensus       131 a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~  210 (598)
T PRK09111        131 ARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVE  210 (598)
T ss_pred             CCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            34557999999763  44666665554334566665544 444443332 345789999999999999988876432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                        ...+.+..|++.++|  .+.-+.
T Consensus       211 --i~~eAl~lIa~~a~G--dlr~al  231 (598)
T PRK09111        211 --VEDEALALIARAAEG--SVRDGL  231 (598)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHHH
Confidence              124567888888988  765543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.33  E-value=0.0055  Score=56.41  Aligned_cols=70  Identities=11%  Similarity=0.076  Sum_probs=42.1

Q ss_pred             eEEEEEeCCCCh-----------hhhhHhhCCCCCCCCCCeEEEEecchhHHhh--C------CCCCeeecCCCChhhhH
Q 040234           77 KVLVVIDDAAHP-----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKL--H------PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        77 ~~LLVLDdv~~~-----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~--~------~~~~~~~l~~L~~~ea~  137 (377)
                      .-+|+||++...           +..+.|...+.....+.+||+++.....-..  .      .-...+++++++.+|-.
T Consensus       122 ~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~  201 (284)
T TIGR02880       122 GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELL  201 (284)
T ss_pred             CcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHH
Confidence            358999998621           2234444444333445567777653321111  0      11356899999999999


Q ss_pred             HHHHHHhcC
Q 040234          138 RLLCLKAFD  146 (377)
Q Consensus       138 ~L~~~~~~~  146 (377)
                      +++...+-.
T Consensus       202 ~I~~~~l~~  210 (284)
T TIGR02880       202 VIAGLMLKE  210 (284)
T ss_pred             HHHHHHHHH
Confidence            998877643

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.

>PRK08116 hypothetical protein; Validated

Probab=97.33  E-value=0.00054  Score=62.50  Aligned_cols=94  Identities=20%  Similarity=0.170  Sum_probs=49.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||.||..+++.+..+....+++           +...++..+.......      . ......+.+.+.+-. |||
T Consensus       123 ~GtGKThLa~aia~~l~~~~~~v~~~-----------~~~~ll~~i~~~~~~~------~-~~~~~~~~~~l~~~d-lLv  183 (268)
T PRK08116        123 VGTGKTYLAACIANELIEKGVPVIFV-----------NFPQLLNRIKSTYKSS------G-KEDENEIIRSLVNAD-LLI  183 (268)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCeEEEE-----------EHHHHHHHHHHHHhcc------c-cccHHHHHHHhcCCC-EEE
Confidence            69999999999999776553233333           3334444444433211      0 111223334445444 899


Q ss_pred             EeCCC--Chhhhh--HhhCCCCCC-CCCCeEEEEecch
Q 040234           82 IDDAA--HPDHLR--RLVGEPDWF-GPGSRIIITTRNE  114 (377)
Q Consensus        82 LDdv~--~~~~~~--~l~~~l~~~-~~gs~IIvTTR~~  114 (377)
                      |||+.  ....|.  .+..-+... ..+..+|+||...
T Consensus       184 iDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        184 LDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             EecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            99993  222222  122111111 3456789998753

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.33  E-value=0.002  Score=62.30  Aligned_cols=96  Identities=10%  Similarity=0.038  Sum_probs=61.2

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEe-cchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITT-RNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|++...  +.++.++..+..-.+.+.+|++| +...+...+ .....+++.++++++..+.+...+..... 
T Consensus       126 ~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~-  204 (397)
T PRK14955        126 GRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGI-  204 (397)
T ss_pred             CCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCC-
Confidence            34568899999763  45666665555434566665554 444443322 22456889999999999888877632221 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                       .-..+.+..|++.++|  .+--+
T Consensus       205 -~i~~~al~~l~~~s~g--~lr~a  225 (397)
T PRK14955        205 -SVDADALQLIGRKAQG--SMRDA  225 (397)
T ss_pred             -CCCHHHHHHHHHHcCC--CHHHH
Confidence             1225678889999999  77544

>PRK04132 replication factor C small subunit; Provisional

Probab=97.30  E-value=0.006  Score=63.76  Aligned_cols=149  Identities=11%  Similarity=0.107  Sum_probs=87.5

Q ss_pred             CCCCcHHHHHHHHHchh-ccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLI-SHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~-~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      +.++||||+|..+++++ .+.+...+.-.+.++..    ++. .++.++.......+.               -..+.-+
T Consensus       574 Ph~lGKTT~A~ala~~l~g~~~~~~~lElNASd~r----gid-~IR~iIk~~a~~~~~---------------~~~~~KV  633 (846)
T PRK04132        574 PTVLHNTTAALALARELFGENWRHNFLELNASDER----GIN-VIREKVKEFARTKPI---------------GGASFKI  633 (846)
T ss_pred             CCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcc----cHH-HHHHHHHHHHhcCCc---------------CCCCCEE
Confidence            35799999999999976 33333333322243321    233 334444332211100               0124569


Q ss_pred             EEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHH
Q 040234           80 VVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYV  155 (377)
Q Consensus        80 LVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~  155 (377)
                      +|||+++..  ++.+.|+..+..-...+++|+++... .+...+ +....+.+.+++.++..+.+.+.+-...-.  -.+
T Consensus       634 vIIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~--i~~  711 (846)
T PRK04132        634 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE--LTE  711 (846)
T ss_pred             EEEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCC--CCH
Confidence            999999874  45566655554334566666665543 333332 446789999999999998887766322111  124


Q ss_pred             HHHHHHHHHhCCCCchhh
Q 040234          156 ELAESVVRICHCQKSTLN  173 (377)
Q Consensus       156 ~~~~~I~~~c~G~~lpla  173 (377)
                      +....|++.++|  -+..
T Consensus       712 e~L~~Ia~~s~G--DlR~  727 (846)
T PRK04132        712 EGLQAILYIAEG--DMRR  727 (846)
T ss_pred             HHHHHHHHHcCC--CHHH
Confidence            578899999999  6644

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.30  E-value=0.017  Score=53.87  Aligned_cols=94  Identities=13%  Similarity=0.045  Sum_probs=61.9

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|||+++..  +..+.|+..+..-.+++.+|++|.. ..+...+ +....+.+.+++.+++.+.+....     .
T Consensus       112 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~~-----~  186 (319)
T PRK08769        112 GIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQG-----V  186 (319)
T ss_pred             CCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHcC-----C
Confidence            35568999999863  3455555544433557777777765 3344333 446788999999999998886531     1


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      .   .+.+..++..++|  .|+......
T Consensus       187 ~---~~~a~~~~~l~~G--~p~~A~~~~  209 (319)
T PRK08769        187 S---ERAAQEALDAARG--HPGLAAQWL  209 (319)
T ss_pred             C---hHHHHHHHHHcCC--CHHHHHHHh
Confidence            1   2336678999999  998765443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.28  E-value=0.0049  Score=59.02  Aligned_cols=94  Identities=9%  Similarity=0.058  Sum_probs=56.6

Q ss_pred             ceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEe-cchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           76 KKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITT-RNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        76 k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTT-R~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      ++-++++|+++..  ..++.++..+......+.+|++| +...+... ......+++.++++++....+...+....-. 
T Consensus       108 ~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~-  186 (367)
T PRK14970        108 KYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIK-  186 (367)
T ss_pred             CcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHHHHHHHcCCC-
Confidence            4458999998753  34555544433223345555555 33333222 2334578999999999998888766432211 


Q ss_pred             hhHHHHHHHHHHHhCCCCchhh
Q 040234          152 EEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lpla  173 (377)
                       -..+.+..|++.++|  .+-.
T Consensus       187 -i~~~al~~l~~~~~g--dlr~  205 (367)
T PRK14970        187 -FEDDALHIIAQKADG--ALRD  205 (367)
T ss_pred             -CCHHHHHHHHHhCCC--CHHH
Confidence             124677888888888  5553

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.26  E-value=0.0022  Score=65.07  Aligned_cols=94  Identities=12%  Similarity=0.070  Sum_probs=58.3

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEE-EecchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIII-TTRNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIv-TTR~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  ...+.|+..+..-.+.+.+|+ |++...+... ......+++.+++.++....+.+.+......
T Consensus       126 ~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~  205 (620)
T PRK14954        126 GRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQ  205 (620)
T ss_pred             CCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCC
Confidence            34557899999763  345556555543234455544 4444444433 2446789999999999888887765322211


Q ss_pred             chhHHHHHHHHHHHhCCCCchh
Q 040234          151 LEEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpl  172 (377)
                        -..+.+..|++.++|  ..-
T Consensus       206 --I~~eal~~La~~s~G--dlr  223 (620)
T PRK14954        206 --IDADALQLIARKAQG--SMR  223 (620)
T ss_pred             --CCHHHHHHHHHHhCC--CHH
Confidence              124567788888888  554

>PF14516 AAA_35: AAA-like domain

Probab=97.25  E-value=0.013  Score=55.18  Aligned_cols=172  Identities=11%  Similarity=0.062  Sum_probs=94.0

Q ss_pred             CCcHHHHHHHHHchhccccccceEEecchhhcc-cccCHHHHHHHHHHHHhhccccC----------ccchhhhHHHHHH
Q 040234            3 GLGKTTLARVVYDLISHEFDGSSFLADVREKCD-KEGSVISLQKQLLSDLLKLADNN----------IRNVYDGINMLRV   71 (377)
Q Consensus         3 GiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~-~~~~~~~~~~~i~~~l~~~~~~~----------~~~~~~~~~~l~~   71 (377)
                      .+|||+|...+.+..++.=-..+++. +..... ...+....++.+...+.......          ..+.......+.+
T Consensus        41 q~GKTSll~~l~~~l~~~~~~~v~id-~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~  119 (331)
T PF14516_consen   41 QMGKTSLLLRLLERLQQQGYRCVYID-LQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEE  119 (331)
T ss_pred             cCCHHHHHHHHHHHHHHCCCEEEEEE-eecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHH
Confidence            58999999999986654312233443 554321 22256666666666654332211          1122223333444


Q ss_pred             Hh---cCceEEEEEeCCCChhh----hhHhhCCCC----C---C-CCCC-e-EEEEecchhHHhh-----CCCCCeeecC
Q 040234           72 RL---RRKKVLVVIDDAAHPDH----LRRLVGEPD----W---F-GPGS-R-IIITTRNEHLLKL-----HPVKKVYKLE  129 (377)
Q Consensus        72 ~l---~~k~~LLVLDdv~~~~~----~~~l~~~l~----~---~-~~gs-~-IIvTTR~~~v~~~-----~~~~~~~~l~  129 (377)
                      .+   .+++.+|+||+++..-.    ...+...+.    .   . .... + |++.+........     ......++|+
T Consensus       120 ~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~  199 (331)
T PF14516_consen  120 YLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSPFNIGQPIELP  199 (331)
T ss_pred             HHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCCcccccceeCC
Confidence            32   25899999999975211    111111110    0   0 0111 1 2222211111111     1335678999


Q ss_pred             CCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhhc
Q 040234          130 ALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVS  183 (377)
Q Consensus       130 ~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~  183 (377)
                      +++.+|..+|+.++-..   ..   ....++|....||  +|.-+..+...+..
T Consensus       200 ~Ft~~ev~~L~~~~~~~---~~---~~~~~~l~~~tgG--hP~Lv~~~~~~l~~  245 (331)
T PF14516_consen  200 DFTPEEVQELAQRYGLE---FS---QEQLEQLMDWTGG--HPYLVQKACYLLVE  245 (331)
T ss_pred             CCCHHHHHHHHHhhhcc---CC---HHHHHHHHHHHCC--CHHHHHHHHHHHHH
Confidence            99999999998776422   11   2238899999999  99888887777644

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0088  Score=59.25  Aligned_cols=97  Identities=13%  Similarity=0.071  Sum_probs=59.7

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEE-EecchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIII-TTRNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIv-TTR~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  +..+.|+..+..-.+...+|+ ||+...+... ......+.+.+++.++....+...+-...- 
T Consensus       118 ~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi-  196 (486)
T PRK14953        118 GKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKI-  196 (486)
T ss_pred             CCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCC-
Confidence            45669999999753  345555555443334455554 4444333322 233567899999999999888876643221 


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                       ....+.+..|++.++|  .+..+.
T Consensus       197 -~id~~al~~La~~s~G--~lr~al  218 (486)
T PRK14953        197 -EYEEKALDLLAQASEG--GMRDAA  218 (486)
T ss_pred             -CCCHHHHHHHHHHcCC--CHHHHH
Confidence             1124567788888888  665443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.18  E-value=0.0075  Score=61.35  Aligned_cols=98  Identities=12%  Similarity=0.036  Sum_probs=62.0

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|||+++.  .+..+.|+..+..-...+.+|++|.+ ..+...+ .....+++..++.++..+.+...+......
T Consensus       119 ~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~  198 (585)
T PRK14950        119 ARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGIN  198 (585)
T ss_pred             CCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            3566899999975  34566665554433445666655543 3333322 335678899999999998888776433211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALM  176 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~  176 (377)
                        ...+.+..|++.++|  .+..+..
T Consensus       199 --i~~eal~~La~~s~G--dlr~al~  220 (585)
T PRK14950        199 --LEPGALEAIARAATG--SMRDAEN  220 (585)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHHHH
Confidence              124567888999999  7765443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.15  E-value=0.0085  Score=59.64  Aligned_cols=96  Identities=11%  Similarity=0.071  Sum_probs=61.1

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|++..  .+..+.|+..+..-.+.+++|++|.+. .+...+ .....+++.+++.++..+.+...+......
T Consensus       116 ~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~  195 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVS  195 (535)
T ss_pred             CCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCC
Confidence            3456899999976  344555655544334566766666553 222211 235788999999999999888766432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        ..++.+..|++.++|  .+.-+
T Consensus       196 --i~~~Al~~Ia~~s~G--dlR~a  215 (535)
T PRK08451        196 --YEPEALEILARSGNG--SLRDT  215 (535)
T ss_pred             --CCHHHHHHHHHHcCC--cHHHH
Confidence              124677888888888  66443

>CHL00181 cbbX CbbX; Provisional

Probab=97.14  E-value=0.0098  Score=54.82  Aligned_cols=69  Identities=12%  Similarity=0.122  Sum_probs=42.9

Q ss_pred             EEEEEeCCCC-----------hhhhhHhhCCCCCCCCCCeEEEEecchhHHhh--------CCCCCeeecCCCChhhhHH
Q 040234           78 VLVVIDDAAH-----------PDHLRRLVGEPDWFGPGSRIIITTRNEHLLKL--------HPVKKVYKLEALTYDEAFR  138 (377)
Q Consensus        78 ~LLVLDdv~~-----------~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~--------~~~~~~~~l~~L~~~ea~~  138 (377)
                      -+|+||++..           .+....|...+.....+.+||+++....+...        -.....+.+++++.++..+
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            4999999864           22344444444433445677777754332110        0224578999999999999


Q ss_pred             HHHHHhcC
Q 040234          139 LLCLKAFD  146 (377)
Q Consensus       139 L~~~~~~~  146 (377)
                      ++...+-.
T Consensus       204 I~~~~l~~  211 (287)
T CHL00181        204 IAKIMLEE  211 (287)
T ss_pred             HHHHHHHH
Confidence            98887743

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.09  E-value=0.011  Score=60.58  Aligned_cols=95  Identities=11%  Similarity=0.041  Sum_probs=59.8

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeE-EEEecchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRI-IITTRNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~I-IvTTR~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|++..  ...+..|+..+..-.....+ ++|++...+... ......+++.+++.++..+.+...+......
T Consensus       117 g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~  196 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENIS  196 (725)
T ss_pred             CCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCCC
Confidence            4566899999975  34566666554432334444 455555555433 2345789999999999998888765322211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                        ...+.+..|++.++|  .+.-
T Consensus       197 --id~eAl~~LA~lS~G--slR~  215 (725)
T PRK07133        197 --YEKNALKLIAKLSSG--SLRD  215 (725)
T ss_pred             --CCHHHHHHHHHHcCC--CHHH
Confidence              113567788888888  6543

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

Probab=97.09  E-value=0.0022  Score=58.16  Aligned_cols=160  Identities=13%  Similarity=0.119  Sum_probs=91.4

Q ss_pred             CCCCcHHHHHHHHHchh--ccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh--cCc
Q 040234            1 MGGLGKTTLARVVYDLI--SHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL--RRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~--~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l--~~k   76 (377)
                      ++|.|||+-|+.+++++  .+-|++++.=.+.+...    ++. +.++=..           +.........+..  ...
T Consensus        65 PpGTGKTStalafar~L~~~~~~~~rvl~lnaSder----Gis-vvr~Kik-----------~fakl~~~~~~~~~~~~~  128 (346)
T KOG0989|consen   65 PPGTGKTSTALAFARALNCEQLFPCRVLELNASDER----GIS-VVREKIK-----------NFAKLTVLLKRSDGYPCP  128 (346)
T ss_pred             CCCCcHhHHHHHHHHHhcCccccccchhhhcccccc----ccc-chhhhhc-----------CHHHHhhccccccCCCCC
Confidence            47999999999999854  34577776533333332    111 1100000           0000000000000  112


Q ss_pred             e-EEEEEeCCCC--hhhhhHhhCCCCCCCCCCe-EEEEecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           77 K-VLVVIDDAAH--PDHLRRLVGEPDWFGPGSR-IIITTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        77 ~-~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~-IIvTTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      + -.+|||+++.  .+.|..|+..+......++ |+||+--..+...+ +....+..++|..++...-|...+....  .
T Consensus       129 ~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~--v  206 (346)
T KOG0989|consen  129 PFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEG--V  206 (346)
T ss_pred             cceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHHHHhC--C
Confidence            3 4789999987  4678888776665455566 44555443332222 3356688999999999999888884433  2


Q ss_pred             hhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          152 EEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      +-..+..+.|++.++| .|--|+.++-+
T Consensus       207 ~~d~~al~~I~~~S~G-dLR~Ait~Lqs  233 (346)
T KOG0989|consen  207 DIDDDALKLIAKISDG-DLRRAITTLQS  233 (346)
T ss_pred             CCCHHHHHHHHHHcCC-cHHHHHHHHHH
Confidence            2235678899999998 45556544433

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.09  E-value=0.005  Score=49.22  Aligned_cols=18  Identities=44%  Similarity=0.575  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+|||++|+.+++...
T Consensus         6 ~~G~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    6 PPGTGKTTLARALAQYLG   23 (132)
T ss_dssp             STTSSHHHHHHHHHHHTT
T ss_pred             cCCCCeeHHHHHHHhhcc
Confidence            379999999999999775

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 ....

>TIGR00767 rho transcription termination factor Rho

Probab=97.07  E-value=0.00069  Score=64.39  Aligned_cols=84  Identities=14%  Similarity=0.172  Sum_probs=51.0

Q ss_pred             CCCCcHHHHHHHHHchhcc-ccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccch-hhh----HHHHHHH-h
Q 040234            1 MGGLGKTTLARVVYDLISH-EFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNV-YDG----INMLRVR-L   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~-~~~----~~~l~~~-l   73 (377)
                      .+|+|||||++.+++.+.. +|+..+|+..+++..   ..+.++++.++..+.......+... ...    .+..+.. -
T Consensus       176 ~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER~---~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~Ae~~~~  252 (415)
T TIGR00767       176 PPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERP---EEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVE  252 (415)
T ss_pred             CCCCChhHHHHHHHHhhcccCCceEEEEEEcCCCC---ccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999996554 488888888443421   1788888888544322211111111 111    1111121 3


Q ss_pred             cCceEEEEEeCCCC
Q 040234           74 RRKKVLVVIDDAAH   87 (377)
Q Consensus        74 ~~k~~LLVLDdv~~   87 (377)
                      .+++.+|++|++..
T Consensus       253 ~GkdVVLlIDEitR  266 (415)
T TIGR00767       253 HKKDVVILLDSITR  266 (415)
T ss_pred             cCCCeEEEEEChhH
Confidence            57899999999865

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

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.04  E-value=0.015  Score=54.68  Aligned_cols=92  Identities=15%  Similarity=0.057  Sum_probs=61.7

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++=++|+|+++.  .+..+.|+..+..-.+++.+|++|.+. .+...+ +....+.+.+++.+++.+.+.+..+    .
T Consensus       107 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~~----~  182 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREVT----M  182 (334)
T ss_pred             CCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHccC----C
Confidence            4566899999986  345566665555435566766666653 344332 4466789999999999988865431    1


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      +   .+.+..+++.++|  .|....
T Consensus       183 ~---~~~a~~~~~la~G--~~~~Al  202 (334)
T PRK07993        183 S---QDALLAALRLSAG--APGAAL  202 (334)
T ss_pred             C---HHHHHHHHHHcCC--CHHHHH
Confidence            1   2346788999999  997543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.03  E-value=0.037  Score=51.78  Aligned_cols=92  Identities=15%  Similarity=0.103  Sum_probs=62.0

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++=++|+|+++.  .+..+.|+..+..-.+++.+|++|.+. .+...+ +....+.+.++++++..+.+......    
T Consensus       106 g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~~~----  181 (325)
T PRK06871        106 GGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQSSA----  181 (325)
T ss_pred             CCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHhcc----
Confidence            4556888999987  345566666555435666777777654 444333 44678999999999999988876421    


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      .   ...+...++.++|  .|+...
T Consensus       182 ~---~~~~~~~~~l~~g--~p~~A~  201 (325)
T PRK06871        182 E---ISEILTALRINYG--RPLLAL  201 (325)
T ss_pred             C---hHHHHHHHHHcCC--CHHHHH
Confidence            1   1235677889999  997443

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.03  E-value=0.012  Score=56.74  Aligned_cols=90  Identities=14%  Similarity=0.199  Sum_probs=51.6

Q ss_pred             CceEEEEEeCCCCh-------------h---hhhHhhCCCCCC--CCCCeEEEEecchhHHhh-C----CCCCeeecCCC
Q 040234           75 RKKVLVVIDDAAHP-------------D---HLRRLVGEPDWF--GPGSRIIITTRNEHLLKL-H----PVKKVYKLEAL  131 (377)
Q Consensus        75 ~k~~LLVLDdv~~~-------------~---~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~~-~----~~~~~~~l~~L  131 (377)
                      ..+.+|+||+++..             +   .+..++..+...  ..+..||.||........ +    .-...+++++.
T Consensus       223 ~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P  302 (389)
T PRK03992        223 KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLP  302 (389)
T ss_pred             cCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCC
Confidence            45689999998752             1   122233222211  234567777765432111 1    22457899999


Q ss_pred             ChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          132 TYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       132 ~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      +.++-.++|..+.....-...   .....+++.+.|
T Consensus       303 ~~~~R~~Il~~~~~~~~~~~~---~~~~~la~~t~g  335 (389)
T PRK03992        303 DEEGRLEILKIHTRKMNLADD---VDLEELAELTEG  335 (389)
T ss_pred             CHHHHHHHHHHHhccCCCCCc---CCHHHHHHHcCC
Confidence            999999999887643221111   124567777777

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.03  E-value=0.0083  Score=61.18  Aligned_cols=96  Identities=13%  Similarity=0.075  Sum_probs=59.4

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEec-chhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTR-NEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR-~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++.  .+..+.|+..+..-.....+|++|. ...+...+ .....+++..++.++....+.+.+......
T Consensus       120 ~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi~  199 (620)
T PRK14948        120 ARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESIE  199 (620)
T ss_pred             CCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCCC
Confidence            3456899999986  3456666665543334455554444 33333322 345678889999999888887766432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        ...+.+..|++.++|  .+..+
T Consensus       200 --is~~al~~La~~s~G--~lr~A  219 (620)
T PRK14948        200 --IEPEALTLVAQRSQG--GLRDA  219 (620)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHH
Confidence              113567888888988  66544

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.99  E-value=0.026  Score=52.63  Aligned_cols=92  Identities=16%  Similarity=0.155  Sum_probs=61.8

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|+|+++.  .+..+.|+..+..-.+++.+|++|.+. .+...+ +....+.+.+++.+++.+.+....   .  
T Consensus       107 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~---~--  181 (319)
T PRK06090        107 NGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQG---I--  181 (319)
T ss_pred             CCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHcC---C--
Confidence            3455899999986  345666666555435567766666554 444443 446789999999999998886532   1  


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      .     .+..+++.++|  .|+......
T Consensus       182 ~-----~~~~~l~l~~G--~p~~A~~~~  202 (319)
T PRK06090        182 T-----VPAYALKLNMG--SPLKTLAMM  202 (319)
T ss_pred             c-----hHHHHHHHcCC--CHHHHHHHh
Confidence            1     13467899999  998765543

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=96.97  E-value=0.0087  Score=61.13  Aligned_cols=111  Identities=15%  Similarity=-0.011  Sum_probs=63.3

Q ss_pred             hHHHHHHHhcCceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEE--EecchhH-HhhC-CCCCeeecCCCChhhhHH
Q 040234           65 GINMLRVRLRRKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIII--TTRNEHL-LKLH-PVKKVYKLEALTYDEAFR  138 (377)
Q Consensus        65 ~~~~l~~~l~~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIv--TTR~~~v-~~~~-~~~~~~~l~~L~~~ea~~  138 (377)
                      .+..+.+.+.+++++++.|+.|..  ..|+.+...+....+...+++  ||++... ...+ .....+.+.+++.++.++
T Consensus       281 ~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~  360 (615)
T TIGR02903       281 LQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIAL  360 (615)
T ss_pred             HHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHH
Confidence            456677777777777776665543  335555544444344444554  5664321 1111 223467899999999999


Q ss_pred             HHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          139 LLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       139 L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ++.+.+.......  .+++.+.|.+....  -+-++..+..
T Consensus       361 Il~~~a~~~~v~l--s~eal~~L~~ys~~--gRraln~L~~  397 (615)
T TIGR02903       361 IVLNAAEKINVHL--AAGVEELIARYTIE--GRKAVNILAD  397 (615)
T ss_pred             HHHHHHHHcCCCC--CHHHHHHHHHCCCc--HHHHHHHHHH
Confidence            9998774322111  13455556555555  5666654443

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.96  E-value=0.0099  Score=60.59  Aligned_cols=90  Identities=11%  Similarity=0.086  Sum_probs=56.5

Q ss_pred             ceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEE-EecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           76 KKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIII-TTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        76 k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIv-TTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      ++-++|+|++...  +..+.|+..+..-...+.+|+ ||+...+...+ .....+++.+++.++....+.+.+....-. 
T Consensus       121 ~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~-  199 (614)
T PRK14971        121 KYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGIT-  199 (614)
T ss_pred             CcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCC-
Confidence            4558899999763  445566555543334555554 54545554432 446789999999999998888766432211 


Q ss_pred             hhHHHHHHHHHHHhCC
Q 040234          152 EEYVELAESVVRICHC  167 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G  167 (377)
                       ...+.+..|++.+||
T Consensus       200 -i~~~al~~La~~s~g  214 (614)
T PRK14971        200 -AEPEALNVIAQKADG  214 (614)
T ss_pred             -CCHHHHHHHHHHcCC
Confidence             113456777777777

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.90  E-value=0.0037  Score=50.06  Aligned_cols=27  Identities=33%  Similarity=0.386  Sum_probs=19.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      .+|+||||+|+.++..........+++
T Consensus        10 ~~G~GKTtl~~~l~~~~~~~~~~~~~~   36 (148)
T smart00382       10 PPGSGKTTLARALARELGPPGGGVIYI   36 (148)
T ss_pred             CCCCcHHHHHHHHHhccCCCCCCEEEE
Confidence            379999999999999766554233333

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.90  E-value=0.021  Score=56.08  Aligned_cols=94  Identities=13%  Similarity=0.071  Sum_probs=58.3

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEec-chhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTR-NEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR-~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  +..+.|+..+..-.....+|++|. ...+...+ .....+++.++++++..+.+...+..... 
T Consensus       120 ~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~-  198 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGI-  198 (451)
T ss_pred             CCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCC-
Confidence            45668999998753  344555555444344556665553 33333222 33567899999999999888876633211 


Q ss_pred             chhHHHHHHHHHHHhCCCCchh
Q 040234          151 LEEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpl  172 (377)
                       ....+.+..|++.++|  ...
T Consensus       199 -~i~~~al~~L~~~s~g--dlr  217 (451)
T PRK06305        199 -ETSREALLPIARAAQG--SLR  217 (451)
T ss_pred             -CCCHHHHHHHHHHcCC--CHH
Confidence             1124567888888888  554

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.87  E-value=0.026  Score=56.96  Aligned_cols=96  Identities=13%  Similarity=0.089  Sum_probs=60.5

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEec-chhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTR-NEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR-~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|++..  ...++.|+..+..-.+...+|.+|. ...+...+ .....+++.+++.++..+.+.+.+......
T Consensus       118 ~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi~  197 (563)
T PRK06647        118 SRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIK  197 (563)
T ss_pred             CCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            4556899999876  3456677666654344556655554 34443322 335678999999999988888766332211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        ..++.+..|++.++|  .+..+
T Consensus       198 --id~eAl~lLa~~s~G--dlR~a  217 (563)
T PRK06647        198 --YEDEALKWIAYKSTG--SVRDA  217 (563)
T ss_pred             --CCHHHHHHHHHHcCC--CHHHH
Confidence              124567778888888  66533

>COG3899 Predicted ATPase [General function prediction only]

Probab=96.85  E-value=0.012  Score=62.44  Aligned_cols=104  Identities=13%  Similarity=0.069  Sum_probs=64.5

Q ss_pred             CceEEEEEeCC-CCh-hh---hhHhhCCCCC-CCCCCeEEE--Eecch--hHHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           75 RKKVLVVIDDA-AHP-DH---LRRLVGEPDW-FGPGSRIII--TTRNE--HLLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        75 ~k~~LLVLDdv-~~~-~~---~~~l~~~l~~-~~~gs~IIv--TTR~~--~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      .++.++|+||+ |-+ ..   ++.+.....- ......|..  |.+..  .+-........+.|.||+..+...|.....
T Consensus       153 ~~plVi~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l  232 (849)
T COG3899         153 EHPLVIVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATL  232 (849)
T ss_pred             cCCeEEEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHh
Confidence            45999999998 332 22   2233222210 000112332  33322  222223446789999999999999998888


Q ss_pred             cCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhhc
Q 040234          145 FDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVS  183 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~  183 (377)
                      +......   .+....|.++..|  +|+-+...-..++.
T Consensus       233 ~~~~~~~---~p~~~~i~~kt~G--nPfFi~e~lk~l~~  266 (849)
T COG3899         233 GCTKLLP---APLLELIFEKTKG--NPFFIEEFLKALYE  266 (849)
T ss_pred             CCccccc---chHHHHHHHHhcC--CCccHHHHHHHHHh
Confidence            5533222   4567899999999  99999888887654

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

Probab=96.84  E-value=0.027  Score=51.58  Aligned_cols=167  Identities=15%  Similarity=-0.017  Sum_probs=89.9

Q ss_pred             CCCcHHHHHHHHHchhccccccc-----eEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcC-
Q 040234            2 GGLGKTTLARVVYDLISHEFDGS-----SFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRR-   75 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~-----~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~-   75 (377)
                      +|.|||++++++.+.....++..     +++.......    +...+...|+.+++..... ..+...........++. 
T Consensus        70 snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p----~~~~~Y~~IL~~lgaP~~~-~~~~~~~~~~~~~llr~~  144 (302)
T PF05621_consen   70 SNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEP----DERRFYSAILEALGAPYRP-RDRVAKLEQQVLRLLRRL  144 (302)
T ss_pred             CCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCC----ChHHHHHHHHHHhCcccCC-CCCHHHHHHHHHHHHHHc
Confidence            68999999999998554444311     3333232222    8899999999998765332 23444444444555554 


Q ss_pred             ceEEEEEeCCCCh-----hhhh---HhhCCCCCCCCCCeEEEEecchhHHhhC-----CCCCeeecCCCChhh-hHHHHH
Q 040234           76 KKVLVVIDDAAHP-----DHLR---RLVGEPDWFGPGSRIIITTRNEHLLKLH-----PVKKVYKLEALTYDE-AFRLLC  141 (377)
Q Consensus        76 k~~LLVLDdv~~~-----~~~~---~l~~~l~~~~~gs~IIvTTR~~~v~~~~-----~~~~~~~l~~L~~~e-a~~L~~  141 (377)
                      +--+||+|++-+.     .+-+   ..+..+.+.-.=+-|.+-|++-.-+-..     +....+.++.-..++ ...|+.
T Consensus       145 ~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~  224 (302)
T PF05621_consen  145 GVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLASRFEPFELPRWELDEEFRRLLA  224 (302)
T ss_pred             CCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHHhccCCccCCCCCCCcHHHHHHH
Confidence            4558999998652     1111   1112222212334566666543221111     113445555544433 344443


Q ss_pred             HHhc---CCCCCchhHHHHHHHHHHHhCCCCchhhHH
Q 040234          142 LKAF---DTHKPLEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       142 ~~~~---~~~~~~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      ....   ......-...++++.|...++|  +.-.+.
T Consensus       225 s~e~~LPLr~~S~l~~~~la~~i~~~s~G--~iG~l~  259 (302)
T PF05621_consen  225 SFERALPLRKPSNLASPELARRIHERSEG--LIGELS  259 (302)
T ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHcCC--chHHHH
Confidence            3221   1112223447889999999999  665543

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

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

Probab=96.82  E-value=0.0039  Score=56.53  Aligned_cols=45  Identities=27%  Similarity=0.344  Sum_probs=32.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+||+++++.++.+|+..+++..+++..+   .+.++.+.+..
T Consensus        78 ~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer~~---Ev~e~~~~~~~  122 (274)
T cd01133          78 AGVGKTVLIMELINNIAKAHGGYSVFAGVGERTR---EGNDLYHEMKE  122 (274)
T ss_pred             CCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcH---HHHHHHHHHHh
Confidence            6999999999999988878887777776666532   44455555443

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.

>CHL00176 ftsH cell division protein; Validated

Probab=96.81  E-value=0.026  Score=57.71  Aligned_cols=140  Identities=16%  Similarity=0.184  Sum_probs=76.8

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++....     ++. ++.        .++....    .+.      ......+.+.+.....+.+|
T Consensus       224 PpGTGKT~LAralA~e~~~p-----~i~-is~--------s~f~~~~----~g~------~~~~vr~lF~~A~~~~P~IL  279 (638)
T CHL00176        224 PPGTGKTLLAKAIAGEAEVP-----FFS-ISG--------SEFVEMF----VGV------GAARVRDLFKKAKENSPCIV  279 (638)
T ss_pred             CCCCCHHHHHHHHHHHhCCC-----eee-ccH--------HHHHHHh----hhh------hHHHHHHHHHHHhcCCCcEE
Confidence            47999999999999865322     222 211        1111110    000      11122334445556678999


Q ss_pred             EEeCCCCh----------------hhhhHhhCCCCCC--CCCCeEEEEecchhHHhh-C----CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHP----------------DHLRRLVGEPDWF--GPGSRIIITTRNEHLLKL-H----PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~----------------~~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~~-~----~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++..                ..+..++..+...  ..+-.||.||........ +    .-...+.++..+.++-.
T Consensus       280 fIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~  359 (638)
T CHL00176        280 FIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRL  359 (638)
T ss_pred             EEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHH
Confidence            99999642                1233444333211  234456666665433221 1    23467889999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ++|+.++..... .  .......+++.+.|
T Consensus       360 ~IL~~~l~~~~~-~--~d~~l~~lA~~t~G  386 (638)
T CHL00176        360 DILKVHARNKKL-S--PDVSLELIARRTPG  386 (638)
T ss_pred             HHHHHHHhhccc-c--hhHHHHHHHhcCCC
Confidence            999887743211 1  12345677777776

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

Probab=96.80  E-value=0.011  Score=57.08  Aligned_cols=63  Identities=21%  Similarity=0.211  Sum_probs=47.6

Q ss_pred             ceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHH-----hhC-CCCCeeecCCCChhhhHHH
Q 040234           76 KKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLL-----KLH-PVKKVYKLEALTYDEAFRL  139 (377)
Q Consensus        76 k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~-----~~~-~~~~~~~l~~L~~~ea~~L  139 (377)
                      ++.+++||.|.....|...+..+.+.++. +|++|+-+....     ... +....+++-||+-.|-..+
T Consensus        94 ~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~~  162 (398)
T COG1373          94 EKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLKL  162 (398)
T ss_pred             CCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHhh
Confidence            77899999999999998877777665665 788888765432     222 3367789999999888664

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.80  E-value=0.028  Score=56.83  Aligned_cols=95  Identities=11%  Similarity=0.038  Sum_probs=58.5

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEE-EecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIII-TTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIv-TTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++.-++|+|++..  ...++.|+..+..-.....+|+ ||....+...+ .....+++.+++.++..+.+...+....-.
T Consensus       118 ~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~  197 (559)
T PRK05563        118 AKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIE  197 (559)
T ss_pred             CCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCCC
Confidence            4566889999986  3456666655543233444444 44444433322 335678899999999998888766432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                        ...+.+..|++.++|  -+..
T Consensus       198 --i~~~al~~ia~~s~G--~~R~  216 (559)
T PRK05563        198 --YEDEALRLIARAAEG--GMRD  216 (559)
T ss_pred             --CCHHHHHHHHHHcCC--CHHH
Confidence              124567778888887  6543

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.79  E-value=0.078  Score=49.54  Aligned_cols=97  Identities=16%  Similarity=0.147  Sum_probs=60.6

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  ...+.|+..+..-. .+.+|++|.+ ..+...+ +....+++.++++++..+.+.+.....  .
T Consensus       123 ~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~--~  199 (314)
T PRK07399        123 APRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEE--I  199 (314)
T ss_pred             CCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhccc--c
Confidence            45668999999763  34555554443323 4455555544 4443333 446889999999999999998765211  1


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ..   .....++...+|  .|..+.....
T Consensus       200 ~~---~~~~~l~~~a~G--s~~~al~~l~  223 (314)
T PRK07399        200 LN---INFPELLALAQG--SPGAAIANIE  223 (314)
T ss_pred             ch---hHHHHHHHHcCC--CHHHHHHHHH
Confidence            11   113578899999  9976654433

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.77  E-value=0.025  Score=56.42  Aligned_cols=140  Identities=16%  Similarity=0.165  Sum_probs=73.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||+||+.+++...-.|     +. ++        ...+..    ...+.      ......+.+.......+.+|
T Consensus        96 ppGtGKT~la~alA~~~~~~~-----~~-i~--------~~~~~~----~~~g~------~~~~l~~~f~~a~~~~p~Il  151 (495)
T TIGR01241        96 PPGTGKTLLAKAVAGEAGVPF-----FS-IS--------GSDFVE----MFVGV------GASRVRDLFEQAKKNAPCII  151 (495)
T ss_pred             CCCCCHHHHHHHHHHHcCCCe-----ee-cc--------HHHHHH----HHhcc------cHHHHHHHHHHHHhcCCCEE
Confidence            479999999999998643322     21 21        111111    11110      11122333444444567899


Q ss_pred             EEeCCCChh----------------hhhHhhCCCCCC--CCCCeEEEEecchhH-----HhhCCCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHPD----------------HLRRLVGEPDWF--GPGSRIIITTRNEHL-----LKLHPVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~~----------------~~~~l~~~l~~~--~~gs~IIvTTR~~~v-----~~~~~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++...                .+..++..+...  ..+-.||.||.....     .+...-...+.++..+.++-.
T Consensus       152 ~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~  231 (495)
T TIGR01241       152 FIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGRE  231 (495)
T ss_pred             EEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHH
Confidence            999985421                122333322211  223456666655431     111123567889999998889


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ++|..+........   ......+++.+.|
T Consensus       232 ~il~~~l~~~~~~~---~~~l~~la~~t~G  258 (495)
T TIGR01241       232 EILKVHAKNKKLAP---DVDLKAVARRTPG  258 (495)
T ss_pred             HHHHHHHhcCCCCc---chhHHHHHHhCCC
Confidence            99887764322111   1234578888877

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.73  E-value=0.012  Score=55.04  Aligned_cols=67  Identities=18%  Similarity=0.250  Sum_probs=37.3

Q ss_pred             ceEEEEEeCCCCh---hhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCChhhhHHHHHH
Q 040234           76 KKVLVVIDDAAHP---DHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALTYDEAFRLLCL  142 (377)
Q Consensus        76 k~~LLVLDdv~~~---~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~~~ea~~L~~~  142 (377)
                      .+-+||+|+++..   +....+...+.....++++|+||.... +...+ +....+.++..+.++..+++..
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~~  171 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQ  171 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHHH
Confidence            3458899999754   222222222222245678888886542 11111 2234677778888887766543

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

Probab=96.72  E-value=0.02  Score=55.25  Aligned_cols=140  Identities=15%  Similarity=0.099  Sum_probs=72.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++.....|   +.+. . .         .+    .....+.      ......+.+.......+.+|
T Consensus       187 ppGTGKT~LAkalA~~l~~~f---i~i~-~-s---------~l----~~k~~ge------~~~~lr~lf~~A~~~~P~IL  242 (398)
T PTZ00454        187 PPGTGKTMLAKAVAHHTTATF---IRVV-G-S---------EF----VQKYLGE------GPRMVRDVFRLARENAPSII  242 (398)
T ss_pred             CCCCCHHHHHHHHHHhcCCCE---EEEe-h-H---------HH----HHHhcch------hHHHHHHHHHHHHhcCCeEE
Confidence            479999999999998665443   1111 1 1         11    1111110      11112222333334578899


Q ss_pred             EEeCCCCh-------------h---hhhHhhCCCCC--CCCCCeEEEEecchhHHhh--C---CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHP-------------D---HLRRLVGEPDW--FGPGSRIIITTRNEHLLKL--H---PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~-------------~---~~~~l~~~l~~--~~~gs~IIvTTR~~~v~~~--~---~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++..             +   .+..++..+..  ...+..||+||........  .   .-...++++..+.++-.
T Consensus       243 fIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~  322 (398)
T PTZ00454        243 FIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKR  322 (398)
T ss_pred             EEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHH
Confidence            99997632             0   12233322221  1234567777775433211  1   23566889989999888


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ++|......... .+  .-...++++...|
T Consensus       323 ~Il~~~~~~~~l-~~--dvd~~~la~~t~g  349 (398)
T PTZ00454        323 LIFQTITSKMNL-SE--EVDLEDFVSRPEK  349 (398)
T ss_pred             HHHHHHHhcCCC-Cc--ccCHHHHHHHcCC
Confidence            888766532211 11  1124566777777

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.68  E-value=0.017  Score=58.53  Aligned_cols=91  Identities=12%  Similarity=0.052  Sum_probs=54.7

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEE-EecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIII-TTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIv-TTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  ...+.|+..+..-.....+|+ ||....+...+ .....+++.+++.++....+...+......
T Consensus       118 ~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~  197 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGIS  197 (576)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCC
Confidence            34558999999763  445556554443244555554 54445444332 345678899999999888887665322211


Q ss_pred             chhHHHHHHHHHHHhCC
Q 040234          151 LEEYVELAESVVRICHC  167 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G  167 (377)
                        ...+.+..|++.++|
T Consensus       198 --i~~~al~~la~~a~G  212 (576)
T PRK14965        198 --ISDAALALVARKGDG  212 (576)
T ss_pred             --CCHHHHHHHHHHcCC
Confidence              113456667777777

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.66  E-value=0.025  Score=56.07  Aligned_cols=71  Identities=14%  Similarity=0.118  Sum_probs=42.7

Q ss_pred             CceEEEEEeCCCChh--------------hhhHhhCCCCCC--CCCCeEEEEecchhHHh-hC----CCCCeeecCCCCh
Q 040234           75 RKKVLVVIDDAAHPD--------------HLRRLVGEPDWF--GPGSRIIITTRNEHLLK-LH----PVKKVYKLEALTY  133 (377)
Q Consensus        75 ~k~~LLVLDdv~~~~--------------~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~-~~----~~~~~~~l~~L~~  133 (377)
                      +++.+|+||+++...              .+..|+..+...  ..+..||.||....... .+    .-...++++..+.
T Consensus       288 g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~  367 (512)
T TIGR03689       288 GRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDA  367 (512)
T ss_pred             CCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCH
Confidence            478999999997421              122333333221  13344555665443211 11    2245689999999


Q ss_pred             hhhHHHHHHHhc
Q 040234          134 DEAFRLLCLKAF  145 (377)
Q Consensus       134 ~ea~~L~~~~~~  145 (377)
                      ++..++|..+..
T Consensus       368 e~r~~Il~~~l~  379 (512)
T TIGR03689       368 EAAADIFSKYLT  379 (512)
T ss_pred             HHHHHHHHHHhh
Confidence            999999998873

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.

>PRK08181 transposase; Validated

Probab=96.62  E-value=0.0034  Score=57.12  Aligned_cols=27  Identities=22%  Similarity=0.033  Sum_probs=19.1

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      .+|+|||.||..+++...++...++|+
T Consensus       114 p~GtGKTHLa~Aia~~a~~~g~~v~f~  140 (269)
T PRK08181        114 PPGGGKSHLAAAIGLALIENGWRVLFT  140 (269)
T ss_pred             cCCCcHHHHHHHHHHHHHHcCCceeee
Confidence            379999999999998665443333443

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.54  E-value=0.044  Score=51.64  Aligned_cols=91  Identities=15%  Similarity=0.157  Sum_probs=59.4

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++.  .+..+.|+..+..-.+++.+|++|.+ ..+...+ +....+.+.+++.++..+.+....   .  
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~---~--  205 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQG---V--  205 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcC---C--
Confidence            3455889999986  45566666665544566666655554 4444333 446789999999999999887642   1  


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      .+     ...++..++|  .|+.....
T Consensus       206 ~~-----~~~~l~~~~G--sp~~Al~~  225 (342)
T PRK06964        206 AD-----ADALLAEAGG--APLAALAL  225 (342)
T ss_pred             Ch-----HHHHHHHcCC--CHHHHHHH
Confidence            11     1235778899  99755433

>PRK06921 hypothetical protein; Provisional

Probab=96.47  E-value=0.0085  Score=54.59  Aligned_cols=27  Identities=19%  Similarity=0.159  Sum_probs=20.2

Q ss_pred             CCCcHHHHHHHHHchhccc-cccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHE-FDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-f~~~~w~~   28 (377)
                      .|+|||.||..+++.+.++ ...++++.
T Consensus       126 ~G~GKThLa~aia~~l~~~~g~~v~y~~  153 (266)
T PRK06921        126 PGSGKTHLLTAAANELMRKKGVPVLYFP  153 (266)
T ss_pred             CCCcHHHHHHHHHHHHhhhcCceEEEEE
Confidence            6999999999999977654 33445554

>PRK12377 putative replication protein; Provisional

Probab=96.45  E-value=0.007  Score=54.42  Aligned_cols=26  Identities=19%  Similarity=0.179  Sum_probs=19.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      .|+|||+||..+++.+......++++
T Consensus       110 ~GtGKThLa~AIa~~l~~~g~~v~~i  135 (248)
T PRK12377        110 PGTGKNHLAAAIGNRLLAKGRSVIVV  135 (248)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCeEEE
Confidence            69999999999999776554334444

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

Probab=96.43  E-value=0.098  Score=46.52  Aligned_cols=170  Identities=16%  Similarity=0.081  Sum_probs=88.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCcc-chhhhHHHHHHHh-cCce-E
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIR-NVYDGINMLRVRL-RRKK-V   78 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~-~~~~~~~~l~~~l-~~k~-~   78 (377)
                      -|.|||.+++.+....-+.  ..+-+..-.+..    +...+...+...+......... ..+.....+.... ++++ .
T Consensus        60 vGsGKTv~~Ral~~s~~~d--~~~~v~i~~~~~----s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v  133 (269)
T COG3267          60 VGSGKTVLRRALLASLNED--QVAVVVIDKPTL----SDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPV  133 (269)
T ss_pred             CCCchhHHHHHHHHhcCCC--ceEEEEecCcch----hHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCe
Confidence            3899999999555433221  111122111222    5556666676666542211111 1222222333333 3566 8


Q ss_pred             EEEEeCCCC--hhhhh---HhhCCCCCCCCCCeEEEEecc--------hhHHhhCCCCCe-eecCCCChhhhHHHHHHHh
Q 040234           79 LVVIDDAAH--PDHLR---RLVGEPDWFGPGSRIIITTRN--------EHLLKLHPVKKV-YKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        79 LLVLDdv~~--~~~~~---~l~~~l~~~~~gs~IIvTTR~--------~~v~~~~~~~~~-~~l~~L~~~ea~~L~~~~~  144 (377)
                      .+++|++.+  .+.++   .|...-......-+|+..-.-        ............ |++.|++.++...++..+.
T Consensus       134 ~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~~t~~yl~~~L  213 (269)
T COG3267         134 VLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETGLYLRHRL  213 (269)
T ss_pred             EEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChHHHHHHHHHHH
Confidence            999999865  23333   332222221222234433221        111111111233 8999999999888888776


Q ss_pred             cCCCCC-chhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          145 FDTHKP-LEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       145 ~~~~~~-~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      .....+ .--..+....|.....|  .|.++..+..
T Consensus       214 e~a~~~~~l~~~~a~~~i~~~sqg--~P~lin~~~~  247 (269)
T COG3267         214 EGAGLPEPLFSDDALLLIHEASQG--IPRLINNLAT  247 (269)
T ss_pred             hccCCCcccCChhHHHHHHHHhcc--chHHHHHHHH
Confidence            443222 22235677889999999  9999876554

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.37  E-value=0.0056  Score=50.91  Aligned_cols=46  Identities=15%  Similarity=0.149  Sum_probs=26.5

Q ss_pred             HHHHhcCc-eEEEEEeCCCCh-----hhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           69 LRVRLRRK-KVLVVIDDAAHP-----DHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        69 l~~~l~~k-~~LLVLDdv~~~-----~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      .++.+... -=|||||++-..     -..+.+...+.....+..||+|.|+.
T Consensus        87 a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          87 AKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence            34444443 459999997432     11222333333335567899999985

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.

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

Probab=96.36  E-value=0.0089  Score=50.88  Aligned_cols=20  Identities=35%  Similarity=0.556  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+|||+|.+++..++..+
T Consensus        32 ~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen   32 ESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             -TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhc
Confidence            47999999999999977666

>PRK06526 transposase; Provisional

Probab=96.34  E-value=0.0052  Score=55.55  Aligned_cols=19  Identities=32%  Similarity=0.113  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+|||+||..+..+...
T Consensus       106 p~GtGKThLa~al~~~a~~  124 (254)
T PRK06526        106 PPGTGKTHLAIGLGIRACQ  124 (254)
T ss_pred             CCCCchHHHHHHHHHHHHH
Confidence            3799999999999985543

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

Probab=96.34  E-value=0.026  Score=59.07  Aligned_cols=123  Identities=15%  Similarity=0.097  Sum_probs=63.6

Q ss_pred             CCCCcHHHHHHHHHchhccc-----c-ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-
Q 040234            1 MGGLGKTTLARVVYDLISHE-----F-DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-----f-~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-   73 (377)
                      .+|+|||+||+.+++++...     + ...+|..          +...+...       .  ....+.++....+.+.+ 
T Consensus       211 ~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~----------~~~~l~a~-------~--~~~g~~e~~l~~i~~~~~  271 (731)
T TIGR02639       211 EPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSL----------DMGSLLAG-------T--KYRGDFEERLKAVVSEIE  271 (731)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEe----------cHHHHhhh-------c--cccchHHHHHHHHHHHHh
Confidence            37999999999999965332     1 2334444          22222110       0  00011222222233222 


Q ss_pred             cCceEEEEEeCCCCh-----------hhhhHhhCCCCCCCCCCeEEEEecchhHHh------hC-CCCCeeecCCCChhh
Q 040234           74 RRKKVLVVIDDAAHP-----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLK------LH-PVKKVYKLEALTYDE  135 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~-----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~------~~-~~~~~~~l~~L~~~e  135 (377)
                      ..++.+|++|++...           +.-+.|.+.+..  ..-++|-+|.......      .. .....++++.++.++
T Consensus       272 ~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~--g~i~~IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~  349 (731)
T TIGR02639       272 KEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSS--GKLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEE  349 (731)
T ss_pred             ccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhC--CCeEEEEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHH
Confidence            245789999998631           223334444321  1234454444321110      01 123578999999999


Q ss_pred             hHHHHHHHh
Q 040234          136 AFRLLCLKA  144 (377)
Q Consensus       136 a~~L~~~~~  144 (377)
                      ..+++....
T Consensus       350 ~~~il~~~~  358 (731)
T TIGR02639       350 TVKILKGLK  358 (731)
T ss_pred             HHHHHHHHH
Confidence            999998654

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.31  E-value=0.076  Score=50.02  Aligned_cols=68  Identities=18%  Similarity=0.178  Sum_probs=45.5

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHH
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCL  142 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~  142 (377)
                      +.+=++|+|+++.  .+..+.|+..+..-.+++.+|++|.++ .+...+ +....+++.+++.++..+.+..
T Consensus       109 ~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        109 SNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             cCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHH
Confidence            3455799999976  334556665555435667777777653 333332 3467899999999999888865

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.24  E-value=0.041  Score=50.05  Aligned_cols=18  Identities=44%  Similarity=0.331  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+|||+||+.+++...
T Consensus        29 ~~GtGKT~lA~~la~~lg   46 (262)
T TIGR02640        29 PAGTGKTTLAMHVARKRD   46 (262)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998543

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).

>PRK09183 transposase/IS protein; Provisional

Probab=96.22  E-value=0.0089  Score=54.27  Aligned_cols=18  Identities=33%  Similarity=0.241  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+|||+||..++....
T Consensus       110 p~GtGKThLa~al~~~a~  127 (259)
T PRK09183        110 PSGVGKTHLAIALGYEAV  127 (259)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            379999999999988543

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.20  E-value=0.015  Score=55.02  Aligned_cols=81  Identities=12%  Similarity=0.184  Sum_probs=47.2

Q ss_pred             CCCcHHHHHHHHHchhccccccc-eEEecchhhcccccCHHHHHHHHHHHHhhccccCccch--------hhhHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGS-SFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNV--------YDGINMLRVR   72 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~-~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~--------~~~~~~l~~~   72 (377)
                      .|+|||||++.+++.+....+.. +.+.-+++..   ..+.++++.+...+...........        .+.++.++. 
T Consensus       142 pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~---~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~Ae~f~~-  217 (380)
T PRK12608        142 PRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERP---EEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERAKRLVE-  217 (380)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCC---CCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHHHHHHH-
Confidence            69999999999999776554433 3333244432   2677777777665443211111110        011122222 


Q ss_pred             hcCceEEEEEeCCCC
Q 040234           73 LRRKKVLVVIDDAAH   87 (377)
Q Consensus        73 l~~k~~LLVLDdv~~   87 (377)
                       .+++.+||+|++..
T Consensus       218 -~GkdVVLvlDsltr  231 (380)
T PRK12608        218 -QGKDVVILLDSLTR  231 (380)
T ss_pred             -cCCCEEEEEeCcHH
Confidence             57899999999854

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

Probab=96.13  E-value=0.16  Score=49.03  Aligned_cols=159  Identities=19%  Similarity=0.195  Sum_probs=89.1

Q ss_pred             CCCcHHHHHHHHHchhcccccc--ceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcC--ce
Q 040234            2 GGLGKTTLARVVYDLISHEFDG--SSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRR--KK   77 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~--~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~--k~   77 (377)
                      +|.|||.+...++.+.......  .+++. ...-.    ...+++..|...+....... ....+..+.+.+...+  ..
T Consensus       184 PGtgkt~~l~rvl~~~~~~~~~~~~v~in-c~sl~----~~~aiF~kI~~~~~q~~~s~-~~~~~~~~~~~~h~~q~k~~  257 (529)
T KOG2227|consen  184 PGTGKTALLSRVLDSLSKSSKSPVTVYIN-CTSLT----EASAIFKKIFSSLLQDLVSP-GTGMQHLEKFEKHTKQSKFM  257 (529)
T ss_pred             CCcchHHHHHHHHHhhhhhcccceeEEEe-ecccc----chHHHHHHHHHHHHHHhcCC-chhHHHHHHHHHHHhcccce
Confidence            6999999999999866655543  35555 33222    56677778877764332211 2224455556555554  36


Q ss_pred             EEEEEeCCCChhh--hhHhhCCCCCC-CCCCeEEEEec--c----hhHHhhC-----CCCCeeecCCCChhhhHHHHHHH
Q 040234           78 VLVVIDDAAHPDH--LRRLVGEPDWF-GPGSRIIITTR--N----EHLLKLH-----PVKKVYKLEALTYDEAFRLLCLK  143 (377)
Q Consensus        78 ~LLVLDdv~~~~~--~~~l~~~l~~~-~~gs~IIvTTR--~----~~v~~~~-----~~~~~~~l~~L~~~ea~~L~~~~  143 (377)
                      +|+|||.++....  -..+...+.|- -+++++|+.--  .    ...+..+     -.-..+..+|.+.++..++|..+
T Consensus       258 ~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~r  337 (529)
T KOG2227|consen  258 LLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQR  337 (529)
T ss_pred             EEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHH
Confidence            8999999986321  11111111111 34555554321  1    1111111     12456788999999999999999


Q ss_pred             hcCCCCCchhHHHHHHHHHHHhCC
Q 040234          144 AFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       144 ~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      +.... ........++-+++++.|
T Consensus       338 l~~~~-t~~~~~~Aie~~ArKvaa  360 (529)
T KOG2227|consen  338 LSEES-TSIFLNAAIELCARKVAA  360 (529)
T ss_pred             Hhccc-ccccchHHHHHHHHHhcc
Confidence            84332 222333445555666655

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

Probab=96.11  E-value=0.0081  Score=53.44  Aligned_cols=27  Identities=33%  Similarity=0.550  Sum_probs=22.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .|+|||+|...+.......|+...++.
T Consensus        22 sGSGKT~li~~lL~~~~~~f~~I~l~t   48 (241)
T PF04665_consen   22 SGSGKTTLIKSLLYYLRHKFDHIFLIT   48 (241)
T ss_pred             CCCCHHHHHHHHHHhhcccCCEEEEEe
Confidence            699999999999998888996665554

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

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.10  E-value=0.015  Score=52.22  Aligned_cols=25  Identities=20%  Similarity=0.194  Sum_probs=18.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSF   26 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w   26 (377)
                      +|+|||+||..+++.+...-..+++
T Consensus       108 ~GtGKThLa~aia~~l~~~g~~v~~  132 (244)
T PRK07952        108 PGTGKNHLAAAICNELLLRGKSVLI  132 (244)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEE
Confidence            7999999999999976554333333

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.07  E-value=0.047  Score=51.24  Aligned_cols=68  Identities=15%  Similarity=0.105  Sum_probs=40.0

Q ss_pred             ceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCChhhhHHHHHHH
Q 040234           76 KKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALTYDEAFRLLCLK  143 (377)
Q Consensus        76 k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~~~ea~~L~~~~  143 (377)
                      ++-++|+|++...  +..+.++..+..-..+..+|++|.+.. +...+ +....+.+.+++.+++.+.+.+.
T Consensus       113 ~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~  184 (325)
T PRK08699        113 GLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRER  184 (325)
T ss_pred             CceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhc
Confidence            3345566887653  333333333222234566777777643 33332 34677899999999999888653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.06  E-value=0.036  Score=58.15  Aligned_cols=140  Identities=16%  Similarity=0.129  Sum_probs=73.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++....|     +. +..        ..+    +....+.      +.....+.+...-...+.+|
T Consensus       495 ppGtGKT~lakalA~e~~~~f-----i~-v~~--------~~l----~~~~vGe------se~~i~~~f~~A~~~~p~ii  550 (733)
T TIGR01243       495 PPGTGKTLLAKAVATESGANF-----IA-VRG--------PEI----LSKWVGE------SEKAIREIFRKARQAAPAII  550 (733)
T ss_pred             CCCCCHHHHHHHHHHhcCCCE-----EE-Eeh--------HHH----hhcccCc------HHHHHHHHHHHHHhcCCEEE
Confidence            479999999999999765443     11 211        111    1111111      11122233333334567899


Q ss_pred             EEeCCCCh--------------hhhhHhhCCCCCC--CCCCeEEEEecchhHHhh-C----CCCCeeecCCCChhhhHHH
Q 040234           81 VIDDAAHP--------------DHLRRLVGEPDWF--GPGSRIIITTRNEHLLKL-H----PVKKVYKLEALTYDEAFRL  139 (377)
Q Consensus        81 VLDdv~~~--------------~~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~~-~----~~~~~~~l~~L~~~ea~~L  139 (377)
                      +||+++..              .....++..+...  ..+-.||.||........ +    .-...+.++..+.++-.++
T Consensus       551 fiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i  630 (733)
T TIGR01243       551 FFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEI  630 (733)
T ss_pred             EEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHH
Confidence            99998632              1123333333211  233446666655433221 1    2356788999999998999


Q ss_pred             HHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          140 LCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      |..+........   ......+++.+.|
T Consensus       631 ~~~~~~~~~~~~---~~~l~~la~~t~g  655 (733)
T TIGR01243       631 FKIHTRSMPLAE---DVDLEELAEMTEG  655 (733)
T ss_pred             HHHHhcCCCCCc---cCCHHHHHHHcCC
Confidence            876653222111   1124567788887

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.

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

Probab=96.06  E-value=0.019  Score=55.86  Aligned_cols=140  Identities=17%  Similarity=0.108  Sum_probs=72.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++....|   +.+. .+.          +.    ....+.      ......+.+.......+.+|
T Consensus       225 PPGTGKT~LAraIA~el~~~f---i~V~-~se----------L~----~k~~Ge------~~~~vr~lF~~A~~~~P~IL  280 (438)
T PTZ00361        225 PPGTGKTLLAKAVANETSATF---LRVV-GSE----------LI----QKYLGD------GPKLVRELFRVAEENAPSIV  280 (438)
T ss_pred             CCCCCHHHHHHHHHHhhCCCE---EEEe-cch----------hh----hhhcch------HHHHHHHHHHHHHhCCCcEE
Confidence            479999999999999776554   1111 111          11    010010      01111222222334567888


Q ss_pred             EEeCCCChh----------------hhhHhhCCCCC--CCCCCeEEEEecchhHHhh-C----CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHPD----------------HLRRLVGEPDW--FGPGSRIIITTRNEHLLKL-H----PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~~----------------~~~~l~~~l~~--~~~gs~IIvTTR~~~v~~~-~----~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++...                .+..++..+..  ...+.+||+||........ +    .....++++..+.++..
T Consensus       281 fIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~  360 (438)
T PTZ00361        281 FIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKR  360 (438)
T ss_pred             eHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHH
Confidence            999875310                11122222211  1235577877775443222 1    22567899999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ++|..+...-.-...   -....++..+.|
T Consensus       361 ~Il~~~~~k~~l~~d---vdl~~la~~t~g  387 (438)
T PTZ00361        361 RIFEIHTSKMTLAED---VDLEEFIMAKDE  387 (438)
T ss_pred             HHHHHHHhcCCCCcC---cCHHHHHHhcCC
Confidence            999877643221111   123456667766

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.96  E-value=0.058  Score=52.66  Aligned_cols=117  Identities=17%  Similarity=0.120  Sum_probs=66.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHH----HHHHhcCc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINM----LRVRLRRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~----l~~~l~~k   76 (377)
                      .+|+|||+||..++.  ...||-+-.   ++..        ++.        +      .++......    +...-+..
T Consensus       546 p~~sGKTaLAA~iA~--~S~FPFvKi---iSpe--------~mi--------G------~sEsaKc~~i~k~F~DAYkS~  598 (744)
T KOG0741|consen  546 PPGSGKTALAAKIAL--SSDFPFVKI---ISPE--------DMI--------G------LSESAKCAHIKKIFEDAYKSP  598 (744)
T ss_pred             CCCCChHHHHHHHHh--hcCCCeEEE---eChH--------Hcc--------C------ccHHHHHHHHHHHHHHhhcCc
Confidence            379999999999996  455664322   2221        110        0      011112222    22333455


Q ss_pred             eEEEEEeCCCChhhh------------hHhhCCCCCC---CCCCeEEEEecchhHHhhCCC----CCeeecCCCCh-hhh
Q 040234           77 KVLVVIDDAAHPDHL------------RRLVGEPDWF---GPGSRIIITTRNEHLLKLHPV----KKVYKLEALTY-DEA  136 (377)
Q Consensus        77 ~~LLVLDdv~~~~~~------------~~l~~~l~~~---~~gs~IIvTTR~~~v~~~~~~----~~~~~l~~L~~-~ea  136 (377)
                      --.||+||++..-+|            +.|+..+...   ++.--|+-||..+.+...++-    ...+.++.++. ++.
T Consensus       599 lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~  678 (744)
T KOG0741|consen  599 LSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQL  678 (744)
T ss_pred             ceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHH
Confidence            678999998754333            2332222222   233345567777788877642    46788999887 677


Q ss_pred             HHHHHHHh
Q 040234          137 FRLLCLKA  144 (377)
Q Consensus       137 ~~L~~~~~  144 (377)
                      .+.+...-
T Consensus       679 ~~vl~~~n  686 (744)
T KOG0741|consen  679 LEVLEELN  686 (744)
T ss_pred             HHHHHHcc
Confidence            77776543

>PRK10536 hypothetical protein; Provisional

Probab=95.93  E-value=0.053  Score=48.67  Aligned_cols=40  Identities=15%  Similarity=0.393  Sum_probs=28.6

Q ss_pred             HhcCceE---EEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           72 RLRRKKV---LVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        72 ~l~~k~~---LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      +++++.+   +||+|.+.+  ..+...++..+   +.+|++|+|--..
T Consensus       169 ymRGrtl~~~~vIvDEaqn~~~~~~k~~ltR~---g~~sk~v~~GD~~  213 (262)
T PRK10536        169 YMRGRTFENAVVILDEAQNVTAAQMKMFLTRL---GENVTVIVNGDIT  213 (262)
T ss_pred             HhcCCcccCCEEEEechhcCCHHHHHHHHhhc---CCCCEEEEeCChh
Confidence            5566654   999999987  45566665554   6899999886543

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.93  E-value=0.043  Score=54.30  Aligned_cols=142  Identities=12%  Similarity=0.088  Sum_probs=72.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||.+|+.++++..-.|    ...+.+..+              ....+.      +.....+.++..-...+.+|
T Consensus       267 PpGTGKTllAkaiA~e~~~~~----~~l~~~~l~--------------~~~vGe------se~~l~~~f~~A~~~~P~IL  322 (489)
T CHL00195        267 IQGTGKSLTAKAIANDWQLPL----LRLDVGKLF--------------GGIVGE------SESRMRQMIRIAEALSPCIL  322 (489)
T ss_pred             CCCCcHHHHHHHHHHHhCCCE----EEEEhHHhc--------------ccccCh------HHHHHHHHHHHHHhcCCcEE
Confidence            479999999999998654332    222121111              000000      11112222222223468999


Q ss_pred             EEeCCCChh--------------hhhHhhCCCCCCCCCCeEEEEecchhH-----HhhCCCCCeeecCCCChhhhHHHHH
Q 040234           81 VIDDAAHPD--------------HLRRLVGEPDWFGPGSRIIITTRNEHL-----LKLHPVKKVYKLEALTYDEAFRLLC  141 (377)
Q Consensus        81 VLDdv~~~~--------------~~~~l~~~l~~~~~gs~IIvTTR~~~v-----~~~~~~~~~~~l~~L~~~ea~~L~~  141 (377)
                      .+|+++..-              .+..++..+.....+--||.||....-     .+.-.-...+.++.-+.++-.++|.
T Consensus       323 ~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~  402 (489)
T CHL00195        323 WIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFK  402 (489)
T ss_pred             EehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHH
Confidence            999987421              111222222211233345667765432     1111235678888889999999998


Q ss_pred             HHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          142 LKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .+........ ........+++.+.|
T Consensus       403 ~~l~~~~~~~-~~~~dl~~La~~T~G  427 (489)
T CHL00195        403 IHLQKFRPKS-WKKYDIKKLSKLSNK  427 (489)
T ss_pred             HHHhhcCCCc-ccccCHHHHHhhcCC
Confidence            7774422111 001235677777777

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.86  E-value=0.013  Score=55.00  Aligned_cols=27  Identities=19%  Similarity=0.202  Sum_probs=19.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .|+|||.||..+++.+..+-..++++.
T Consensus       192 ~GtGKThLa~aIa~~l~~~g~~V~y~t  218 (329)
T PRK06835        192 TGTGKTFLSNCIAKELLDRGKSVIYRT  218 (329)
T ss_pred             CCCcHHHHHHHHHHHHHHCCCeEEEEE
Confidence            699999999999997655433444443

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

Probab=95.81  E-value=0.028  Score=50.85  Aligned_cols=65  Identities=23%  Similarity=0.203  Sum_probs=37.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      +|+|||.||..+.+++. .....+.+.          ...+++.++......         ......+.+.+.. -=|||
T Consensus       114 ~G~GKThLa~Ai~~~l~-~~g~sv~f~----------~~~el~~~Lk~~~~~---------~~~~~~l~~~l~~-~dlLI  172 (254)
T COG1484         114 PGVGKTHLAIAIGNELL-KAGISVLFI----------TAPDLLSKLKAAFDE---------GRLEEKLLRELKK-VDLLI  172 (254)
T ss_pred             CCCcHHHHHHHHHHHHH-HcCCeEEEE----------EHHHHHHHHHHHHhc---------CchHHHHHHHhhc-CCEEE
Confidence            69999999999999877 433333333          444555555544321         1112223332222 24899


Q ss_pred             EeCCCC
Q 040234           82 IDDAAH   87 (377)
Q Consensus        82 LDdv~~   87 (377)
                      |||+-.
T Consensus       173 iDDlG~  178 (254)
T COG1484         173 IDDIGY  178 (254)
T ss_pred             EecccC
Confidence            999854

>PHA00729 NTP-binding motif containing protein

Probab=95.80  E-value=0.061  Score=47.41  Aligned_cols=17  Identities=41%  Similarity=0.276  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+|||+||..+++++.
T Consensus        26 pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         26 QGSGKTTYALKVARDVF   42 (226)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            79999999999998654

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.77  E-value=0.014  Score=54.20  Aligned_cols=90  Identities=13%  Similarity=0.152  Sum_probs=47.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||.||..+++.+...-..+.++.           ...++..+.......      +..   +. .+.+. +.=|||
T Consensus       165 ~G~GKThLa~Aia~~l~~~g~~v~~~~-----------~~~l~~~lk~~~~~~------~~~---~~-l~~l~-~~dlLi  222 (306)
T PRK08939        165 FGVGKSYLLAAIANELAKKGVSSTLLH-----------FPEFIRELKNSISDG------SVK---EK-IDAVK-EAPVLM  222 (306)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCEEEEE-----------HHHHHHHHHHHHhcC------cHH---HH-HHHhc-CCCEEE
Confidence            699999999999997654422334433           234444444433111      111   22 22233 345899


Q ss_pred             EeCCCC--hhhhh--HhhCCC-CCC-CCCCeEEEEecc
Q 040234           82 IDDAAH--PDHLR--RLVGEP-DWF-GPGSRIIITTRN  113 (377)
Q Consensus        82 LDdv~~--~~~~~--~l~~~l-~~~-~~gs~IIvTTR~  113 (377)
                      |||+..  ...|.  .++..+ ... ..+..+|+||..
T Consensus       223 IDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        223 LDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             EecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence            999853  33343  233322 111 234567778764

>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=95.76  E-value=0.0063  Score=49.44  Aligned_cols=17  Identities=53%  Similarity=0.616  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+|||+||+.+++..
T Consensus         7 ~~G~GKt~l~~~la~~~   23 (139)
T PF07728_consen    7 PPGTGKTTLARELAALL   23 (139)
T ss_dssp             SSSSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            37999999999999977

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.

>TIGR00602 rad24 checkpoint protein rad24

Probab=95.67  E-value=0.051  Score=55.37  Aligned_cols=52  Identities=8%  Similarity=-0.115  Sum_probs=32.2

Q ss_pred             CCeeecCCCChhhhHHHHHHHhcCCCCC--c---hhHHHHHHHHHHHhCCCCchhhHH
Q 040234          123 KKVYKLEALTYDEAFRLLCLKAFDTHKP--L---EEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       123 ~~~~~l~~L~~~ea~~L~~~~~~~~~~~--~---~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      ...+.+.+++..+..+.|.+.+-.....  .   -...+....|+..++| +.--||.
T Consensus       266 v~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~G-DiRsAIn  322 (637)
T TIGR00602       266 VSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCSG-DIRSAIN  322 (637)
T ss_pred             eeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCCC-hHHHHHH
Confidence            4568999999999877777666322110  0   0113567778878877 3555554

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

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

Probab=95.67  E-value=0.05  Score=53.76  Aligned_cols=71  Identities=13%  Similarity=0.116  Sum_probs=48.3

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEE-EEecchhHHhh-CCCCCeeecCCCChhhhHHHHHHHhc
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRII-ITTRNEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAF  145 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~II-vTTR~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~  145 (377)
                      +|-=+.|+|.|.-  ...|+.|+..+..-.+.-+.| .||--+.+... .+..+.|.++.|+.++-...+...+.
T Consensus       118 ~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~  192 (515)
T COG2812         118 GRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILD  192 (515)
T ss_pred             ccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHH
Confidence            3445889999864  567888888776434454444 45555555333 35578899999999988877776663

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.66  E-value=0.091  Score=55.83  Aligned_cols=68  Identities=24%  Similarity=0.158  Sum_probs=39.3

Q ss_pred             CceEEEEEeCCCCh----------hhhhHhhCCCCCCCCCCeEEEEecchhHHhh-------CCCCCeeecCCCChhhhH
Q 040234           75 RKKVLVVIDDAAHP----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKL-------HPVKKVYKLEALTYDEAF  137 (377)
Q Consensus        75 ~k~~LLVLDdv~~~----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~-------~~~~~~~~l~~L~~~ea~  137 (377)
                      +++.+|++|++...          +.-+.|.+.+.  ...-++|-||........       .+....+.+++++.++..
T Consensus       279 ~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~--~G~l~~IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~  356 (852)
T TIGR03345       279 PQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALA--RGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAI  356 (852)
T ss_pred             CCCeEEEEeChHHhccCCCccccccHHHHhhHHhh--CCCeEEEEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHH
Confidence            46899999997432          11123444432  123456655554322110       122468999999999999


Q ss_pred             HHHHHHh
Q 040234          138 RLLCLKA  144 (377)
Q Consensus       138 ~L~~~~~  144 (377)
                      ++|....
T Consensus       357 ~iL~~~~  363 (852)
T TIGR03345       357 RMLRGLA  363 (852)
T ss_pred             HHHHHHH
Confidence            9975433

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.

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

Probab=95.63  E-value=0.0086  Score=51.08  Aligned_cols=26  Identities=27%  Similarity=0.243  Sum_probs=17.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      .|+|||.||..++++...+-..+.|+
T Consensus        56 ~G~GKThLa~ai~~~~~~~g~~v~f~   81 (178)
T PF01695_consen   56 PGTGKTHLAVAIANEAIRKGYSVLFI   81 (178)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--EEEE
T ss_pred             HhHHHHHHHHHHHHHhccCCcceeEe
Confidence            69999999999998654432233444

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.

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

Probab=95.59  E-value=0.24  Score=46.27  Aligned_cols=139  Identities=17%  Similarity=0.245  Sum_probs=75.8

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh---c-Cc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL---R-RK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l---~-~k   76 (377)
                      ++|.|||-||++|+++....|     +..++.             ++.....+.          ....+|..+   + ..
T Consensus       193 PPGTGKTLLAkAVA~~T~AtF-----IrvvgS-------------ElVqKYiGE----------GaRlVRelF~lAreka  244 (406)
T COG1222         193 PPGTGKTLLAKAVANQTDATF-----IRVVGS-------------ELVQKYIGE----------GARLVRELFELAREKA  244 (406)
T ss_pred             CCCCcHHHHHHHHHhccCceE-----EEeccH-------------HHHHHHhcc----------chHHHHHHHHHHhhcC
Confidence            489999999999999776654     332222             122222222          123333332   2 35


Q ss_pred             eEEEEEeCCCCh-------------h---hhhHhhCCCCCCC--CCCeEEEEecchhHHhh-----CCCCCeeecCCCCh
Q 040234           77 KVLVVIDDAAHP-------------D---HLRRLVGEPDWFG--PGSRIIITTRNEHLLKL-----HPVKKVYKLEALTY  133 (377)
Q Consensus        77 ~~LLVLDdv~~~-------------~---~~~~l~~~l~~~~--~gs~IIvTTR~~~v~~~-----~~~~~~~~l~~L~~  133 (377)
                      +.+|.+|.++..             +   .+-.|+..+....  ..-|||..|...++...     -.-.+.++++.-+.
T Consensus       245 PsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~  324 (406)
T COG1222         245 PSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDE  324 (406)
T ss_pred             CeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCH
Confidence            889999998642             1   1223444433332  24478877665444322     13367788885555


Q ss_pred             hhhHHHHHHHhcCCCC-CchhHHHHHHHHHHHhCCCCchhh
Q 040234          134 DEAFRLLCLKAFDTHK-PLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       134 ~ea~~L~~~~~~~~~~-~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      +.=.++|.-+...-.- ..-+    .+.|++.+.|  ..-|
T Consensus       325 ~gR~~Il~IHtrkM~l~~dvd----~e~la~~~~g--~sGA  359 (406)
T COG1222         325 EGRAEILKIHTRKMNLADDVD----LELLARLTEG--FSGA  359 (406)
T ss_pred             HHHHHHHHHHhhhccCccCcC----HHHHHHhcCC--CchH
Confidence            5556677666532211 1222    4567888888  5544

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.59  E-value=0.025  Score=49.13  Aligned_cols=103  Identities=14%  Similarity=0.190  Sum_probs=56.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+||||++..+...+.......++...  +.      .+..... ...+... .....+.....+.++..++..+=+++
T Consensus        10 tGSGKTTll~~ll~~~~~~~~~~i~t~e--~~------~E~~~~~-~~~~i~q-~~vg~~~~~~~~~i~~aLr~~pd~ii   79 (198)
T cd01131          10 TGSGKSTTLAAMIDYINKNKTHHILTIE--DP------IEFVHES-KRSLINQ-REVGLDTLSFENALKAALRQDPDVIL   79 (198)
T ss_pred             CCCCHHHHHHHHHHHhhhcCCcEEEEEc--CC------ccccccC-ccceeee-cccCCCccCHHHHHHHHhcCCcCEEE
Confidence            6999999999988866544444444331  11      0000000 0000000 00111233456677888887788999


Q ss_pred             EeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHH
Q 040234           82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLL  117 (377)
Q Consensus        82 LDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~  117 (377)
                      +|++.+.+.+.......   ..|..++.|+....+.
T Consensus        80 ~gEird~e~~~~~l~~a---~~G~~v~~t~Ha~~~~  112 (198)
T cd01131          80 VGEMRDLETIRLALTAA---ETGHLVMSTLHTNSAA  112 (198)
T ss_pred             EcCCCCHHHHHHHHHHH---HcCCEEEEEecCCcHH
Confidence            99999877665544331   3355677777765443

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.

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

Probab=95.54  E-value=0.034  Score=52.13  Aligned_cols=132  Identities=21%  Similarity=0.234  Sum_probs=76.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHh-hccccCc-----cchhhhHHHHHHH--h
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLL-KLADNNI-----RNVYDGINMLRVR--L   73 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~-~~~~~~~-----~~~~~~~~~l~~~--l   73 (377)
                      +|.|||.+.+++.+....   ..+|++ +.+.+    ....++..|+.+.. .......     .+..+....+.++  .
T Consensus        39 sgTGKT~~~r~~l~~~n~---~~vw~n-~~ecf----t~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~  110 (438)
T KOG2543|consen   39 SGTGKTYLVRQLLRKLNL---ENVWLN-CVECF----TYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAA  110 (438)
T ss_pred             CCCchhHHHHHHHhhcCC---cceeee-hHHhc----cHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHh
Confidence            699999999999986633   347888 66666    88889999998874 1111111     1222334444442  2


Q ss_pred             c--CceEEEEEeCCCChhhhh--------HhhCCCCCCCCCCeEEEEecch---hHHhhCCC--CCeeecCCCChhhhHH
Q 040234           74 R--RKKVLVVIDDAAHPDHLR--------RLVGEPDWFGPGSRIIITTRNE---HLLKLHPV--KKVYKLEALTYDEAFR  138 (377)
Q Consensus        74 ~--~k~~LLVLDdv~~~~~~~--------~l~~~l~~~~~gs~IIvTTR~~---~v~~~~~~--~~~~~l~~L~~~ea~~  138 (377)
                      .  ++.++|||||++...+.+        .+-..++  .+. -+|+++-..   .....++.  .-++..+.-+.+|-.+
T Consensus       111 t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~--~~~-i~iils~~~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~  187 (438)
T KOG2543|consen  111 TNRDQKVFLILDNADALRDMDAILLQCLFRLYELLN--EPT-IVIILSAPSCEKQYLINTGTLEIVVLHFPQYSVEETQV  187 (438)
T ss_pred             hccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhC--CCc-eEEEEeccccHHHhhcccCCCCceEEecCCCCHHHHHH
Confidence            2  358999999998643322        2222222  223 334443321   11221222  3356678889999999


Q ss_pred             HHHHHh
Q 040234          139 LLCLKA  144 (377)
Q Consensus       139 L~~~~~  144 (377)
                      ++.+.-
T Consensus       188 Il~~~~  193 (438)
T KOG2543|consen  188 ILSRDN  193 (438)
T ss_pred             HHhcCC
Confidence            886544

>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=95.50  E-value=0.058  Score=45.22  Aligned_cols=57  Identities=19%  Similarity=0.250  Sum_probs=32.5

Q ss_pred             ceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCC
Q 040234           76 KKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALT  132 (377)
Q Consensus        76 k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~  132 (377)
                      +.=++||||++.  .+..+.|+..+..-..++.+|++|++.. +...+ +....+.+.+||
T Consensus       102 ~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  102 KYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             SSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTSEEEEE----
T ss_pred             CceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhceEEecCCCC
Confidence            456899999987  3455555554443356788888887653 33322 445667776664

...

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.49  E-value=0.021  Score=50.61  Aligned_cols=28  Identities=14%  Similarity=0.093  Sum_probs=21.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+|||+||.+++......-..++|+.
T Consensus        31 ~~GsGKT~l~~~la~~~~~~~~~v~yi~   58 (225)
T PRK09361         31 PPGSGKTNICLQLAVEAAKNGKKVIYID   58 (225)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            3799999999999986654445567766

>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=95.43  E-value=0.032  Score=48.49  Aligned_cols=39  Identities=31%  Similarity=0.677  Sum_probs=24.9

Q ss_pred             hcCc---eEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           73 LRRK---KVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        73 l~~k---~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      ++++   .-.+|+|++.+  ..++..++..+   +.+||+|++--..
T Consensus       113 iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR~---g~~skii~~GD~~  156 (205)
T PF02562_consen  113 IRGRTFDNAFIIVDEAQNLTPEELKMILTRI---GEGSKIIITGDPS  156 (205)
T ss_dssp             GTT--B-SEEEEE-SGGG--HHHHHHHHTTB----TT-EEEEEE---
T ss_pred             hcCccccceEEEEecccCCCHHHHHHHHccc---CCCcEEEEecCce
Confidence            4554   46999999977  56788887664   6799999987644

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

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.42  E-value=0.071  Score=48.99  Aligned_cols=71  Identities=21%  Similarity=0.309  Sum_probs=43.6

Q ss_pred             CCCCcHHHHHHHHHc----hhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCc
Q 040234            1 MGGLGKTTLARVVYD----LISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~----~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k   76 (377)
                      ++|.|||+|.+.+++    |..++|..+..+. +        +..+++..++..-++.       ....-+.+++.+.++
T Consensus       185 PPGTGKTSLCKaLaQkLSIR~~~~y~~~~liE-i--------nshsLFSKWFsESgKl-------V~kmF~kI~ELv~d~  248 (423)
T KOG0744|consen  185 PPGTGKTSLCKALAQKLSIRTNDRYYKGQLIE-I--------NSHSLFSKWFSESGKL-------VAKMFQKIQELVEDR  248 (423)
T ss_pred             CCCCChhHHHHHHHHhheeeecCccccceEEE-E--------ehhHHHHHHHhhhhhH-------HHHHHHHHHHHHhCC
Confidence            589999999999999    4556677666665 3        3345555555442221       223334455555554


Q ss_pred             e--EEEEEeCCCC
Q 040234           77 K--VLVVIDDAAH   87 (377)
Q Consensus        77 ~--~LLVLDdv~~   87 (377)
                      .  +.+.+|.|+.
T Consensus       249 ~~lVfvLIDEVES  261 (423)
T KOG0744|consen  249 GNLVFVLIDEVES  261 (423)
T ss_pred             CcEEEEEeHHHHH
Confidence            3  4566888865

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

Probab=95.32  E-value=0.21  Score=49.85  Aligned_cols=121  Identities=17%  Similarity=0.203  Sum_probs=73.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||-||++|+++-+-.|     +. +.+.            +++....+.      ++......+++.=...+++|
T Consensus       553 PPGCGKTLlAKAVANEag~NF-----is-VKGP------------ELlNkYVGE------SErAVR~vFqRAR~saPCVI  608 (802)
T KOG0733|consen  553 PPGCGKTLLAKAVANEAGANF-----IS-VKGP------------ELLNKYVGE------SERAVRQVFQRARASAPCVI  608 (802)
T ss_pred             CCCccHHHHHHHHhhhccCce-----Ee-ecCH------------HHHHHHhhh------HHHHHHHHHHHhhcCCCeEE
Confidence            489999999999999777665     33 3332            233333332      22223333444445679999


Q ss_pred             EEeCCCCh-------------hhhhHhhCCCCCC--CCCCeEEEEecchhHHhh-----CCCCCeeecCCCChhhhHHHH
Q 040234           81 VIDDAAHP-------------DHLRRLVGEPDWF--GPGSRIIITTRNEHLLKL-----HPVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        81 VLDdv~~~-------------~~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~~-----~~~~~~~~l~~L~~~ea~~L~  140 (377)
                      .+|.++..             ..++.|+..+...  ..|--||-.|..+++...     -.-...+-++.-+.+|-.+++
T Consensus       609 FFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~IL  688 (802)
T KOG0733|consen  609 FFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAIL  688 (802)
T ss_pred             EecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHH
Confidence            99998642             1345555554432  234456655655544221     123677788888899999999


Q ss_pred             HHHhc
Q 040234          141 CLKAF  145 (377)
Q Consensus       141 ~~~~~  145 (377)
                      +...-
T Consensus       689 K~~tk  693 (802)
T KOG0733|consen  689 KTITK  693 (802)
T ss_pred             HHHhc
Confidence            88774

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.27  E-value=0.039  Score=46.60  Aligned_cols=119  Identities=13%  Similarity=0.076  Sum_probs=60.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcC--ceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRR--KKVL   79 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~--k~~L   79 (377)
                      +|+|||++|.+++..   .....+++. .....    +. ++.+.+.+.....  +......+....+.+.+.+  +.-.
T Consensus         8 ~~sGKS~~a~~~~~~---~~~~~~y~a-t~~~~----d~-em~~rI~~H~~~R--~~~w~t~E~~~~l~~~l~~~~~~~~   76 (169)
T cd00544           8 ARSGKSRFAERLAAE---LGGPVTYIA-TAEAF----DD-EMAERIARHRKRR--PAHWRTIETPRDLVSALKELDPGDV   76 (169)
T ss_pred             CCCCHHHHHHHHHHh---cCCCeEEEE-ccCcC----CH-HHHHHHHHHHHhC--CCCceEeecHHHHHHHHHhcCCCCE
Confidence            689999999999865   223445554 44332    22 3444444432111  2222333334445555532  2347


Q ss_pred             EEEeCCCC-------h----------hhhhHhhCCCCCCCCCCeEEEEecchhHHhhCCCCCeeecCCCChhhhHHHHHH
Q 040234           80 VVIDDAAH-------P----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEAFRLLCL  142 (377)
Q Consensus        80 LVLDdv~~-------~----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~~~l~~L~~~ea~~L~~~  142 (377)
                      +++|.+..       .          +.+..+...+.  ..+..+|++|.+-            -.+..+.+..-+.|..
T Consensus        77 VLIDclt~~~~n~l~~~~~~~~~~~~~~i~~l~~~l~--~~~~~~viVsnEv------------G~g~vp~~~~~r~f~d  142 (169)
T cd00544          77 VLIDCLTLWVTNLLFADLEEWEAAIADEIDALLAAVR--NKPGTLILVSNEV------------GLGVVPENALGRRFRD  142 (169)
T ss_pred             EEEEcHhHHHHHhCCCccccchhHHHHHHHHHHHHHH--cCCCcEEEEECCc------------CCCCCCCCHHHHHHHH
Confidence            99999521       0          12222333332  2344566665421            2344556677777877


Q ss_pred             Hhc
Q 040234          143 KAF  145 (377)
Q Consensus       143 ~~~  145 (377)
                      ..+
T Consensus       143 ~lG  145 (169)
T cd00544         143 ELG  145 (169)
T ss_pred             HHH
Confidence            764

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.23  E-value=0.096  Score=54.99  Aligned_cols=144  Identities=15%  Similarity=0.101  Sum_probs=70.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++.....|   +.+. ..          .+...    ..+      .........+.......+.+|
T Consensus       220 ppGtGKT~laraia~~~~~~~---i~i~-~~----------~i~~~----~~g------~~~~~l~~lf~~a~~~~p~il  275 (733)
T TIGR01243       220 PPGTGKTLLAKAVANEAGAYF---ISIN-GP----------EIMSK----YYG------ESEERLREIFKEAEENAPSII  275 (733)
T ss_pred             CCCCChHHHHHHHHHHhCCeE---EEEe-cH----------HHhcc----ccc------HHHHHHHHHHHHHHhcCCcEE
Confidence            379999999999998765433   1111 11          11100    000      011122333333444567899


Q ss_pred             EEeCCCCh-------------hhhhHhhCCCCCC-CCCCeEEE-Eecchh-HHhhC----CCCCeeecCCCChhhhHHHH
Q 040234           81 VIDDAAHP-------------DHLRRLVGEPDWF-GPGSRIII-TTRNEH-LLKLH----PVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        81 VLDdv~~~-------------~~~~~l~~~l~~~-~~gs~IIv-TTR~~~-v~~~~----~~~~~~~l~~L~~~ea~~L~  140 (377)
                      +||+++..             .....|...+... ..+..+++ ||.... +-..+    .-...+.+...+.++-.+++
T Consensus       276 ~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il  355 (733)
T TIGR01243       276 FIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEIL  355 (733)
T ss_pred             EeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHH
Confidence            99998542             1122232222211 22333444 444332 21111    12356778888888888888


Q ss_pred             HHHhcCCCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          141 CLKAFDTHKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      .......... +  ......+++.+.|  ..-+
T Consensus       356 ~~~~~~~~l~-~--d~~l~~la~~t~G--~~ga  383 (733)
T TIGR01243       356 KVHTRNMPLA-E--DVDLDKLAEVTHG--FVGA  383 (733)
T ss_pred             HHHhcCCCCc-c--ccCHHHHHHhCCC--CCHH
Confidence            7554221111 1  1224567777777  5433

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=95.22  E-value=0.022  Score=49.77  Aligned_cols=28  Identities=14%  Similarity=0.170  Sum_probs=21.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+|||+||.+++......-..++|+.
T Consensus        20 ~~GsGKT~l~~~~~~~~~~~g~~v~yi~   47 (209)
T TIGR02237        20 PPGSGKTNICMILAVNAARQGKKVVYID   47 (209)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            4799999999999886655445667776

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=95.17  E-value=0.042  Score=49.76  Aligned_cols=44  Identities=23%  Similarity=0.284  Sum_probs=24.7

Q ss_pred             CCCCcHHHHHHHHHch--hccc---ccc-ceEEecchhhcccccCHHHHHHHHHHH
Q 040234            1 MGGLGKTTLARVVYDL--ISHE---FDG-SSFLADVREKCDKEGSVISLQKQLLSD   50 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~--~~~~---f~~-~~w~~~~~~~~~~~~~~~~~~~~i~~~   50 (377)
                      .+|+|||+|+.+++-.  +...   -.. .+|++ ....+    ...++ .+|+++
T Consensus        46 ~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyid-Te~~f----~~~Rl-~~i~~~   95 (256)
T PF08423_consen   46 ESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYID-TEGTF----SPERL-QQIAER   95 (256)
T ss_dssp             STTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEE-SSSSS-----HHHH-HHHHHH
T ss_pred             ecccccchHHHHHHHHhhcccccccCCCceEEEe-CCCCC----CHHHH-HHHhhc
Confidence            3799999999888752  2222   233 45554 55554    44444 345544

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 ....

>PRK10865 protein disaggregation chaperone; Provisional

Probab=95.15  E-value=0.2  Score=53.45  Aligned_cols=18  Identities=28%  Similarity=0.517  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ..|+|||+||+.+++...
T Consensus       606 p~G~GKT~lA~aLa~~l~  623 (857)
T PRK10865        606 PTGVGKTELCKALANFMF  623 (857)
T ss_pred             CCCCCHHHHHHHHHHHhh
Confidence            379999999999998553

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=95.14  E-value=0.041  Score=49.01  Aligned_cols=27  Identities=22%  Similarity=0.225  Sum_probs=18.7

Q ss_pred             CCCcHHHHHHHHHchhc--cc----cccceEEe
Q 040234            2 GGLGKTTLARVVYDLIS--HE----FDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~--~~----f~~~~w~~   28 (377)
                      +|+|||+||.+++-...  ..    -..++|+.
T Consensus        28 ~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~   60 (235)
T cd01123          28 FGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID   60 (235)
T ss_pred             CCCCHHHHHHHHHHHeeCccccCCCCccEEEEe
Confidence            79999999999985322  21    24566766

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 .

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.12  E-value=0.19  Score=50.43  Aligned_cols=122  Identities=16%  Similarity=0.178  Sum_probs=63.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||++|+.++++-+-.|=.      +...            +++....+.      ++....+.+++.=+--+.++
T Consensus       476 PPGC~KT~lAkalAne~~~nFls------vkgp------------EL~sk~vGe------SEr~ir~iF~kAR~~aP~Ii  531 (693)
T KOG0730|consen  476 PPGCGKTLLAKALANEAGMNFLS------VKGP------------ELFSKYVGE------SERAIREVFRKARQVAPCII  531 (693)
T ss_pred             CCCcchHHHHHHHhhhhcCCeee------ccCH------------HHHHHhcCc------hHHHHHHHHHHHhhcCCeEE
Confidence            58999999999999976666522      2111            011111111      12222222333223345777


Q ss_pred             EEeCCCChh-------------hhhHhhCCCCCCCCCCeEEE---EecchhHHhh-C---CCCCeeecCCCChhhhHHHH
Q 040234           81 VIDDAAHPD-------------HLRRLVGEPDWFGPGSRIII---TTRNEHLLKL-H---PVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        81 VLDdv~~~~-------------~~~~l~~~l~~~~~gs~IIv---TTR~~~v~~~-~---~~~~~~~l~~L~~~ea~~L~  140 (377)
                      .||.++...             .+..|+..+........|+|   |.|-..+-.. +   ...+.+.++.-+.+.-.++|
T Consensus       532 FfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Il  611 (693)
T KOG0730|consen  532 FFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEIL  611 (693)
T ss_pred             ehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHH
Confidence            788775421             23344444433233323333   3343322111 1   24677788888888888999


Q ss_pred             HHHhcC
Q 040234          141 CLKAFD  146 (377)
Q Consensus       141 ~~~~~~  146 (377)
                      +.++-+
T Consensus       612 k~~~kk  617 (693)
T KOG0730|consen  612 KQCAKK  617 (693)
T ss_pred             HHHHhc
Confidence            888843

>PRK04296 thymidine kinase; Provisional

Probab=95.06  E-value=0.017  Score=49.85  Aligned_cols=104  Identities=13%  Similarity=0.005  Sum_probs=52.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcccc-CccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN-NIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|.||||+|..++.+...+-..++.+.   +.+    +.......++++++..... ......+..+.+++ ..++.-+|
T Consensus        11 ~GsGKTT~~l~~~~~~~~~g~~v~i~k---~~~----d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~~~dvv   82 (190)
T PRK04296         11 MNSGKSTELLQRAYNYEERGMKVLVFK---PAI----DDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGEKIDCV   82 (190)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCeEEEEe---ccc----cccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCCCCCEE
Confidence            499999999999987655533333331   111    0001111223333211110 01233344444444 23344589


Q ss_pred             EEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh
Q 040234           81 VIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH  115 (377)
Q Consensus        81 VLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~  115 (377)
                      |+|.+.-  .+++..+...+.  ..|..||+|.++..
T Consensus        83 iIDEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~~~  117 (190)
T PRK04296         83 LIDEAQFLDKEQVVQLAEVLD--DLGIPVICYGLDTD  117 (190)
T ss_pred             EEEccccCCHHHHHHHHHHHH--HcCCeEEEEecCcc
Confidence            9999954  333444433322  45778999998753

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=95.05  E-value=0.23  Score=51.21  Aligned_cols=122  Identities=16%  Similarity=0.185  Sum_probs=64.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||++|+.++++..-.|     +. ++.        ..+...    ..+.      ......+.+.......+.+|
T Consensus       193 ~~G~GKt~~~~~~a~~~~~~f-----~~-is~--------~~~~~~----~~g~------~~~~~~~~f~~a~~~~P~Ii  248 (644)
T PRK10733        193 PPGTGKTLLAKAIAGEAKVPF-----FT-ISG--------SDFVEM----FVGV------GASRVRDMFEQAKKAAPCII  248 (644)
T ss_pred             CCCCCHHHHHHHHHHHcCCCE-----EE-Eeh--------HHhHHh----hhcc------cHHHHHHHHHHHHhcCCcEE
Confidence            479999999999998665433     11 111        111110    0000      11122223333334567899


Q ss_pred             EEeCCCChh----------------hhhHhhCCCCCC--CCCCeEEEEecchhHHhh-C----CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHPD----------------HLRRLVGEPDWF--GPGSRIIITTRNEHLLKL-H----PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~~----------------~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~~-~----~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++...                .+..++..+...  ..+.-||.||........ .    .-...+.++..+.++-.
T Consensus       249 fIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~  328 (644)
T PRK10733        249 FIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGRE  328 (644)
T ss_pred             EehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHH
Confidence            999986531                123343332221  223345557766543221 1    22567888888888888


Q ss_pred             HHHHHHhcC
Q 040234          138 RLLCLKAFD  146 (377)
Q Consensus       138 ~L~~~~~~~  146 (377)
                      +++..+...
T Consensus       329 ~Il~~~~~~  337 (644)
T PRK10733        329 QILKVHMRR  337 (644)
T ss_pred             HHHHHHhhc
Confidence            888877643

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

Probab=95.05  E-value=0.13  Score=47.96  Aligned_cols=60  Identities=17%  Similarity=0.152  Sum_probs=35.8

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChh
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYD  134 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~  134 (377)
                      ++.-+++||+++..  +....++..+..-...+.+|++|... .+...+ +....+++.+.+..
T Consensus       108 ~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~tI~SRc~~i~f~~~~~~  171 (325)
T COG0470         108 GGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRL  171 (325)
T ss_pred             CCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccchhhhcceeeecCCchHH
Confidence            45679999999873  34455555444435677888777743 333322 33566777763333

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.04  E-value=0.23  Score=50.42  Aligned_cols=155  Identities=15%  Similarity=0.070  Sum_probs=77.3

Q ss_pred             CCCcHHHHHHHHHchhcc-ccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISH-EFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+|||+||+.+++.+.. ++-...++. ++...+.  .+..++..+                  ...+...+.-.+-++
T Consensus       440 ~GsGKT~L~kal~~~~~k~~~~hv~~v~-Cs~l~~~--~~e~iQk~l------------------~~vfse~~~~~PSiI  498 (952)
T KOG0735|consen  440 KGSGKTNLVKALFDYYSKDLIAHVEIVS-CSTLDGS--SLEKIQKFL------------------NNVFSEALWYAPSII  498 (952)
T ss_pred             CCCCHhHHHHHHHHHhccccceEEEEEe-chhccch--hHHHHHHHH------------------HHHHHHHHhhCCcEE
Confidence            699999999999995543 222333333 3332211  222332222                  122334455678899


Q ss_pred             EEeCCCChh--------hh-------h----HhhCCCCCCCCCCeEEEEecchhH-HhhC----CCCCeeecCCCChhhh
Q 040234           81 VIDDAAHPD--------HL-------R----RLVGEPDWFGPGSRIIITTRNEHL-LKLH----PVKKVYKLEALTYDEA  136 (377)
Q Consensus        81 VLDdv~~~~--------~~-------~----~l~~~l~~~~~gs~IIvTTR~~~v-~~~~----~~~~~~~l~~L~~~ea  136 (377)
                      ||||++...        +|       .    .+..-+...+..-++|.|.....- -..+    -...+..|..+...+-
T Consensus       499 vLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R  578 (952)
T KOG0735|consen  499 VLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRR  578 (952)
T ss_pred             EEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHH
Confidence            999986311        11       1    111111111222245555544321 1111    1244677888988888


Q ss_pred             HHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhh
Q 040234          137 FRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSY  180 (377)
Q Consensus       137 ~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~  180 (377)
                      .++|........  .....+..+-+..+|+| =++.-+.+...+
T Consensus       579 ~~IL~~~~s~~~--~~~~~~dLd~ls~~TEG-y~~~DL~ifVeR  619 (952)
T KOG0735|consen  579 KEILTTIFSKNL--SDITMDDLDFLSVKTEG-YLATDLVIFVER  619 (952)
T ss_pred             HHHHHHHHHhhh--hhhhhHHHHHHHHhcCC-ccchhHHHHHHH
Confidence            888776653322  11122333447888876 145555555443

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

Probab=95.04  E-value=0.18  Score=52.91  Aligned_cols=18  Identities=33%  Similarity=0.538  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+|||+||+.+++.+.
T Consensus       492 p~GvGKT~lA~~la~~l~  509 (731)
T TIGR02639       492 PTGVGKTELAKQLAEALG  509 (731)
T ss_pred             CCCccHHHHHHHHHHHhc
Confidence            479999999999998663

>PRK08118 topology modulation protein; Reviewed

Probab=95.04  E-value=0.04  Score=46.44  Aligned_cols=26  Identities=38%  Similarity=0.609  Sum_probs=19.0

Q ss_pred             CCCCcHHHHHHHHHchhc---cccccceE
Q 040234            1 MGGLGKTTLARVVYDLIS---HEFDGSSF   26 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~---~~f~~~~w   26 (377)
                      ++|+||||||+.++++..   -+++..+|
T Consensus         9 ~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          9 SGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             CCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            489999999999998643   23454444

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

Probab=95.01  E-value=0.069  Score=55.14  Aligned_cols=87  Identities=22%  Similarity=0.299  Sum_probs=49.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceE-E
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKV-L   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~-L   79 (377)
                      +.|+|||.||+.++..+-+.=...+-+. +|+....         .-.+.|.+.++.-.. -++ --.|.+..+.++| +
T Consensus       529 PTGVGKTELAkaLA~~Lfg~e~aliR~D-MSEy~Ek---------HsVSrLIGaPPGYVG-yee-GG~LTEaVRr~PySV  596 (786)
T COG0542         529 PTGVGKTELAKALAEALFGDEQALIRID-MSEYMEK---------HSVSRLIGAPPGYVG-YEE-GGQLTEAVRRKPYSV  596 (786)
T ss_pred             CCcccHHHHHHHHHHHhcCCCccceeec-hHHHHHH---------HHHHHHhCCCCCCce-ecc-ccchhHhhhcCCCeE
Confidence            4799999999999996654333334343 5554321         222333333222111 111 2345566677877 8


Q ss_pred             EEEeCCCC--hhhhhHhhCCCC
Q 040234           80 VVIDDAAH--PDHLRRLVGEPD   99 (377)
Q Consensus        80 LVLDdv~~--~~~~~~l~~~l~   99 (377)
                      |+||+++.  ++.++-|+..+.
T Consensus       597 iLlDEIEKAHpdV~nilLQVlD  618 (786)
T COG0542         597 ILLDEIEKAHPDVFNLLLQVLD  618 (786)
T ss_pred             EEechhhhcCHHHHHHHHHHhc
Confidence            88999974  666666665544

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.99  E-value=0.051  Score=50.73  Aligned_cols=28  Identities=25%  Similarity=0.109  Sum_probs=20.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+||||||.+++......-...+|+.
T Consensus        63 p~GsGKTtLal~~~~~~~~~g~~~vyId   90 (325)
T cd00983          63 PESSGKTTLALHAIAEAQKLGGTVAFID   90 (325)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCEEEEC
Confidence            4799999999998875544444556665

RecA couples ATP hydrolysis to DNA strand exchange.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=94.94  E-value=0.15  Score=54.08  Aligned_cols=121  Identities=15%  Similarity=0.098  Sum_probs=61.6

Q ss_pred             CCCCcHHHHHHHHHchhccc-----c-ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-
Q 040234            1 MGGLGKTTLARVVYDLISHE-----F-DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-----f-~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-   73 (377)
                      .+|+|||+||..+++++...     . ...+|..          +...++.       +.  ....+.++....+.+.+ 
T Consensus       208 ~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l----------~~~~l~a-------g~--~~~ge~e~rl~~i~~~~~  268 (821)
T CHL00095        208 EPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITL----------DIGLLLA-------GT--KYRGEFEERLKRIFDEIQ  268 (821)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEe----------eHHHHhc-------cC--CCccHHHHHHHHHHHHHH
Confidence            47999999999999865421     1 1345544          2222211       00  00111222222222222 


Q ss_pred             cCceEEEEEeCCCCh----------hhhhHhhCCCCCCCCCCeEEEEecchhHHhh-------CCCCCeeecCCCChhhh
Q 040234           74 RRKKVLVVIDDAAHP----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKL-------HPVKKVYKLEALTYDEA  136 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~-------~~~~~~~~l~~L~~~ea  136 (377)
                      ..++.+|++|++...          +.-+.|.+.+.  ...-++|.+|........       ......++++..+.++.
T Consensus       269 ~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~--rg~l~~IgaTt~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~  346 (821)
T CHL00095        269 ENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALA--RGELQCIGATTLDEYRKHIEKDPALERRFQPVYVGEPSVEET  346 (821)
T ss_pred             hcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHh--CCCcEEEEeCCHHHHHHHHhcCHHHHhcceEEecCCCCHHHH
Confidence            346789999998421          12223333332  122355555554433111       12345678888888888


Q ss_pred             HHHHHH
Q 040234          137 FRLLCL  142 (377)
Q Consensus       137 ~~L~~~  142 (377)
                      ..++..
T Consensus       347 ~aILr~  352 (821)
T CHL00095        347 IEILFG  352 (821)
T ss_pred             HHHHHH
Confidence            887754

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=94.92  E-value=0.48  Score=43.61  Aligned_cols=66  Identities=17%  Similarity=0.183  Sum_probs=41.9

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHH
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLC  141 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~  141 (377)
                      +++-++|+|+++.  .+..+.|+..+..-.+++.+|++|.+. .+...+ +....+.+.+ +.++..+.+.
T Consensus       103 ~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        103 GKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             CCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHH
Confidence            4556899999987  445666766665435566677666554 444443 3456777766 6666666664

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=94.90  E-value=0.053  Score=44.73  Aligned_cols=28  Identities=29%  Similarity=0.186  Sum_probs=19.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+|||+++..++......-...+++.
T Consensus         7 ~~G~GKT~l~~~i~~~~~~~~~~v~~~~   34 (165)
T cd01120           7 PTGSGKTTLALQLALNIATKGGKVVYVD   34 (165)
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCEEEEEE
Confidence            3799999999999986654333444444

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.88  E-value=0.2  Score=53.38  Aligned_cols=19  Identities=32%  Similarity=0.544  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ..|+|||+||+.+++....
T Consensus       603 p~GvGKt~lA~~La~~l~~  621 (852)
T TIGR03346       603 PTGVGKTELAKALAEFLFD  621 (852)
T ss_pred             CCCCCHHHHHHHHHHHhcC
Confidence            4799999999999986543

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.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=94.86  E-value=0.24  Score=44.29  Aligned_cols=17  Identities=35%  Similarity=0.456  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+|||+||.+++..+
T Consensus         9 ~~G~GKS~lal~la~~v   25 (239)
T cd01125           9 PGGTGKSSLLLVLALAM   25 (239)
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            48999999999998744

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.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.85  E-value=0.11  Score=45.86  Aligned_cols=27  Identities=19%  Similarity=0.036  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhcccc------ccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEF------DGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f------~~~~w~~   28 (377)
                      +|+|||+||.+++.......      ..++|+.
T Consensus        28 ~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~   60 (226)
T cd01393          28 FGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID   60 (226)
T ss_pred             CCCChhHHHHHHHHHhhcccccCCCcceEEEEe
Confidence            79999999999987543333      3446665

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.

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=94.75  E-value=0.83  Score=43.34  Aligned_cols=20  Identities=25%  Similarity=0.365  Sum_probs=17.1

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+|||.+|+.++++..-.
T Consensus       156 PPGcGKTllAraiA~elg~~  175 (413)
T PLN00020        156 GKGQGKSFQCELVFKKMGIE  175 (413)
T ss_pred             CCCCCHHHHHHHHHHHcCCC
Confidence            37999999999999977554

>TIGR02012 tigrfam_recA protein RecA

Probab=94.75  E-value=0.068  Score=49.84  Aligned_cols=76  Identities=16%  Similarity=0.080  Sum_probs=40.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc----ccCccchhhhHHHHHHHhc-C
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA----DNNIRNVYDGINMLRVRLR-R   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~----~~~~~~~~~~~~~l~~~l~-~   75 (377)
                      .+|+||||||.+++......-...+|+. .-+..    +.     ..+++++...    -..+.+.++..+.+...++ +
T Consensus        63 ~~GsGKTtLaL~~~~~~~~~g~~v~yId-~E~~~----~~-----~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~~~  132 (321)
T TIGR02012        63 PESSGKTTLALHAIAEAQKAGGTAAFID-AEHAL----DP-----VYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSG  132 (321)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCcEEEEc-ccchh----HH-----HHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhcc
Confidence            3799999999998875544434455664 32221    11     1233322111    1122344555555555544 3


Q ss_pred             ceEEEEEeCCC
Q 040234           76 KKVLVVIDDAA   86 (377)
Q Consensus        76 k~~LLVLDdv~   86 (377)
                      ..-++|+|.+.
T Consensus       133 ~~~lIVIDSv~  143 (321)
T TIGR02012       133 AVDIIVVDSVA  143 (321)
T ss_pred             CCcEEEEcchh
Confidence            45688888874

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.

>PTZ00202 tuzin; Provisional

Probab=94.67  E-value=0.13  Score=49.62  Aligned_cols=128  Identities=16%  Similarity=0.126  Sum_probs=72.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-----c-
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-----R-   74 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-----~-   74 (377)
                      ++|+|||||++.+.....    ..+++.+..       +..++++.++.+|+....   ....++.+.+++.+     . 
T Consensus       294 ~~G~GKTTLlR~~~~~l~----~~qL~vNpr-------g~eElLr~LL~ALGV~p~---~~k~dLLrqIqeaLl~~~~e~  359 (550)
T PTZ00202        294 FRGCGKSSLCRSAVRKEG----MPAVFVDVR-------GTEDTLRSVVKALGVPNV---EACGDLLDFISEACRRAKKMN  359 (550)
T ss_pred             CCCCCHHHHHHHHHhcCC----ceEEEECCC-------CHHHHHHHHHHHcCCCCc---ccHHHHHHHHHHHHHHHHHhC
Confidence            479999999999997554    225555443       457899999999875322   12223334433333     2 


Q ss_pred             CceEEEEEeCCC--Chh-hhhHhhCCCCCCCCCCeEEEEecchhHHhh---CCCCCeeecCCCChhhhHHHHHHH
Q 040234           75 RKKVLVVIDDAA--HPD-HLRRLVGEPDWFGPGSRIIITTRNEHLLKL---HPVKKVYKLEALTYDEAFRLLCLK  143 (377)
Q Consensus        75 ~k~~LLVLDdv~--~~~-~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~---~~~~~~~~l~~L~~~ea~~L~~~~  143 (377)
                      +++.+||+-=-+  +.. .+++.. .+-....-|+|++---.+.+...   ++.-..|-+++++.++|.+.-.+.
T Consensus       360 GrtPVLII~lreg~~l~rvyne~v-~la~drr~ch~v~evpleslt~~~~~lprldf~~vp~fsr~qaf~y~~h~  433 (550)
T PTZ00202        360 GETPLLVLKLREGSSLQRVYNEVV-ALACDRRLCHVVIEVPLESLTIANTLLPRLDFYLVPNFSRSQAFAYTQHA  433 (550)
T ss_pred             CCCEEEEEEecCCCcHHHHHHHHH-HHHccchhheeeeeehHhhcchhcccCccceeEecCCCCHHHHHHHHhhc
Confidence            566666665332  211 122211 11122445778776555443211   133456778999999988765543

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

Probab=94.66  E-value=0.38  Score=42.33  Aligned_cols=25  Identities=20%  Similarity=0.185  Sum_probs=18.1

Q ss_pred             CCCCcHHHHHHHHHchhc-cccccce
Q 040234            1 MGGLGKTTLARVVYDLIS-HEFDGSS   25 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~-~~f~~~~   25 (377)
                      |+|+||||-+..+++++- ..|..++
T Consensus        56 pPG~GKTTsi~~LAr~LLG~~~ke~v   81 (333)
T KOG0991|consen   56 PPGTGKTTSILCLARELLGDSYKEAV   81 (333)
T ss_pred             CCCCchhhHHHHHHHHHhChhhhhHh
Confidence            689999999999888643 3344443

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

Probab=94.58  E-value=0.16  Score=53.11  Aligned_cols=67  Identities=9%  Similarity=0.054  Sum_probs=38.0

Q ss_pred             CceEEEEEeCCCCh----------hhhh-HhhCCCCCCCCCCeEEEEecchhHHhh-------CCCCCeeecCCCChhhh
Q 040234           75 RKKVLVVIDDAAHP----------DHLR-RLVGEPDWFGPGSRIIITTRNEHLLKL-------HPVKKVYKLEALTYDEA  136 (377)
Q Consensus        75 ~k~~LLVLDdv~~~----------~~~~-~l~~~l~~~~~gs~IIvTTR~~~v~~~-------~~~~~~~~l~~L~~~ea  136 (377)
                      .++.+|+||++...          .+.. .+.+.+.  ...-++|-+|....+...       .+....+.+++++.++.
T Consensus       277 ~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~--~g~i~vIgATt~~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~  354 (758)
T PRK11034        277 DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEET  354 (758)
T ss_pred             cCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHh--CCCeEEEecCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHH
Confidence            45679999998631          1222 2333332  123345544443332110       12235789999999999


Q ss_pred             HHHHHHH
Q 040234          137 FRLLCLK  143 (377)
Q Consensus       137 ~~L~~~~  143 (377)
                      .+++...
T Consensus       355 ~~IL~~~  361 (758)
T PRK11034        355 VQIINGL  361 (758)
T ss_pred             HHHHHHH
Confidence            9998754

>PRK09354 recA recombinase A; Provisional

Probab=94.57  E-value=0.076  Score=50.01  Aligned_cols=76  Identities=17%  Similarity=0.087  Sum_probs=40.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc----ccCccchhhhHHHHHHHhcC-
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA----DNNIRNVYDGINMLRVRLRR-   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~----~~~~~~~~~~~~~l~~~l~~-   75 (377)
                      .+|+||||||.+++......-...+|+. .-+..    +.     ..+++++...    -..+.+.++..+.+...++. 
T Consensus        68 ~~GsGKTtLal~~~~~~~~~G~~~~yId-~E~s~----~~-----~~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~s~  137 (349)
T PRK09354         68 PESSGKTTLALHAIAEAQKAGGTAAFID-AEHAL----DP-----VYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSG  137 (349)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCcEEEEC-Cccch----HH-----HHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhcC
Confidence            3799999999998875554444556665 32222    21     2233332111    11223444455555554433 


Q ss_pred             ceEEEEEeCCC
Q 040234           76 KKVLVVIDDAA   86 (377)
Q Consensus        76 k~~LLVLDdv~   86 (377)
                      ..-|+|+|.+.
T Consensus       138 ~~~lIVIDSva  148 (349)
T PRK09354        138 AVDLIVVDSVA  148 (349)
T ss_pred             CCCEEEEeChh
Confidence            45577888764

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

Probab=94.57  E-value=0.058  Score=52.35  Aligned_cols=33  Identities=21%  Similarity=0.267  Sum_probs=22.7

Q ss_pred             CCCCcHHHHHHHHHchhcc--ccccceEEecchhhc
Q 040234            1 MGGLGKTTLARVVYDLISH--EFDGSSFLADVREKC   34 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~--~f~~~~w~~~~~~~~   34 (377)
                      ++|+|||++|+.+++.+..  .+....|+. +++..
T Consensus       202 ppGtGKT~lA~~la~~l~~~~~~~~v~~Vt-FHpsy  236 (459)
T PRK11331        202 PPGVGKTFVARRLAYLLTGEKAPQRVNMVQ-FHQSY  236 (459)
T ss_pred             CCCCCHHHHHHHHHHHhcCCcccceeeEEe-ecccc
Confidence            6899999999999986543  333444444 65544

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=94.48  E-value=0.063  Score=50.89  Aligned_cols=101  Identities=17%  Similarity=0.185  Sum_probs=56.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+||||+...+.+.+.......++..  .       +..+....-...+... .....+.....+.++..|+..+=.|+
T Consensus       131 tGSGKTT~l~al~~~i~~~~~~~i~ti--E-------dp~E~~~~~~~~~i~q-~evg~~~~~~~~~l~~~lr~~pd~i~  200 (343)
T TIGR01420       131 TGSGKSTTLASMIDYINKNAAGHIITI--E-------DPIEYVHRNKRSLINQ-REVGLDTLSFANALRAALREDPDVIL  200 (343)
T ss_pred             CCCCHHHHHHHHHHhhCcCCCCEEEEE--c-------CChhhhccCccceEEc-cccCCCCcCHHHHHHHhhccCCCEEE
Confidence            699999999999887665555555543  1       1111110000000000 00111223456778888888999999


Q ss_pred             EeCCCChhhhhHhhCCCCCCCCCCeEEEEecchh
Q 040234           82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEH  115 (377)
Q Consensus        82 LDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~  115 (377)
                      +|.+.+.+.+.......   ..|-.|+.|.....
T Consensus       201 vgEird~~~~~~~l~aa---~tGh~v~~T~Ha~~  231 (343)
T TIGR01420       201 IGEMRDLETVELALTAA---ETGHLVFGTLHTNS  231 (343)
T ss_pred             EeCCCCHHHHHHHHHHH---HcCCcEEEEEcCCC
Confidence            99999977665433321   34545666665443

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.

>cd01394 radB RadB

Probab=94.46  E-value=0.052  Score=47.79  Aligned_cols=28  Identities=18%  Similarity=0.145  Sum_probs=20.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+||||||.+++.....+-..++|+.
T Consensus        27 ~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394          27 PPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            3799999999999986544433455664

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=94.46  E-value=0.097  Score=44.16  Aligned_cols=46  Identities=17%  Similarity=0.127  Sum_probs=27.9

Q ss_pred             HHHHHHHhcCce-EEEEEeCCCC--------hhhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           66 INMLRVRLRRKK-VLVVIDDAAH--------PDHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        66 ~~~l~~~l~~k~-~LLVLDdv~~--------~~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      .+..++.+...+ =|||||.+-.        .+++-.++.   ...++..||+|-|+.
T Consensus        86 ~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~---~rp~~~evVlTGR~~  140 (173)
T TIGR00708        86 WQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQ---ERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHH---hCCCCCEEEEECCCC
Confidence            334455555544 4999999753        233333333   235567899999975

Alternate name: corrinoid adenosyltransferase.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=94.46  E-value=0.11  Score=49.40  Aligned_cols=76  Identities=22%  Similarity=0.199  Sum_probs=41.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-cCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-RRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-~~k~~LL   80 (377)
                      +|||||||..+++.++.++- ...++.  ++.     +..++-. -+++++........-.+.-.+.+.+.+ +.++-|+
T Consensus       102 PGIGKSTLLLQva~~lA~~~-~vLYVs--GEE-----S~~Qikl-RA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~p~lv  172 (456)
T COG1066         102 PGIGKSTLLLQVAARLAKRG-KVLYVS--GEE-----SLQQIKL-RADRLGLPTNNLYLLAETNLEDIIAELEQEKPDLV  172 (456)
T ss_pred             CCCCHHHHHHHHHHHHHhcC-cEEEEe--CCc-----CHHHHHH-HHHHhCCCccceEEehhcCHHHHHHHHHhcCCCEE
Confidence            69999999999999888776 444443  332     4444322 233333211111111112223333333 4678899


Q ss_pred             EEeCCC
Q 040234           81 VIDDAA   86 (377)
Q Consensus        81 VLDdv~   86 (377)
                      |+|.+.
T Consensus       173 VIDSIQ  178 (456)
T COG1066         173 VIDSIQ  178 (456)
T ss_pred             EEeccc
Confidence            999974

>PRK05541 adenylylsulfate kinase; Provisional

Probab=94.45  E-value=0.12  Score=43.88  Aligned_cols=27  Identities=30%  Similarity=0.682  Sum_probs=22.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      +.|+||||+|+.+++++...+...+++
T Consensus        15 ~~GsGKst~a~~l~~~l~~~~~~~~~~   41 (176)
T PRK05541         15 LAGSGKTTIAKALYERLKLKYSNVIYL   41 (176)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            479999999999999887666665555

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.42  E-value=0.29  Score=52.30  Aligned_cols=123  Identities=13%  Similarity=0.066  Sum_probs=62.9

Q ss_pred             CCCCcHHHHHHHHHchhcccc------ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-
Q 040234            1 MGGLGKTTLARVVYDLISHEF------DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f------~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-   73 (377)
                      .+|+|||+||..+++++...+      ...+|..++          ..++...         ....+.+.....+.+.+ 
T Consensus       202 ~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~----------~~l~a~~---------~~~g~~e~~l~~~l~~~~  262 (852)
T TIGR03346       202 EPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDM----------GALIAGA---------KYRGEFEERLKAVLNEVT  262 (852)
T ss_pred             CCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeH----------HHHhhcc---------hhhhhHHHHHHHHHHHHH
Confidence            379999999999998764432      223444322          2211000         00011222222222222 


Q ss_pred             c-CceEEEEEeCCCCh----------hhhhHhhCCCCCCCCCCeEEEEecchhHHhh-------CCCCCeeecCCCChhh
Q 040234           74 R-RKKVLVVIDDAAHP----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKL-------HPVKKVYKLEALTYDE  135 (377)
Q Consensus        74 ~-~k~~LLVLDdv~~~----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~-------~~~~~~~~l~~L~~~e  135 (377)
                      + +++.+|++|++...          +..+.|.+.+.  ...-++|.+|........       ......+.++..+.++
T Consensus       263 ~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~--~g~i~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~  340 (852)
T TIGR03346       263 KSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALA--RGELHCIGATTLDEYRKYIEKDAALERRFQPVFVDEPTVED  340 (852)
T ss_pred             hcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhh--cCceEEEEeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHH
Confidence            2 46899999998642          12333444432  122345544443322110       1224567899999999


Q ss_pred             hHHHHHHHh
Q 040234          136 AFRLLCLKA  144 (377)
Q Consensus       136 a~~L~~~~~  144 (377)
                      ..+++....
T Consensus       341 ~~~iL~~~~  349 (852)
T TIGR03346       341 TISILRGLK  349 (852)
T ss_pred             HHHHHHHHH
Confidence            999887553

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.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=94.42  E-value=0.02  Score=48.48  Aligned_cols=16  Identities=19%  Similarity=0.152  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||++|..++.+.
T Consensus        10 ~~sGKS~~a~~l~~~~   25 (170)
T PRK05800         10 ARSGKSRFAERLAAQS   25 (170)
T ss_pred             CCccHHHHHHHHHHHc
Confidence            6899999999998754

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=94.41  E-value=0.23  Score=41.83  Aligned_cols=48  Identities=15%  Similarity=0.297  Sum_probs=29.2

Q ss_pred             HHHHhcCceEEEEEeCCCC---h---hhhhHhhCCCCCCCCCCeEEEEecchhHHhh
Q 040234           69 LRVRLRRKKVLVVIDDAAH---P---DHLRRLVGEPDWFGPGSRIIITTRNEHLLKL  119 (377)
Q Consensus        69 l~~~l~~k~~LLVLDdv~~---~---~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~  119 (377)
                      +-+.+..++-+++||+-..   .   +.+..++..+.   .+..||++|.+......
T Consensus       107 la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~---~~~tii~~sh~~~~~~~  160 (171)
T cd03228         107 IARALLRDPPILILDEATSALDPETEALILEALRALA---KGKTVIVIAHRLSTIRD  160 (171)
T ss_pred             HHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhc---CCCEEEEEecCHHHHHh
Confidence            4455666778999999753   1   23333333332   34678888888766543

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.41  E-value=0.28  Score=52.26  Aligned_cols=68  Identities=10%  Similarity=-0.017  Sum_probs=37.8

Q ss_pred             CceEEEEEeCCCCh----------hhhhHhhCCCCCCCCCCeEEEEecchhHHh------hC-CCCCeeecCCCChhhhH
Q 040234           75 RKKVLVVIDDAAHP----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLK------LH-PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        75 ~k~~LLVLDdv~~~----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~------~~-~~~~~~~l~~L~~~ea~  137 (377)
                      +++.+|++|++...          +.-+.|.+.+.  ...-++|-+|.......      .. .....+.+...+.++..
T Consensus       270 ~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~--~g~l~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~~~  347 (857)
T PRK10865        270 EGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTI  347 (857)
T ss_pred             CCCeEEEEecHHHhccCCCCccchhHHHHhcchhh--cCCCeEEEcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHHHH
Confidence            46889999998542          12333444442  22345555554433211      01 12335667777889998


Q ss_pred             HHHHHHh
Q 040234          138 RLLCLKA  144 (377)
Q Consensus       138 ~L~~~~~  144 (377)
                      +++....
T Consensus       348 ~iL~~l~  354 (857)
T PRK10865        348 AILRGLK  354 (857)
T ss_pred             HHHHHHh
Confidence            8886544

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.33  E-value=0.034  Score=45.90  Aligned_cols=33  Identities=30%  Similarity=0.495  Sum_probs=25.2

Q ss_pred             CCCCcHHHHHHHHHchhccc-cc-cceEEecchhh
Q 040234            1 MGGLGKTTLARVVYDLISHE-FD-GSSFLADVREK   33 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-f~-~~~w~~~~~~~   33 (377)
                      |+|+|||||++.+++.+++. |. +++|...++..
T Consensus        13 ~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR~g   47 (179)
T COG1618          13 RPGVGKTTLVLKIAEKLREKGYKVGGFITPEVREG   47 (179)
T ss_pred             CCCccHHHHHHHHHHHHHhcCceeeeEEeeeeecC
Confidence            68999999999999987766 76 45665555543

>TIGR00763 lon ATP-dependent protease La

Probab=94.26  E-value=0.29  Score=51.69  Aligned_cols=21  Identities=29%  Similarity=0.589  Sum_probs=17.3

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      .+|+|||+||+.+++.+...|
T Consensus       355 ppG~GKT~lAk~iA~~l~~~~  375 (775)
T TIGR00763       355 PPGVGKTSLGKSIAKALNRKF  375 (775)
T ss_pred             CCCCCHHHHHHHHHHHhcCCe
Confidence            479999999999999775443

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.

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.15  E-value=0.078  Score=48.38  Aligned_cols=80  Identities=23%  Similarity=0.103  Sum_probs=42.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHH-HhhccccCccchhhhHHHHHHH---hcCc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSD-LLKLADNNIRNVYDGINMLRVR---LRRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~-l~~~~~~~~~~~~~~~~~l~~~---l~~k   76 (377)
                      ..|+||||||.+++-..+..-...+|+...+..     ++..+ .++... +....-..+.+.++..+.+...   ..++
T Consensus        68 ~~gsGKT~lal~~~~~aq~~g~~a~fIDtE~~l-----~p~r~-~~l~~~~~d~l~v~~~~~~e~q~~i~~~~~~~~~~~  141 (279)
T COG0468          68 PESSGKTTLALQLVANAQKPGGKAAFIDTEHAL-----DPERA-KQLGVDLLDNLLVSQPDTGEQQLEIAEKLARSGAEK  141 (279)
T ss_pred             CCCcchhhHHHHHHHHhhcCCCeEEEEeCCCCC-----CHHHH-HHHHHhhhcceeEecCCCHHHHHHHHHHHHHhccCC
Confidence            368999999999887555555577888744332     33333 233333 2111112233333333333333   2333


Q ss_pred             eEEEEEeCCC
Q 040234           77 KVLVVIDDAA   86 (377)
Q Consensus        77 ~~LLVLDdv~   86 (377)
                      --|+|+|.+-
T Consensus       142 i~LvVVDSva  151 (279)
T COG0468         142 IDLLVVDSVA  151 (279)
T ss_pred             CCEEEEecCc
Confidence            5588888874

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

Probab=94.10  E-value=0.45  Score=43.17  Aligned_cols=71  Identities=21%  Similarity=0.018  Sum_probs=47.5

Q ss_pred             EEEEecchhHHhhC--CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhh
Q 040234          107 IIITTRNEHLLKLH--PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYT  181 (377)
Q Consensus       107 IIvTTR~~~v~~~~--~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l  181 (377)
                      |=.|||.-.+...+  .-.-+.+++-.+++|-.++..+.+..-.  .+-.++.+.+|+++..|  -|--..-+-.+.
T Consensus       155 IGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~--i~i~~~~a~eIA~rSRG--TPRIAnRLLrRV  227 (332)
T COG2255         155 IGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILG--IEIDEEAALEIARRSRG--TPRIANRLLRRV  227 (332)
T ss_pred             eeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhC--CCCChHHHHHHHHhccC--CcHHHHHHHHHH
Confidence            44688865443332  2245678899999999999988873221  12225678999999999  997655554443

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=94.08  E-value=0.17  Score=46.06  Aligned_cols=40  Identities=18%  Similarity=0.304  Sum_probs=30.2

Q ss_pred             CceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHH
Q 040234           75 RKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLL  117 (377)
Q Consensus        75 ~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~  117 (377)
                      ..+=++++|.+...+.+..+...+   ..|..||+||....+.
T Consensus       193 ~~P~villDE~~~~e~~~~l~~~~---~~G~~vI~ttH~~~~~  232 (270)
T TIGR02858       193 MSPDVIVVDEIGREEDVEALLEAL---HAGVSIIATAHGRDVE  232 (270)
T ss_pred             CCCCEEEEeCCCcHHHHHHHHHHH---hCCCEEEEEechhHHH
Confidence            578899999998877777665554   2477899999976553

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.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=94.05  E-value=0.091  Score=45.01  Aligned_cols=49  Identities=16%  Similarity=0.142  Sum_probs=28.1

Q ss_pred             HHHHHHHhcCce-EEEEEeCCCChh-----hhhHhhCCCCCCCCCCeEEEEecch
Q 040234           66 INMLRVRLRRKK-VLVVIDDAAHPD-----HLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        66 ~~~l~~~l~~k~-~LLVLDdv~~~~-----~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      .+..++.+...+ =|||||.+-..-     ..+.+...+.....+..||+|-|..
T Consensus       104 ~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986        104 WEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence            334455555444 499999975421     1222322233335567899999975

>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=93.99  E-value=0.82  Score=42.72  Aligned_cols=18  Identities=17%  Similarity=0.475  Sum_probs=16.1

Q ss_pred             CCcHHHHHHHHHchhccc
Q 040234            3 GLGKTTLARVVYDLISHE   20 (377)
Q Consensus         3 GiGKTtLA~~v~~~~~~~   20 (377)
                      |+|||++.+.+.+++++.
T Consensus        30 GsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen   30 GSGKSSFLNMLKEELKED   47 (325)
T ss_pred             CCCHHHHHHHHHHHHhcc
Confidence            999999999999977766

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 [].

>PRK07261 topology modulation protein; Provisional

Probab=93.99  E-value=0.18  Score=42.65  Aligned_cols=17  Identities=41%  Similarity=0.513  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||||+++....
T Consensus         8 ~~GsGKSTla~~l~~~~   24 (171)
T PRK07261          8 YSGSGKSTLARKLSQHY   24 (171)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999998743

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=93.87  E-value=0.16  Score=54.04  Aligned_cols=19  Identities=32%  Similarity=0.412  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      +.|+|||.||+.+++.+..
T Consensus       604 p~GvGKT~lA~~La~~l~~  622 (852)
T TIGR03345       604 PSGVGKTETALALAELLYG  622 (852)
T ss_pred             CCCCCHHHHHHHHHHHHhC
Confidence            4799999999999986543

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.

>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=93.80  E-value=0.11  Score=44.95  Aligned_cols=49  Identities=16%  Similarity=0.073  Sum_probs=27.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhh
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLK   53 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~   53 (377)
                      +.|+||||.+.+++.+.+.+ ...+-+... +.++ . ...+-++..++.++.
T Consensus         9 ptGvGKTTt~aKLAa~~~~~-~~~v~lis~-D~~R-~-ga~eQL~~~a~~l~v   57 (196)
T PF00448_consen    9 PTGVGKTTTIAKLAARLKLK-GKKVALISA-DTYR-I-GAVEQLKTYAEILGV   57 (196)
T ss_dssp             STTSSHHHHHHHHHHHHHHT-T--EEEEEE-STSS-T-HHHHHHHHHHHHHTE
T ss_pred             CCCCchHhHHHHHHHHHhhc-cccceeecC-CCCC-c-cHHHHHHHHHHHhcc
Confidence            47999999998888865555 433333212 2221 1 444555666666543

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 ....

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

Probab=93.69  E-value=0.25  Score=43.98  Aligned_cols=19  Identities=21%  Similarity=0.487  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      .|.|||+|++.+.++....
T Consensus        61 rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   61 RGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             CCCCHHHHHHHHHHHHhhc
Confidence            5999999999999866543

>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=93.62  E-value=0.044  Score=43.13  Aligned_cols=17  Identities=35%  Similarity=0.479  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         7 ~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    7 PPGSGKSTLAKELAERL   23 (121)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            47999999999999865

...

>PRK06762 hypothetical protein; Provisional

Probab=93.56  E-value=0.32  Score=40.69  Aligned_cols=17  Identities=35%  Similarity=0.536  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.+++++
T Consensus        10 ~~GsGKST~A~~L~~~l   26 (166)
T PRK06762         10 NSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999866

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.55  E-value=0.23  Score=44.42  Aligned_cols=27  Identities=15%  Similarity=0.074  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||+||.+++......-..++|+.
T Consensus        30 pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877        30 PGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            799999999998774333334556665

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.

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=93.52  E-value=0.32  Score=42.71  Aligned_cols=78  Identities=18%  Similarity=0.212  Sum_probs=41.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc-----ccCccch----------hhhH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA-----DNNIRNV----------YDGI   66 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~-----~~~~~~~----------~~~~   66 (377)
                      +|+|||+|+.++++.......  +++. +++..+   .+.++.+++...-....     .......          -...
T Consensus        24 ~g~GKt~Ll~~i~~~~~~d~~--V~~~-iGer~~---Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~a~t~A   97 (215)
T PF00006_consen   24 AGVGKTVLLQEIANNQDADVV--VYAL-IGERGR---EVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYTALTIA   97 (215)
T ss_dssp             TTSSHHHHHHHHHHHCTTTEE--EEEE-ESECHH---HHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHHHHHHH
T ss_pred             cccccchhhHHHHhcccccce--eeee-ccccch---hHHHHHHHHhhcccccccccccccchhhHHHHhhhhccchhhh
Confidence            699999999999986643322  4443 544321   44455544432200000     0000110          1123


Q ss_pred             HHHHHHhcCceEEEEEeCCCC
Q 040234           67 NMLRVRLRRKKVLVVIDDAAH   87 (377)
Q Consensus        67 ~~l~~~l~~k~~LLVLDdv~~   87 (377)
                      +.++.  ++++.|+++||+-.
T Consensus        98 Eyfrd--~G~dVlli~Dsltr  116 (215)
T PF00006_consen   98 EYFRD--QGKDVLLIIDSLTR  116 (215)
T ss_dssp             HHHHH--TTSEEEEEEETHHH
T ss_pred             HHHhh--cCCceeehhhhhHH
Confidence            33444  68999999999844

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 ....

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

Probab=93.43  E-value=0.55  Score=46.96  Aligned_cols=63  Identities=19%  Similarity=0.262  Sum_probs=39.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||.||+.++.+..--|     +. ++..            +++..+.+      .+++...+.+.+....-++++
T Consensus       231 PPGCGKT~lA~AiAgel~vPf-----~~-isAp------------eivSGvSG------ESEkkiRelF~~A~~~aPciv  286 (802)
T KOG0733|consen  231 PPGCGKTSLANAIAGELGVPF-----LS-ISAP------------EIVSGVSG------ESEKKIRELFDQAKSNAPCIV  286 (802)
T ss_pred             CCCccHHHHHHHHhhhcCCce-----Ee-ecch------------hhhcccCc------ccHHHHHHHHHHHhccCCeEE
Confidence            489999999999999765433     22 2111            11222111      244455556666666789999


Q ss_pred             EEeCCCC
Q 040234           81 VIDDAAH   87 (377)
Q Consensus        81 VLDdv~~   87 (377)
                      .+|+++-
T Consensus       287 FiDeIDA  293 (802)
T KOG0733|consen  287 FIDEIDA  293 (802)
T ss_pred             Eeecccc
Confidence            9999864

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=93.41  E-value=0.33  Score=41.90  Aligned_cols=20  Identities=35%  Similarity=0.458  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+||||+|+++++.+++.
T Consensus         9 yPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           9 YPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             CCCCCchHHHHHHHHHHHHh
Confidence            48999999999999966554

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=93.36  E-value=0.25  Score=48.45  Aligned_cols=44  Identities=32%  Similarity=0.363  Sum_probs=26.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLL   48 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~   48 (377)
                      +|+|||+|+.++++....+..+.+-+..+++..+   .+.++...+.
T Consensus       152 ~G~GKt~Ll~~~~~~~~~~~~dv~V~~liGER~r---Ev~ef~~~~~  195 (461)
T PRK12597        152 AGVGKTVLMMELIFNISKQHSGSSVFAGVGERSR---EGHELYHEMK  195 (461)
T ss_pred             CCCChhHHHHHHHHHHHhhCCCEEEEEcCCcchH---HHHHHHHHHH
Confidence            6999999999999866543444433343554331   4444544444

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=93.29  E-value=0.47  Score=40.23  Aligned_cols=47  Identities=21%  Similarity=0.202  Sum_probs=28.2

Q ss_pred             HHHHhcCceEEEEEeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           69 LRVRLRRKKVLVVIDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        69 l~~~l~~k~~LLVLDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      +-+.+..++=+++||+...   ..   .+..++..+   ..+..||++|.+.....
T Consensus       109 laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~---~~~~tii~~sh~~~~~~  161 (178)
T cd03247         109 LARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEV---LKDKTLIWITHHLTGIE  161 (178)
T ss_pred             HHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHH---cCCCEEEEEecCHHHHH
Confidence            4455567778999999754   22   222222222   23567888888876654

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.

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=93.25  E-value=0.16  Score=48.38  Aligned_cols=92  Identities=22%  Similarity=0.257  Sum_probs=48.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      -|.|||-|.-.+|+.+...-..++             .....+.++-+.+....     ...+....+.+.+.++..||.
T Consensus        71 vG~GKT~Lmd~f~~~lp~~~k~R~-------------HFh~Fm~~vh~~l~~~~-----~~~~~l~~va~~l~~~~~lLc  132 (362)
T PF03969_consen   71 VGRGKTMLMDLFYDSLPIKRKRRV-------------HFHEFMLDVHSRLHQLR-----GQDDPLPQVADELAKESRLLC  132 (362)
T ss_pred             CCCchhHHHHHHHHhCCccccccc-------------cccHHHHHHHHHHHHHh-----CCCccHHHHHHHHHhcCCEEE
Confidence            489999999999985443211111             11123333333322211     122334556667778888999


Q ss_pred             EeCC--CChh---hhhHhhCCCCCCCCCCeEEEEecch
Q 040234           82 IDDA--AHPD---HLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        82 LDdv--~~~~---~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      +|..  .|..   .+..|...+-  ..| .|||+|-+.
T Consensus       133 fDEF~V~DiaDAmil~rLf~~l~--~~g-vvlVaTSN~  167 (362)
T PF03969_consen  133 FDEFQVTDIADAMILKRLFEALF--KRG-VVLVATSNR  167 (362)
T ss_pred             EeeeeccchhHHHHHHHHHHHHH--HCC-CEEEecCCC
Confidence            9995  3432   2444444332  234 456666554

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

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

Probab=93.23  E-value=1.8  Score=38.91  Aligned_cols=140  Identities=16%  Similarity=0.110  Sum_probs=74.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|.|||.+|+.++++.+--|     +. +        ...+++   .+.. +.      ......+...+.-+.-++++
T Consensus       159 ppGTGKTm~Akalane~kvp~-----l~-v--------kat~li---GehV-Gd------gar~Ihely~rA~~~aPciv  214 (368)
T COG1223         159 PPGTGKTMMAKALANEAKVPL-----LL-V--------KATELI---GEHV-GD------GARRIHELYERARKAAPCIV  214 (368)
T ss_pred             CCCccHHHHHHHHhcccCCce-----EE-e--------chHHHH---HHHh-hh------HHHHHHHHHHHHHhcCCeEE
Confidence            479999999999999665432     11 1        111111   1111 11      01111222222334468999


Q ss_pred             EEeCCCCh--------------hhhhHhhCCCCCC--CCCCeEEEEecchhHHhhC---CCCCeeecCCCChhhhHHHHH
Q 040234           81 VIDDAAHP--------------DHLRRLVGEPDWF--GPGSRIIITTRNEHLLKLH---PVKKVYKLEALTYDEAFRLLC  141 (377)
Q Consensus        81 VLDdv~~~--------------~~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~~~---~~~~~~~l~~L~~~ea~~L~~  141 (377)
                      .||..+..              +.+++|+..+..-  +.|-..|..|....++...   .-...++...-+.+|-.+++.
T Consensus       215 FiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile  294 (368)
T COG1223         215 FIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILE  294 (368)
T ss_pred             EehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHH
Confidence            99987642              2345565554432  3354555555555443221   224456677777888888888


Q ss_pred             HHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          142 LKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .++-.-.-+   .....+.++++.+|
T Consensus       295 ~y~k~~Plp---v~~~~~~~~~~t~g  317 (368)
T COG1223         295 YYAKKFPLP---VDADLRYLAAKTKG  317 (368)
T ss_pred             HHHHhCCCc---cccCHHHHHHHhCC
Confidence            877321111   12236678888888

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=93.22  E-value=0.34  Score=45.16  Aligned_cols=76  Identities=21%  Similarity=0.125  Sum_probs=40.7

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc----cCccchhhhHHHHHHHhcCc-
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD----NNIRNVYDGINMLRVRLRRK-   76 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~----~~~~~~~~~~~~l~~~l~~k-   76 (377)
                      .|+||||||.++..+....-...+|+. .-..         +-...+++++....    ..+.+.++..+...+.++.. 
T Consensus        62 ~ssGKttLaL~~ia~~q~~g~~~a~ID-~e~~---------ld~~~a~~lGvdl~rllv~~P~~~E~al~~~e~lirsg~  131 (322)
T PF00154_consen   62 ESSGKTTLALHAIAEAQKQGGICAFID-AEHA---------LDPEYAESLGVDLDRLLVVQPDTGEQALWIAEQLIRSGA  131 (322)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT-EEEEEE-SSS------------HHHHHHTT--GGGEEEEE-SSHHHHHHHHHHHHHTTS
T ss_pred             CCCchhhhHHHHHHhhhcccceeEEec-Cccc---------chhhHHHhcCccccceEEecCCcHHHHHHHHHHHhhccc
Confidence            588999999999986655545567776 3222         22233344333221    12334455555555655543 


Q ss_pred             eEEEEEeCCCC
Q 040234           77 KVLVVIDDAAH   87 (377)
Q Consensus        77 ~~LLVLDdv~~   87 (377)
                      .-++|+|.|..
T Consensus       132 ~~lVVvDSv~a  142 (322)
T PF00154_consen  132 VDLVVVDSVAA  142 (322)
T ss_dssp             ESEEEEE-CTT
T ss_pred             ccEEEEecCcc
Confidence            45888888865

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 ....

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=93.17  E-value=0.26  Score=43.93  Aligned_cols=77  Identities=13%  Similarity=0.093  Sum_probs=41.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-------------------cCccch
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-------------------NNIRNV   62 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-------------------~~~~~~   62 (377)
                      +|+|||+||.+++.....+=..++|+. ..+      ...++++++. +++-...                   ....+.
T Consensus        34 ~GsGKt~l~~~~~~~~~~~g~~~~y~~-~e~------~~~~~~~~~~-~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~~~  105 (234)
T PRK06067         34 HGTGKSVLSQQFVYGALKQGKKVYVIT-TEN------TSKSYLKQME-SVKIDISDFFLWGYLRIFPLNTEGFEWNSTLA  105 (234)
T ss_pred             CCCChHHHHHHHHHHHHhCCCEEEEEE-cCC------CHHHHHHHHH-HCCCChhHHHhCCCceEEeccccccccCcchH
Confidence            799999999999764323333445554 322      4444444432 2210000                   011223


Q ss_pred             hhhHHHHHHHhcC-ceEEEEEeCCC
Q 040234           63 YDGINMLRVRLRR-KKVLVVIDDAA   86 (377)
Q Consensus        63 ~~~~~~l~~~l~~-k~~LLVLDdv~   86 (377)
                      +...+.+.+.+.. +.-++|+|.+.
T Consensus       106 ~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067        106 NKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEecHH
Confidence            4556666666654 56689999975

>CHL00095 clpC Clp protease ATP binding subunit

Probab=93.16  E-value=0.21  Score=53.06  Aligned_cols=101  Identities=24%  Similarity=0.252  Sum_probs=49.8

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCce-EE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKK-VL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~-~L   79 (377)
                      +.|+|||+||+.+++.+-..-...+-+ +++.....+ ....        +.+...... ..++ ...+.+.++.++ -+
T Consensus       547 p~GvGKt~lA~~LA~~l~~~~~~~~~~-d~s~~~~~~-~~~~--------l~g~~~gyv-g~~~-~~~l~~~~~~~p~~V  614 (821)
T CHL00095        547 PTGVGKTELTKALASYFFGSEDAMIRL-DMSEYMEKH-TVSK--------LIGSPPGYV-GYNE-GGQLTEAVRKKPYTV  614 (821)
T ss_pred             CCCCcHHHHHHHHHHHhcCCccceEEE-Echhccccc-cHHH--------hcCCCCccc-CcCc-cchHHHHHHhCCCeE
Confidence            479999999999998654322222222 244332111 1111        111111000 0111 123444555554 58


Q ss_pred             EEEeCCCC--hhhhhHhhCCCCCC-----------CCCCeEEEEecc
Q 040234           80 VVIDDAAH--PDHLRRLVGEPDWF-----------GPGSRIIITTRN  113 (377)
Q Consensus        80 LVLDdv~~--~~~~~~l~~~l~~~-----------~~gs~IIvTTR~  113 (377)
                      ++||+++.  .+.++.|+..+...           ...+-+|+||..
T Consensus       615 vllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~  661 (821)
T CHL00095        615 VLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNL  661 (821)
T ss_pred             EEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCc
Confidence            99999975  44555555544331           234557777764

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=93.16  E-value=0.29  Score=47.91  Aligned_cols=83  Identities=20%  Similarity=0.179  Sum_probs=43.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-----cCccchhhh------HHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-----NNIRNVYDG------INMLR   70 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~------~~~l~   70 (377)
                      +|+|||||+.+++.......+..+-+..+++..+   .+.++++.+...-.....     ....+...+      .-.+-
T Consensus       153 ~GvGKt~Ll~~i~~~~~~~~~~v~V~~liGER~r---Ev~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~~a~tiA  229 (463)
T PRK09280        153 AGVGKTVLIQELINNIAKEHGGYSVFAGVGERTR---EGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVALTGLTMA  229 (463)
T ss_pred             CCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcH---HHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            6999999999998855444344444444555431   444555555432110000     001111110      11123


Q ss_pred             HHh---cCceEEEEEeCCCC
Q 040234           71 VRL---RRKKVLVVIDDAAH   87 (377)
Q Consensus        71 ~~l---~~k~~LLVLDdv~~   87 (377)
                      +++   +++++||++|++-.
T Consensus       230 Eyfrd~~G~~VLll~DslTR  249 (463)
T PRK09280        230 EYFRDVEGQDVLLFIDNIFR  249 (463)
T ss_pred             HHHHHhcCCceEEEecchHH
Confidence            333   67899999999854

>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=93.08  E-value=0.1  Score=42.24  Aligned_cols=18  Identities=33%  Similarity=0.418  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+.....
T Consensus         7 ~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    7 PPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             STTSSHHHHHHHHHHHST
T ss_pred             CCCCCHHHHHHHHHHHCC
Confidence            589999999999987544

...

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=93.05  E-value=0.61  Score=46.59  Aligned_cols=142  Identities=16%  Similarity=0.124  Sum_probs=76.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|.|||.||+.+++.....|-....-              .++...    .+      .+.....+.+....+..+..|
T Consensus       284 pPGtGKT~lAkava~~~~~~fi~v~~~--------------~l~sk~----vG------esek~ir~~F~~A~~~~p~ii  339 (494)
T COG0464         284 PPGTGKTLLAKAVALESRSRFISVKGS--------------ELLSKW----VG------ESEKNIRELFEKARKLAPSII  339 (494)
T ss_pred             CCCCCHHHHHHHHHhhCCCeEEEeeCH--------------HHhccc----cc------hHHHHHHHHHHHHHcCCCcEE
Confidence            589999999999999666655322111              111111    11      122223334444446678999


Q ss_pred             EEeCCCCh-------------hhhhHhhCCCCCCC--CCCeEEEEecchhHHhh---C--CCCCeeecCCCChhhhHHHH
Q 040234           81 VIDDAAHP-------------DHLRRLVGEPDWFG--PGSRIIITTRNEHLLKL---H--PVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        81 VLDdv~~~-------------~~~~~l~~~l~~~~--~gs~IIvTTR~~~v~~~---~--~~~~~~~l~~L~~~ea~~L~  140 (377)
                      .+|+++..             .....++..+....  .+-.||-||-.+.....   .  .-...+.+++-+.++..++|
T Consensus       340 FiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~  419 (494)
T COG0464         340 FIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIF  419 (494)
T ss_pred             EEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHH
Confidence            99998642             12333333332222  23334555544433221   1  23567889999999999999


Q ss_pred             HHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          141 CLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ..+....... -...-..+.+++...|
T Consensus       420 ~~~~~~~~~~-~~~~~~~~~l~~~t~~  445 (494)
T COG0464         420 KIHLRDKKPP-LAEDVDLEELAEITEG  445 (494)
T ss_pred             HHHhcccCCc-chhhhhHHHHHHHhcC
Confidence            9888533321 0112234455555555

>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=92.96  E-value=1.3  Score=42.68  Aligned_cols=101  Identities=16%  Similarity=0.083  Sum_probs=68.4

Q ss_pred             eEEEEEeCCCC-----------hhhhhHhhCCCCCCCCCCeEEEEecchhH----HhhCC--CCCeeecCCCChhhhHHH
Q 040234           77 KVLVVIDDAAH-----------PDHLRRLVGEPDWFGPGSRIIITTRNEHL----LKLHP--VKKVYKLEALTYDEAFRL  139 (377)
Q Consensus        77 ~~LLVLDdv~~-----------~~~~~~l~~~l~~~~~gs~IIvTTR~~~v----~~~~~--~~~~~~l~~L~~~ea~~L  139 (377)
                      +=++||||..+           ..+|...+..    .+-.+||++|-+...    ...++  ..+.+.|...+++.|.++
T Consensus       149 ~PVVVIdnF~~k~~~~~~iy~~laeWAa~Lv~----~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~y  224 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEENDFIYDKLAEWAASLVQ----NNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQY  224 (431)
T ss_pred             CCEEEEcchhccCcccchHHHHHHHHHHHHHh----cCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHH
Confidence            56899999643           2356665544    455689988876543    33443  357789999999999999


Q ss_pred             HHHHhcCCCCC------------------chhHHHHHHHHHHHhCCCCchhhHHHHHhhhhc
Q 040234          140 LCLKAFDTHKP------------------LEEYVELAESVVRICHCQKSTLNALMSVSYTVS  183 (377)
Q Consensus       140 ~~~~~~~~~~~------------------~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~  183 (377)
                      ...+.......                  .....+.....+..+||  ==+-|..++.++.+
T Consensus       225 V~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGG--RltDLe~lvrRiks  284 (431)
T PF10443_consen  225 VLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGG--RLTDLEFLVRRIKS  284 (431)
T ss_pred             HHHHhcccccccccccccccccccccccccccchHHHHHHHHHcCC--cHHHHHHHHHHHHc
Confidence            98887543110                  02345567788889999  77777777776544

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 [].

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=92.93  E-value=0.074  Score=45.00  Aligned_cols=33  Identities=24%  Similarity=0.259  Sum_probs=22.7

Q ss_pred             CCCCcHHHHHHHHHchhc-cccccceEEecchhhc
Q 040234            1 MGGLGKTTLARVVYDLIS-HEFDGSSFLADVREKC   34 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~-~~f~~~~w~~~~~~~~   34 (377)
                      +.|+|||.||+.+++.+. +.....+-+. +++..
T Consensus        11 psGvGKT~la~~la~~l~~~~~~~~~~~d-~s~~~   44 (171)
T PF07724_consen   11 PSGVGKTELAKALAELLFVGSERPLIRID-MSEYS   44 (171)
T ss_dssp             STTSSHHHHHHHHHHHHT-SSCCEEEEEE-GGGHC
T ss_pred             CCCCCHHHHHHHHHHHhccCCccchHHHh-hhccc
Confidence            479999999999999776 4444434333 55553

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=92.92  E-value=0.27  Score=44.75  Aligned_cols=81  Identities=16%  Similarity=0.137  Sum_probs=45.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+||||++..+.+.+...-...+.+.+..+.     ....     ..++    ...........+.++..|+..+=.++
T Consensus        89 tGSGKTT~l~all~~i~~~~~~iitiEdp~E~-----~~~~-----~~q~----~v~~~~~~~~~~~l~~~lR~~PD~i~  154 (264)
T cd01129          89 TGSGKTTTLYSALSELNTPEKNIITVEDPVEY-----QIPG-----INQV----QVNEKAGLTFARGLRAILRQDPDIIM  154 (264)
T ss_pred             CCCcHHHHHHHHHhhhCCCCCeEEEECCCcee-----cCCC-----ceEE----EeCCcCCcCHHHHHHHHhccCCCEEE
Confidence            59999999998887664321122233221111     0000     0000    00111112456778888888888999


Q ss_pred             EeCCCChhhhhHhhC
Q 040234           82 IDDAAHPDHLRRLVG   96 (377)
Q Consensus        82 LDdv~~~~~~~~l~~   96 (377)
                      ++++.+.+....+..
T Consensus       155 vgEiR~~e~a~~~~~  169 (264)
T cd01129         155 VGEIRDAETAEIAVQ  169 (264)
T ss_pred             eccCCCHHHHHHHHH
Confidence            999999876554433

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>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=92.90  E-value=0.48  Score=39.92  Aligned_cols=20  Identities=30%  Similarity=0.403  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+||||++..++....+.
T Consensus         8 ~~G~GKTt~~~~la~~~~~~   27 (173)
T cd03115           8 LQGVGKTTTAAKLALYLKKK   27 (173)
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            48999999999999866554

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.

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=92.88  E-value=0.37  Score=43.79  Aligned_cols=45  Identities=13%  Similarity=0.107  Sum_probs=25.9

Q ss_pred             CCCcHHHHHHHHHchhc---cccccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLIS---HEFDGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~---~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      .|+|||+|+..++++..   +.-...+-+..+++..+   ...++...+..
T Consensus        78 ~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~r---ev~e~~~~~~~  125 (276)
T cd01135          78 SGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITME---DARFFKDDFEE  125 (276)
T ss_pred             CCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccH---HHHHHHHHhhh
Confidence            68999999999987543   11123333333666542   44555555443

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.

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.86  E-value=2.6  Score=40.79  Aligned_cols=53  Identities=8%  Similarity=-0.054  Sum_probs=35.7

Q ss_pred             CCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhh
Q 040234          123 KKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTV  182 (377)
Q Consensus       123 ~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~  182 (377)
                      ...+.+.--+.+.-..|+..+.+... +    ..+..+|.+...+  --+.-..++..+.
T Consensus       362 DmhI~mgyCtf~~fK~La~nYL~~~~-~----h~L~~eie~l~~~--~~~tPA~V~e~lm  414 (457)
T KOG0743|consen  362 DMHIYMGYCTFEAFKTLASNYLGIEE-D----HRLFDEIERLIEE--TEVTPAQVAEELM  414 (457)
T ss_pred             eeEEEcCCCCHHHHHHHHHHhcCCCC-C----cchhHHHHHHhhc--CccCHHHHHHHHh
Confidence            45677888888888889888885433 2    3456667777777  6666556666543

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

Probab=92.71  E-value=0.31  Score=43.03  Aligned_cols=82  Identities=22%  Similarity=0.331  Sum_probs=45.4

Q ss_pred             CCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEEE
Q 040234            3 GLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVI   82 (377)
Q Consensus         3 GiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLVL   82 (377)
                      |.|||+|++.+.+++.+....  .|. +...     ++.                   ++..+.+.++.  ..+|++|..
T Consensus        95 GtGKSSLVKA~~~e~~~~glr--LVE-V~k~-----dl~-------------------~Lp~l~~~Lr~--~~~kFIlFc  145 (287)
T COG2607          95 GTGKSSLVKALLNEYADEGLR--LVE-VDKE-----DLA-------------------TLPDLVELLRA--RPEKFILFC  145 (287)
T ss_pred             CCChHHHHHHHHHHHHhcCCe--EEE-EcHH-----HHh-------------------hHHHHHHHHhc--CCceEEEEe
Confidence            889999999999877776544  222 3222     111                   11122222222  467999999


Q ss_pred             eCCC---ChhhhhHhhCCCCCC---CCCCeEEEEecc
Q 040234           83 DDAA---HPDHLRRLVGEPDWF---GPGSRIIITTRN  113 (377)
Q Consensus        83 Ddv~---~~~~~~~l~~~l~~~---~~gs~IIvTTR~  113 (377)
                      ||..   +.+.++.+...+..+   .+...++..|.+
T Consensus       146 DDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSN  182 (287)
T COG2607         146 DDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSN  182 (287)
T ss_pred             cCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecC
Confidence            9983   344566665554432   334445544443

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=92.71  E-value=0.37  Score=47.05  Aligned_cols=44  Identities=30%  Similarity=0.402  Sum_probs=27.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLL   48 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~   48 (377)
                      +|+|||+|+.+++.......+..+-+..+++..+   .+.++++.+.
T Consensus       152 ~G~GKt~L~~~~~~~~~~~~~~v~V~alIGER~r---Ev~ef~~~~~  195 (461)
T TIGR01039       152 AGVGKTVLIQELINNIAKEHGGYSVFAGVGERTR---EGNDLYHEMK  195 (461)
T ss_pred             CCCChHHHHHHHHHHHHhcCCCeEEEEEecCCch---HHHHHHHHHH
Confidence            6999999999998855443344444444655431   4445555553

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.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=92.58  E-value=3.3  Score=38.40  Aligned_cols=94  Identities=13%  Similarity=0.050  Sum_probs=57.5

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEec-chhHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTR-NEHLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR-~~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +.+=++|+|+++..  ...+.|+..+..-.+.+.+|++|. ...+... ......+++.++++++..+.+... +    .
T Consensus        89 ~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~~~-~----~  163 (299)
T PRK07132         89 SQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLLSK-N----K  163 (299)
T ss_pred             CCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHHHc-C----C
Confidence            46678999998763  335555555544355666666554 3444433 345788999999999998877654 1    1


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      .   .+.+..++...+|  .--|+..+.
T Consensus       164 ~---~~~a~~~a~~~~~--~~~a~~~~~  186 (299)
T PRK07132        164 E---KEYNWFYAYIFSN--FEQAEKYIN  186 (299)
T ss_pred             C---hhHHHHHHHHcCC--HHHHHHHHh
Confidence            1   2345556666666  555555443

>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=92.51  E-value=0.27  Score=44.82  Aligned_cols=19  Identities=26%  Similarity=0.291  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||+|+++...+.+
T Consensus         9 ~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    9 LPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -TTSSHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHh
Confidence            4899999999999986554

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>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=92.45  E-value=0.35  Score=39.55  Aligned_cols=94  Identities=14%  Similarity=0.165  Sum_probs=46.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|.|||||++.++...+. ..+.+++.......    -+.+                .+.-+...-.+-+.+..++-+++
T Consensus        35 nGsGKStLl~~l~G~~~~-~~G~i~~~~~~~i~----~~~~----------------lS~G~~~rv~laral~~~p~ill   93 (144)
T cd03221          35 NGAGKSTLLKLIAGELEP-DEGIVTWGSTVKIG----YFEQ----------------LSGGEKMRLALAKLLLENPNLLL   93 (144)
T ss_pred             CCCCHHHHHHHHcCCCCC-CceEEEECCeEEEE----EEcc----------------CCHHHHHHHHHHHHHhcCCCEEE
Confidence            699999999999984432 24445554210000    0000                11111222233445556677899


Q ss_pred             EeCCCC---hhhhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           82 IDDAAH---PDHLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        82 LDdv~~---~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      +|+.-.   ......+...+...  +..||++|.+.....
T Consensus        94 lDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~  131 (144)
T cd03221          94 LDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLD  131 (144)
T ss_pred             EeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHH
Confidence            999743   22222222222111  246888888765544

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.

>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=92.38  E-value=0.6  Score=39.68  Aligned_cols=112  Identities=18%  Similarity=0.203  Sum_probs=53.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHH------HHHHHHHHHhhcc--cc---CccchhhhHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVIS------LQKQLLSDLLKLA--DN---NIRNVYDGINMLR   70 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~------~~~~i~~~l~~~~--~~---~~~~~~~~~~~l~   70 (377)
                      .|+|||||++.++..... ..+.+++... +.. .. +...      ...++++.++...  ..   ..+.-+...-.+-
T Consensus        34 nGsGKStLl~~i~G~~~~-~~G~v~~~g~-~~~-~~-~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G~~qrl~la  109 (180)
T cd03214          34 NGAGKSTLLKTLAGLLKP-SSGEILLDGK-DLA-SL-SPKELARKIAYVPQALELLGLAHLADRPFNELSGGERQRVLLA  109 (180)
T ss_pred             CCCCHHHHHHHHhCCCCC-CCcEEEECCE-ECC-cC-CHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHHHHHHHHHH
Confidence            699999999999985432 3444555311 100 00 1111      1111333322111  01   1111122223345


Q ss_pred             HHhcCceEEEEEeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           71 VRLRRKKVLVVIDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        71 ~~l~~k~~LLVLDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      +.+...+-+++||+.-.   .+   .+..++..+.. ..+..||++|.+.....
T Consensus       110 ral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~-~~~~tiii~sh~~~~~~  162 (180)
T cd03214         110 RALAQEPPILLLDEPTSHLDIAHQIELLELLRRLAR-ERGKTVVMVLHDLNLAA  162 (180)
T ss_pred             HHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHH-hcCCEEEEEeCCHHHHH
Confidence            55667788999999743   22   22222222211 11567888888766543

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.

>PRK08233 hypothetical protein; Provisional

Probab=92.34  E-value=0.25  Score=41.79  Aligned_cols=18  Identities=33%  Similarity=0.429  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+||||||..++..+.
T Consensus        11 ~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233         11 VSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             CCCCCHHHHHHHHHhhCC
Confidence            379999999999998653

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=92.26  E-value=0.15  Score=43.66  Aligned_cols=18  Identities=39%  Similarity=0.372  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+|||+++.+++..+.
T Consensus        40 ~~g~GKT~~~~~l~~~~~   57 (193)
T PF13481_consen   40 PPGSGKTTLALQLAAALA   57 (193)
T ss_dssp             CSTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999988543

>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=92.22  E-value=0.12  Score=42.89  Aligned_cols=27  Identities=33%  Similarity=0.284  Sum_probs=20.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      ++|+||||||+.+.+++.+.-....++
T Consensus        10 lsGsGKtTlA~~L~~~L~~~g~~~~~L   36 (156)
T PF01583_consen   10 LSGSGKTTLARALERRLFARGIKVYLL   36 (156)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTS-EEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCcEEEe
Confidence            589999999999999887664444443

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 ....

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=92.20  E-value=1.8  Score=40.27  Aligned_cols=141  Identities=16%  Similarity=0.100  Sum_probs=76.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCc---cchhhhHHHHHHHhc---
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNI---RNVYDGINMLRVRLR---   74 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~---~~~~~~~~~l~~~l~---   74 (377)
                      +.|.|||+|......+ .+.+.....++.+.+...   .-+-+++.|.+++........   .+..+-...+-..|+   
T Consensus        57 prgsgkT~li~~~Ls~-~q~~~E~~l~v~Lng~~~---~dk~al~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~  132 (408)
T KOG2228|consen   57 PRGSGKTILIDTRLSD-IQENGENFLLVRLNGELQ---TDKIALKGITRQLALELNRIVKSFGSFTENLSKLLEALKKGD  132 (408)
T ss_pred             cCCCCceEeeHHHHhh-HHhcCCeEEEEEECccch---hhHHHHHHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCC
Confidence            3699999998777765 445555455544544331   112245555555543322111   222233333444443   


Q ss_pred             ---CceEEEEEeCCCCh----hh---hhHhhCCCCCCCCCCeEEEEecch-------hHHhhCCCCCeeecCCCChhhhH
Q 040234           75 ---RKKVLVVIDDAAHP----DH---LRRLVGEPDWFGPGSRIIITTRNE-------HLLKLHPVKKVYKLEALTYDEAF  137 (377)
Q Consensus        75 ---~k~~LLVLDdv~~~----~~---~~~l~~~l~~~~~gs~IIvTTR~~-------~v~~~~~~~~~~~l~~L~~~ea~  137 (377)
                         .-++..|+|..+--    .|   ++.+-..-....|-|-|-+|||-.       .|-.+.+-..++-++.++-++-.
T Consensus       133 ~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv  212 (408)
T KOG2228|consen  133 ETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDILELLEKRVKSRFSHRVIFMLPSLPLGDYV  212 (408)
T ss_pred             CCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHHhhcccceeeccCCCChHHHH
Confidence               23688889887641    11   222222222235667788999953       33333333345566778889999


Q ss_pred             HHHHHHhc
Q 040234          138 RLLCLKAF  145 (377)
Q Consensus       138 ~L~~~~~~  145 (377)
                      .+++....
T Consensus       213 ~l~r~ll~  220 (408)
T KOG2228|consen  213 DLYRKLLS  220 (408)
T ss_pred             HHHHHHhc
Confidence            99888764

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=92.18  E-value=0.084  Score=45.75  Aligned_cols=34  Identities=24%  Similarity=0.489  Sum_probs=20.4

Q ss_pred             eEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEec
Q 040234           77 KVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTR  112 (377)
Q Consensus        77 ~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR  112 (377)
                      .-+||+|++.-  ..++..+.....  ..+.++|+.--
T Consensus        94 ~~vliVDEasmv~~~~~~~ll~~~~--~~~~klilvGD  129 (196)
T PF13604_consen   94 KDVLIVDEASMVDSRQLARLLRLAK--KSGAKLILVGD  129 (196)
T ss_dssp             TSEEEESSGGG-BHHHHHHHHHHS---T-T-EEEEEE-
T ss_pred             ccEEEEecccccCHHHHHHHHHHHH--hcCCEEEEECC
Confidence            34999999875  346666665544  24778876654

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

Probab=92.16  E-value=0.43  Score=44.80  Aligned_cols=34  Identities=29%  Similarity=0.654  Sum_probs=25.2

Q ss_pred             eEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecc
Q 040234           77 KVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRN  113 (377)
Q Consensus        77 ~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~  113 (377)
                      +-++|+|.+.+  ..++..+...   .+.|+||+.|---
T Consensus       352 ~~FiIIDEaQNLTpheikTiltR---~G~GsKIVl~gd~  387 (436)
T COG1875         352 DSFIIIDEAQNLTPHELKTILTR---AGEGSKIVLTGDP  387 (436)
T ss_pred             cceEEEehhhccCHHHHHHHHHh---ccCCCEEEEcCCH
Confidence            45899999988  4566666544   2889999988653

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=92.12  E-value=0.52  Score=41.74  Aligned_cols=27  Identities=19%  Similarity=0.076  Sum_probs=18.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||+||.+++......-..++|+.
T Consensus        29 ~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881        29 PGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             CCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            699999999988764333334556665

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.

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

Probab=92.12  E-value=0.52  Score=49.67  Aligned_cols=41  Identities=15%  Similarity=0.118  Sum_probs=26.2

Q ss_pred             CCeEEEEecchhHHhhC-CCCCeeecCCCChhhhHHHHHHHh
Q 040234          104 GSRIIITTRNEHLLKLH-PVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus       104 gs~IIvTTR~~~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      +.-+|.|+....+...+ .....+++.+++.++-.++..++.
T Consensus       465 ~v~~i~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        465 DVMFVATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             ceEEEEcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHHHhh
Confidence            44455666544332222 334678999999999988877665

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=92.11  E-value=0.95  Score=41.16  Aligned_cols=43  Identities=23%  Similarity=0.260  Sum_probs=26.7

Q ss_pred             CCCcHHHHHHHHHchhccc-cccceEEecchhhcccccCHHHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHE-FDGSSFLADVREKCDKEGSVISLQKQLLSDL   51 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l   51 (377)
                      +|+|||+|+.+++...... -..++|+. +-.      ...++...+...+
T Consensus        39 ~G~GKT~l~~~~~~~~~~~~g~~vl~iS-~E~------~~~~~~~r~~~~~   82 (271)
T cd01122          39 TGVGKTTFLREYALDLITQHGVRVGTIS-LEE------PVVRTARRLLGQY   82 (271)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCceEEEEE-ccc------CHHHHHHHHHHHH
Confidence            6999999999998865333 23455554 222      4455666655544

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=92.07  E-value=0.33  Score=46.41  Aligned_cols=27  Identities=22%  Similarity=0.286  Sum_probs=19.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||||+.+++......-..++|+.
T Consensus        91 pG~GKStLllq~a~~~a~~g~~VlYvs  117 (372)
T cd01121          91 PGIGKSTLLLQVAARLAKRGGKVLYVS  117 (372)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            799999999999986654433444544

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.

>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=92.06  E-value=0.098  Score=41.36  Aligned_cols=17  Identities=35%  Similarity=0.571  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ..|+||||||+++.++.
T Consensus         6 ~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    6 IPGSGKTTIAKELAERL   22 (129)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            47999999999999975

...

>PRK04328 hypothetical protein; Provisional

Probab=91.99  E-value=0.34  Score=43.64  Aligned_cols=27  Identities=15%  Similarity=0.084  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||+||.+++.+-...-..++|+.
T Consensus        32 pGsGKT~l~~~fl~~~~~~ge~~lyis   58 (249)
T PRK04328         32 PGTGKSIFSQQFLWNGLQMGEPGVYVA   58 (249)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            799999999998775333334556665

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=91.91  E-value=0.69  Score=41.14  Aligned_cols=27  Identities=15%  Similarity=0.108  Sum_probs=17.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .|+||||||.+++......-..++++.
T Consensus        33 ~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         33 ESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            799999999777764422223345544

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=91.91  E-value=2.6  Score=43.70  Aligned_cols=96  Identities=14%  Similarity=0.181  Sum_probs=58.6

Q ss_pred             CceEEEEEeCCCCh-----------------hhhhHhhCCCCCCCCCCeE--EEEecchhHHhhC-----CCCCeeecCC
Q 040234           75 RKKVLVVIDDAAHP-----------------DHLRRLVGEPDWFGPGSRI--IITTRNEHLLKLH-----PVKKVYKLEA  130 (377)
Q Consensus        75 ~k~~LLVLDdv~~~-----------------~~~~~l~~~l~~~~~gs~I--IvTTR~~~v~~~~-----~~~~~~~l~~  130 (377)
                      ..+..+-+|+++..                 ..++.|+...........|  |.+|+..++....     .-++.+.++.
T Consensus       402 ~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~  481 (774)
T KOG0731|consen  402 NAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDL  481 (774)
T ss_pred             cCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccceeccC
Confidence            45677888876531                 2356666655544333333  3455555443221     2366788888


Q ss_pred             CChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhH
Q 040234          131 LTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       131 L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                      -+...-.++|.-++...... .+..++.+ |+...-|  .+-|-
T Consensus       482 p~~~~r~~i~~~h~~~~~~~-~e~~dl~~-~a~~t~g--f~gad  521 (774)
T KOG0731|consen  482 PDVKGRASILKVHLRKKKLD-DEDVDLSK-LASLTPG--FSGAD  521 (774)
T ss_pred             CchhhhHHHHHHHhhccCCC-cchhhHHH-HHhcCCC--CcHHH
Confidence            88888999998888543332 34456666 8888888  77664

>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=91.68  E-value=0.59  Score=39.17  Aligned_cols=107  Identities=20%  Similarity=0.192  Sum_probs=49.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEec------chhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcC
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLAD------VREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRR   75 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~------~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~   75 (377)
                      .|+|||||++.++..... ..+.+++..      +.+... . ....+...+...   . ....+.-+...-.+.+.+..
T Consensus        36 nGsGKSTLl~~l~G~~~~-~~G~i~~~~~~~i~~~~q~~~-~-~~~tv~~nl~~~---~-~~~LS~G~~~rv~laral~~  108 (166)
T cd03223          36 SGTGKSSLFRALAGLWPW-GSGRIGMPEGEDLLFLPQRPY-L-PLGTLREQLIYP---W-DDVLSGGEQQRLAFARLLLH  108 (166)
T ss_pred             CCCCHHHHHHHHhcCCCC-CCceEEECCCceEEEECCCCc-c-ccccHHHHhhcc---C-CCCCCHHHHHHHHHHHHHHc
Confidence            699999999999984432 123233221      111110 0 111222222110   1 11112222233334455566


Q ss_pred             ceEEEEEeCCCC---hhhhhHhhCCCCCCCCCCeEEEEecchhHH
Q 040234           76 KKVLVVIDDAAH---PDHLRRLVGEPDWFGPGSRIIITTRNEHLL  117 (377)
Q Consensus        76 k~~LLVLDdv~~---~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~  117 (377)
                      ++=+++||+--.   .+..+.+...+...  +..||++|.+....
T Consensus       109 ~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~  151 (166)
T cd03223         109 KPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLW  151 (166)
T ss_pred             CCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHH
Confidence            777889999643   22222222222111  35688888877654

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

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=91.67  E-value=0.28  Score=46.31  Aligned_cols=14  Identities=36%  Similarity=0.226  Sum_probs=12.3

Q ss_pred             CCCcHHHHHHHHHc
Q 040234            2 GGLGKTTLARVVYD   15 (377)
Q Consensus         2 gGiGKTtLA~~v~~   15 (377)
                      +|+|||+|+.+++-
T Consensus       135 ~GsGKTql~lqlav  148 (344)
T PLN03187        135 FRSGKTQLAHTLCV  148 (344)
T ss_pred             CCCChhHHHHHHHH
Confidence            79999999998864

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

Probab=91.64  E-value=1  Score=38.55  Aligned_cols=55  Identities=13%  Similarity=0.201  Sum_probs=36.4

Q ss_pred             hhHHHHHHHhcCceEEEEEeCC----CChhhhh--HhhCCCCCCCCCCeEEEEecchhHHhhC
Q 040234           64 DGINMLRVRLRRKKVLVVIDDA----AHPDHLR--RLVGEPDWFGPGSRIIITTRNEHLLKLH  120 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv----~~~~~~~--~l~~~l~~~~~gs~IIvTTR~~~v~~~~  120 (377)
                      +..-.+-+.+-+++-||+-|.-    +..-.|+  .+...+.  ..|..||++|.+..+...+
T Consensus       143 QQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeein--r~GtTVl~ATHd~~lv~~~  203 (223)
T COG2884         143 QQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEIN--RLGTTVLMATHDLELVNRM  203 (223)
T ss_pred             HHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHh--hcCcEEEEEeccHHHHHhc
Confidence            3344456677788899999974    3333343  2333332  5689999999999887765

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=91.63  E-value=1.1  Score=37.90  Aligned_cols=17  Identities=24%  Similarity=0.196  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         7 ~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         7 GPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            48999999999999855

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=91.47  E-value=0.43  Score=44.67  Aligned_cols=17  Identities=24%  Similarity=0.175  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+|||+||.+++...
T Consensus       110 ~~GsGKT~l~~~~~~~~  126 (317)
T PRK04301        110 EFGSGKTQICHQLAVNV  126 (317)
T ss_pred             CCCCCHhHHHHHHHHHh
Confidence            37999999999998743

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=91.35  E-value=1.9  Score=38.02  Aligned_cols=51  Identities=22%  Similarity=0.314  Sum_probs=31.0

Q ss_pred             HhcCceEEEEEeCCCCh---hhhhHh---hCCCCCCCCCCeEEEEecchhHHhhCCCCC
Q 040234           72 RLRRKKVLVVIDDAAHP---DHLRRL---VGEPDWFGPGSRIIITTRNEHLLKLHPVKK  124 (377)
Q Consensus        72 ~l~~k~~LLVLDdv~~~---~~~~~l---~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~  124 (377)
                      .+-=++-|.|||..++-   +.++.+   ...+.  .+++.+|+.|..+.++.......
T Consensus       158 ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr--~~~~~~liITHy~rll~~i~pD~  214 (251)
T COG0396         158 LLLLEPKLAILDEPDSGLDIDALKIVAEGINALR--EEGRGVLIITHYQRLLDYIKPDK  214 (251)
T ss_pred             HHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHh--cCCCeEEEEecHHHHHhhcCCCE
Confidence            33446779999999873   222221   11222  34777888888888887765433

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=91.31  E-value=0.34  Score=41.27  Aligned_cols=16  Identities=38%  Similarity=0.430  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      .+|+||||+|+.++++
T Consensus         8 ~pGaGK~T~A~~La~~   23 (178)
T COG0563           8 PPGAGKSTLAKKLAKK   23 (178)
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            3799999999999996

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.29  E-value=0.95  Score=43.47  Aligned_cols=19  Identities=26%  Similarity=0.123  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||++..++..+..
T Consensus       249 ptGvGKTTTiaKLA~~L~~  267 (436)
T PRK11889        249 PTGVGKTTTLAKMAWQFHG  267 (436)
T ss_pred             CCCCcHHHHHHHHHHHHHH
Confidence            3799999999999986543

>PRK10867 signal recognition particle protein; Provisional

Probab=91.21  E-value=0.56  Score=45.77  Aligned_cols=20  Identities=30%  Similarity=0.421  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+||||+|..++...+..
T Consensus       108 ~~GsGKTTtaakLA~~l~~~  127 (433)
T PRK10867        108 LQGAGKTTTAGKLAKYLKKK  127 (433)
T ss_pred             CCCCcHHHHHHHHHHHHHHh
Confidence            47999999998888755544

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=91.16  E-value=0.56  Score=45.78  Aligned_cols=44  Identities=23%  Similarity=0.343  Sum_probs=26.2

Q ss_pred             CCCcHHHHHHHHHchhc-cccccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLIS-HEFDGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+|+.++++... .+-+..++. .+++..+   .+.++.+.+..
T Consensus       147 ~G~GKt~l~~~~~~~~~~~~~~v~V~~-~iGeR~r---Ev~e~~~~~~~  191 (449)
T TIGR03305       147 AGVGKTVLLTEMIHNMVGQHQGVSIFC-GIGERCR---EGEELYREMKE  191 (449)
T ss_pred             CCCChhHHHHHHHHHHHhcCCCEEEEE-EeccCcH---HHHHHHHHHhh
Confidence            69999999999988543 322344443 3655431   44455555443

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.

>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=91.13  E-value=0.096  Score=41.75  Aligned_cols=22  Identities=36%  Similarity=0.546  Sum_probs=16.3

Q ss_pred             CCCcHHHHHHHHHchhcccccc
Q 040234            2 GGLGKTTLARVVYDLISHEFDG   23 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~   23 (377)
                      +|+|||+||+.++..+...|..
T Consensus         8 PG~GKT~la~~lA~~~~~~f~R   29 (131)
T PF07726_consen    8 PGVGKTTLAKALARSLGLSFKR   29 (131)
T ss_dssp             --HHHHHHHHHHHHHTT--EEE
T ss_pred             CccHHHHHHHHHHHHcCCceeE
Confidence            7999999999999988888865

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.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=91.05  E-value=0.49  Score=42.55  Aligned_cols=19  Identities=26%  Similarity=0.539  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||+|+.+++....
T Consensus         7 ~pGSGKST~a~~La~~l~~   25 (249)
T TIGR03574         7 LPGVGKSTFSKELAKKLSE   25 (249)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            5899999999999986643

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.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=91.04  E-value=1.3  Score=36.46  Aligned_cols=18  Identities=33%  Similarity=0.578  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+||||||+.+...+.
T Consensus         7 ~~GsGKSTla~~L~~~l~   24 (149)
T cd02027           7 LSGSGKSTIARALEEKLF   24 (149)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            379999999999998654

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=90.96  E-value=0.96  Score=42.62  Aligned_cols=18  Identities=33%  Similarity=0.469  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+++.+.+.+.
T Consensus         7 l~GaGKST~~~~l~~~l~   24 (340)
T TIGR03575         7 LPAAGKSTLARSLSATLR   24 (340)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            589999999999998654

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=90.94  E-value=0.65  Score=45.41  Aligned_cols=20  Identities=30%  Similarity=0.370  Sum_probs=16.4

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ..|+||||+|..++..++..
T Consensus       103 ~~GsGKTTtaakLA~~L~~~  122 (437)
T PRK00771        103 LQGSGKTTTAAKLARYFKKK  122 (437)
T ss_pred             CCCCcHHHHHHHHHHHHHHc
Confidence            47999999999999866543

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=90.93  E-value=4.1  Score=41.65  Aligned_cols=162  Identities=13%  Similarity=0.114  Sum_probs=85.6

Q ss_pred             CCCcHHHHHHHHHchhc-----cccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhc--
Q 040234            2 GGLGKTTLARVVYDLIS-----HEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLR--   74 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~-----~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~--   74 (377)
                      +|.|||..+..|.+.++     ..-+.-.++. +...  ..+...++...|..++.+...    ......+.+..++.  
T Consensus       431 PGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yve-INgm--~l~~~~~~Y~~I~~~lsg~~~----~~~~al~~L~~~f~~~  503 (767)
T KOG1514|consen  431 PGTGKTATVLEVMKELQTSSAQKELPKFDYVE-INGL--RLASPREIYEKIWEALSGERV----TWDAALEALNFRFTVP  503 (767)
T ss_pred             CCCCceehHHHHHHHHHHHHhhcCCCCccEEE-Ecce--eecCHHHHHHHHHHhcccCcc----cHHHHHHHHHHhhccC
Confidence            69999999999998443     1222222222 2211  111677888888888766543    33444555555554  


Q ss_pred             ---CceEEEEEeCCCCh-----hhhhHhhCCCCCCCCCCeEEEEecc-------h----hHHhhCCCCCeeecCCCChhh
Q 040234           75 ---RKKVLVVIDDAAHP-----DHLRRLVGEPDWFGPGSRIIITTRN-------E----HLLKLHPVKKVYKLEALTYDE  135 (377)
Q Consensus        75 ---~k~~LLVLDdv~~~-----~~~~~l~~~l~~~~~gs~IIvTTR~-------~----~v~~~~~~~~~~~l~~L~~~e  135 (377)
                         .+..+|++|+++..     +.+-.+..-..  .++++++|.+=.       +    .+...++ ...+...+.+.++
T Consensus       504 k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt--~~~sKLvvi~IaNTmdlPEr~l~nrvsSRlg-~tRi~F~pYth~q  580 (767)
T KOG1514|consen  504 KPKRSTTVVLIDELDILVTRSQDVLYNIFDWPT--LKNSKLVVIAIANTMDLPERLLMNRVSSRLG-LTRICFQPYTHEQ  580 (767)
T ss_pred             CCCCCCEEEEeccHHHHhcccHHHHHHHhcCCc--CCCCceEEEEecccccCHHHHhccchhhhcc-ceeeecCCCCHHH
Confidence               35789999998652     23333322211  467776654421       1    1122222 3446677777777


Q ss_pred             hHHHHHHHhcCCCC-CchhHHHHHHHHHHHhCCCCchhhHH
Q 040234          136 AFRLLCLKAFDTHK-PLEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       136 a~~L~~~~~~~~~~-~~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      -.++...+...... .....+-++++++...|-  .-.|+.
T Consensus       581 Lq~Ii~~RL~~~~~f~~~aielvarkVAavSGD--aRrald  619 (767)
T KOG1514|consen  581 LQEIISARLKGLDAFENKAIELVARKVAAVSGD--ARRALD  619 (767)
T ss_pred             HHHHHHHhhcchhhcchhHHHHHHHHHHhcccc--HHHHHH
Confidence            77766655532211 122233344455554554  444443

>PRK03839 putative kinase; Provisional

Probab=90.89  E-value=0.15  Score=43.34  Aligned_cols=18  Identities=28%  Similarity=0.589  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      |+|+||||+|+.++++..
T Consensus         8 ~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          8 TPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            689999999999999764

>PF07015 VirC1: VirC1 protein; InterPro: IPR009744 This family consists of several bacterial VirC1 proteins

Probab=90.88  E-value=0.47  Score=41.87  Aligned_cols=26  Identities=27%  Similarity=0.330  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      ||.||||++..++..+..+=..+..+
T Consensus        11 GGaGKTT~~~~LAs~la~~G~~V~lI   36 (231)
T PF07015_consen   11 GGAGKTTAAMALASELAARGARVALI   36 (231)
T ss_pred             CCCcHHHHHHHHHHHHHHCCCeEEEE
Confidence            89999999999999765543333333

In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon, which enhances T-DNA processing probably, does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA [].

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=90.73  E-value=0.57  Score=42.50  Aligned_cols=28  Identities=11%  Similarity=0.090  Sum_probs=19.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+|||+||.+++..-...=..++++.
T Consensus        44 ~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        44 VSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            3799999999998774333333456655

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR00959 ffh signal recognition particle protein

Probab=90.60  E-value=1  Score=43.88  Aligned_cols=18  Identities=28%  Similarity=0.322  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+||||+|..++....
T Consensus       107 ~~GsGKTTtaakLA~~l~  124 (428)
T TIGR00959       107 LQGSGKTTTCGKLAYYLK  124 (428)
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            479999999999988653

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=90.56  E-value=0.63  Score=43.39  Aligned_cols=16  Identities=25%  Similarity=0.227  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||+|+.+++...
T Consensus       104 ~g~GKT~l~~~~~~~~  119 (310)
T TIGR02236       104 FGSGKTQICHQLAVNV  119 (310)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            7999999999998754

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.

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

Probab=90.56  E-value=0.61  Score=47.57  Aligned_cols=64  Identities=22%  Similarity=0.288  Sum_probs=35.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh--cCceE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL--RRKKV   78 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l--~~k~~   78 (377)
                      ++|+||||||.-++++-.  |.. +=+. .++..    ....+-..|...+...                ..+  .+++.
T Consensus       334 ppGlGKTTLAHViAkqaG--YsV-vEIN-ASDeR----t~~~v~~kI~~avq~~----------------s~l~adsrP~  389 (877)
T KOG1969|consen  334 PPGLGKTTLAHVIAKQAG--YSV-VEIN-ASDER----TAPMVKEKIENAVQNH----------------SVLDADSRPV  389 (877)
T ss_pred             CCCCChhHHHHHHHHhcC--ceE-EEec-ccccc----cHHHHHHHHHHHHhhc----------------cccccCCCcc
Confidence            489999999999998432  211 1122 33322    3334444444433221                112  25788


Q ss_pred             EEEEeCCCCh
Q 040234           79 LVVIDDAAHP   88 (377)
Q Consensus        79 LLVLDdv~~~   88 (377)
                      -||+|.++-.
T Consensus       390 CLViDEIDGa  399 (877)
T KOG1969|consen  390 CLVIDEIDGA  399 (877)
T ss_pred             eEEEecccCC
Confidence            8999999863

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=90.53  E-value=0.94  Score=46.13  Aligned_cols=32  Identities=19%  Similarity=0.422  Sum_probs=21.4

Q ss_pred             EEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecc
Q 040234           79 LVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRN  113 (377)
Q Consensus        79 LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~  113 (377)
                      +||+|.+.-  ...+..+...+   .+++++|+.--.
T Consensus       262 vlIiDEaSMvd~~l~~~ll~al---~~~~rlIlvGD~  295 (586)
T TIGR01447       262 VLVVDEASMVDLPLMAKLLKAL---PPNTKLILLGDK  295 (586)
T ss_pred             EEEEcccccCCHHHHHHHHHhc---CCCCEEEEECCh
Confidence            899999864  44566666665   356788776543

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.

>KOG3022 consensus Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]

Probab=90.46  E-value=0.56  Score=42.25  Aligned_cols=105  Identities=22%  Similarity=0.180  Sum_probs=55.3

Q ss_pred             CCCcHHHHHHHHHchhc-cccccceEEecchhhcccccCHHHHHHHHHHHHhh------------------------c-c
Q 040234            2 GGLGKTTLARVVYDLIS-HEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLK------------------------L-A   55 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~------------------------~-~   55 (377)
                      ||+||||.+..++..+. ..+..++.=.|+...     ++-.++..--+....                        . .
T Consensus        57 GGVGKSTvt~nla~~La~~g~~vglLD~Dl~GP-----SiP~m~g~e~~~~~~~~~g~~Pv~~~~~l~~mS~gfLl~~~~  131 (300)
T KOG3022|consen   57 GGVGKSTVTVNLALALASEGKKVGLLDADLCGP-----SIPRMMGLEGEVVHQSDNGWIPVVVNKNLKLMSMGFLLKPRD  131 (300)
T ss_pred             CCCchhHHHHHHHHHHhcCCCcEEEEeecccCC-----CchhhcCCCCceeeecCCCceeeeecCCeEEEEeeeecCCCC
Confidence            89999999999998655 445555555545443     222222111111000                        0 0


Q ss_pred             ccCccchhhhHHHHHHHhcCceE----EEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           56 DNNIRNVYDGINMLRVRLRRKKV----LVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        56 ~~~~~~~~~~~~~l~~~l~~k~~----LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      ....+.-......+++.|++..|    .||+|=--..  +++. +...++. . ...|||||-..
T Consensus       132 ~~vIwRGpkk~~~I~qflk~vdwg~lDyLviDtPPGtsDehls-~~~~~~~-~-~gAviVTTPQ~  193 (300)
T KOG3022|consen  132 DSVIWRGPKKNSMIKQFLKDVDWGELDYLVIDTPPGTSDEHLS-LVQFLRE-S-DGAVIVTTPQE  193 (300)
T ss_pred             ccceeechHHHHHHHHHHhcCCCCCcCEEEEeCCCCCChhhhh-eeecccc-c-CceEEEeCchh
Confidence            01112223446678899988877    7888875332  2222 2222221 1 33799999754

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=90.37  E-value=0.6  Score=39.00  Aligned_cols=106  Identities=16%  Similarity=0.222  Sum_probs=51.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||||.+.++.... ...+.+++... ... .. +.....   -+.++ . ..+.+.-+...-.+-+.+..++-+++
T Consensus        35 nGsGKSTLl~~i~G~~~-~~~G~v~~~g~-~~~-~~-~~~~~~---~~~i~-~-~~qLS~G~~qrl~laral~~~p~ill  105 (163)
T cd03216          35 NGAGKSTLMKILSGLYK-PDSGEILVDGK-EVS-FA-SPRDAR---RAGIA-M-VYQLSVGERQMVEIARALARNARLLI  105 (163)
T ss_pred             CCCCHHHHHHHHhCCCC-CCCeEEEECCE-ECC-cC-CHHHHH---hcCeE-E-EEecCHHHHHHHHHHHHHhcCCCEEE
Confidence            69999999999998543 23455555421 110 00 111110   00111 0 00111222223334455566778899


Q ss_pred             EeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           82 IDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        82 LDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      ||+.-.   ..   .+..++..+.  ..+..||++|.+.....
T Consensus       106 lDEP~~~LD~~~~~~l~~~l~~~~--~~~~tiii~sh~~~~~~  146 (163)
T cd03216         106 LDEPTAALTPAEVERLFKVIRRLR--AQGVAVIFISHRLDEVF  146 (163)
T ss_pred             EECCCcCCCHHHHHHHHHHHHHHH--HCCCEEEEEeCCHHHHH
Confidence            999743   22   2222222221  23667888888876443

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.

>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=90.35  E-value=0.23  Score=44.98  Aligned_cols=31  Identities=29%  Similarity=0.362  Sum_probs=21.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVRE   32 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~   32 (377)
                      ||+||||+|..++..+..+-..++.+.|...
T Consensus        12 GGvGKTT~a~nLa~~La~~~~~kVLliDlDp   42 (259)
T COG1192          12 GGVGKTTTAVNLAAALAKRGGKKVLLIDLDP   42 (259)
T ss_pred             CCccHHHHHHHHHHHHHHhcCCcEEEEeCCC
Confidence            8999999999999976633323344443433

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=90.31  E-value=0.7  Score=37.97  Aligned_cols=17  Identities=29%  Similarity=0.206  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+||||+|..++.+.
T Consensus         4 ~PgsGK~t~~~~la~~~   20 (151)
T PF00406_consen    4 PPGSGKGTQAKRLAKRY   20 (151)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHhc
Confidence            48999999999999854

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=90.28  E-value=1  Score=41.35  Aligned_cols=19  Identities=26%  Similarity=0.179  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||++..++.....
T Consensus       202 ptGvGKTTt~~kLa~~~~~  220 (282)
T TIGR03499       202 PTGVGKTTTLAKLAARFVL  220 (282)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3799999999999885543

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=90.28  E-value=0.42  Score=44.61  Aligned_cols=15  Identities=27%  Similarity=0.151  Sum_probs=12.7

Q ss_pred             CCCCcHHHHHHHHHc
Q 040234            1 MGGLGKTTLARVVYD   15 (377)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (377)
                      .+|+|||+|+.+++-
T Consensus       104 ~~GsGKTql~lqla~  118 (313)
T TIGR02238       104 EFRCGKTQLSHTLCV  118 (313)
T ss_pred             CCCCCcCHHHHHHHH
Confidence            379999999988774

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.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=90.28  E-value=0.19  Score=47.83  Aligned_cols=88  Identities=15%  Similarity=0.140  Sum_probs=46.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+||||++..+.+.+....+...-+..+-+... . ....+... . ....+ .....+.......++..|+..+-.++
T Consensus       143 TGSGKTTtL~aLl~~i~~~~~~~~~Ivt~EdpiE-~-~~~~~~~~-~-~~v~Q-~~v~~~~~~~~~~l~~aLR~~Pd~i~  217 (358)
T TIGR02524       143 TGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIE-F-VYDEIETI-S-ASVCQ-SEIPRHLNNFAAGVRNALRRKPHAIL  217 (358)
T ss_pred             CCCCHHHHHHHHHHHHhhcCCCCcEEEEeCCCce-E-eccccccc-c-ceeee-eeccccccCHHHHHHHHhccCCCEEe
Confidence            6999999999999866544332211111111110 0 11110000 0 00001 01111223456778888999999999


Q ss_pred             EeCCCChhhhhHh
Q 040234           82 IDDAAHPDHLRRL   94 (377)
Q Consensus        82 LDdv~~~~~~~~l   94 (377)
                      +..+.+.+.....
T Consensus       218 vGEiRd~et~~~a  230 (358)
T TIGR02524       218 VGEARDAETISAA  230 (358)
T ss_pred             eeeeCCHHHHHHH
Confidence            9999998776543

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=90.24  E-value=0.94  Score=41.20  Aligned_cols=86  Identities=15%  Similarity=0.109  Sum_probs=42.9

Q ss_pred             CCCcHHHHH-HHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc-----ccCccch----------hhh
Q 040234            2 GGLGKTTLA-RVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA-----DNNIRNV----------YDG   65 (377)
Q Consensus         2 gGiGKTtLA-~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~-----~~~~~~~----------~~~   65 (377)
                      +|+|||+|| ..+.++.  +-+..+.+..+++..+   .+.++.+++...-....     .....+.          -..
T Consensus        78 ~g~GKt~L~l~~i~~~~--~~~v~~V~~~iGer~~---ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a~~~a~ai  152 (274)
T cd01132          78 RQTGKTAIAIDTIINQK--GKKVYCIYVAIGQKAS---TVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAPYTGCAM  152 (274)
T ss_pred             CCCCccHHHHHHHHHhc--CCCeEEEEEecccchH---HHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHHHHHHHHH
Confidence            579999996 5555532  2234434554555431   44555555543210000     0001111          112


Q ss_pred             HHHHHHHhcCceEEEEEeCCCC-hhhhhHh
Q 040234           66 INMLRVRLRRKKVLVVIDDAAH-PDHLRRL   94 (377)
Q Consensus        66 ~~~l~~~l~~k~~LLVLDdv~~-~~~~~~l   94 (377)
                      ++.++.  +++..||++||+-. ...++.+
T Consensus       153 AE~fr~--~G~~Vlvl~DslTr~A~A~rEi  180 (274)
T cd01132         153 GEYFMD--NGKHALIIYDDLSKQAVAYRQM  180 (274)
T ss_pred             HHHHHH--CCCCEEEEEcChHHHHHHHHHH
Confidence            333333  57899999999965 3444444

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.

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

Probab=90.24  E-value=0.65  Score=48.65  Aligned_cols=18  Identities=22%  Similarity=0.342  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+|||+||+.++..+.
T Consensus       496 P~GvGKT~lAk~LA~~l~  513 (758)
T PRK11034        496 PTGVGKTEVTVQLSKALG  513 (758)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            469999999999998663

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=90.17  E-value=0.54  Score=49.05  Aligned_cols=75  Identities=17%  Similarity=0.103  Sum_probs=42.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc----ccCccchhhhHHHHHHHhcC-c
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA----DNNIRNVYDGINMLRVRLRR-K   76 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~----~~~~~~~~~~~~~l~~~l~~-k   76 (377)
                      +|+||||||.+++......-...+|+. .-+.+    +     ...+++++...    -..+.+.+.....+...++. +
T Consensus        69 ~GsGKTtLal~~~~~a~~~G~~v~yId-~E~t~----~-----~~~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~~~~  138 (790)
T PRK09519         69 ESSGKTTVALHAVANAQAAGGVAAFID-AEHAL----D-----PDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGA  138 (790)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCcEEEEC-Cccch----h-----HHHHHHcCCChhHeEEecCCCHHHHHHHHHHHhhcCC
Confidence            699999999887764433334456665 32222    2     12444443221    11223445556666665544 5


Q ss_pred             eEEEEEeCCC
Q 040234           77 KVLVVIDDAA   86 (377)
Q Consensus        77 ~~LLVLDdv~   86 (377)
                      .-|||+|.+.
T Consensus       139 ~~LVVIDSI~  148 (790)
T PRK09519        139 LDIVVIDSVA  148 (790)
T ss_pred             CeEEEEcchh
Confidence            6689999975

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=90.16  E-value=1.9  Score=36.30  Aligned_cols=49  Identities=18%  Similarity=0.314  Sum_probs=29.6

Q ss_pred             HHHHHhcCceEEEEEeCCCC---h---hhhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           68 MLRVRLRRKKVLVVIDDAAH---P---DHLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        68 ~l~~~l~~k~~LLVLDdv~~---~---~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      .+-+.+..++=++++|+.-.   .   ..+..++..+.  ..|..||++|.+.....
T Consensus       105 ~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~--~~g~tiii~th~~~~~~  159 (173)
T cd03230         105 ALAQALLHDPELLILDEPTSGLDPESRREFWELLRELK--KEGKTILLSSHILEEAE  159 (173)
T ss_pred             HHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHH--HCCCEEEEECCCHHHHH
Confidence            35556677888999999743   2   22223322222  23567888888876554

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=90.14  E-value=1.2  Score=39.76  Aligned_cols=43  Identities=23%  Similarity=0.258  Sum_probs=26.5

Q ss_pred             CCCcHHHHHHHHHchhccc-cccceEEecchhhcccccCHHHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHE-FDGSSFLADVREKCDKEGSVISLQKQLLSDL   51 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l   51 (377)
                      +|+|||++|.+++...... =..++|+. .-.      ...+++..++...
T Consensus        22 ~G~GKT~~~~~~~~~~~~~~g~~vly~s-~E~------~~~~~~~r~~~~~   65 (242)
T cd00984          22 PSMGKTAFALNIAENIAKKQGKPVLFFS-LEM------SKEQLLQRLLASE   65 (242)
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCceEEEe-CCC------CHHHHHHHHHHHh
Confidence            7999999999988754333 23445544 221      5556666665443

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.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=90.04  E-value=1.2  Score=45.45  Aligned_cols=103  Identities=21%  Similarity=0.226  Sum_probs=50.8

Q ss_pred             CCCcHHHHHHHHHchhcccc---ccceEEecchhhcccccCHHHHHHHHHHHHhhcccc--CccchhhhHHHHHHHhcC-
Q 040234            2 GGLGKTTLARVVYDLISHEF---DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN--NIRNVYDGINMLRVRLRR-   75 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f---~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~~l~~~l~~-   75 (377)
                      +|.||||++..+...+.+..   ...+.+.+.+..     ...++.+.+...+......  ...........+.+.|.. 
T Consensus       176 pGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgk-----AA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiHrlLg~~  250 (615)
T PRK10875        176 PGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGK-----AAARLTESLGKALRQLPLTDEQKKRIPEEASTLHRLLGAQ  250 (615)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHH-----HHHHHHHHHHhhhhccccchhhhhcCCCchHHHHHHhCcC
Confidence            79999999998887543322   234555433222     3333333333222111000  000111123444544432 


Q ss_pred             -----------ce---EEEEEeCCC--ChhhhhHhhCCCCCCCCCCeEEEEec
Q 040234           76 -----------KK---VLVVIDDAA--HPDHLRRLVGEPDWFGPGSRIIITTR  112 (377)
Q Consensus        76 -----------k~---~LLVLDdv~--~~~~~~~l~~~l~~~~~gs~IIvTTR  112 (377)
                                 .+   =+||+|.+.  +......+...++   +++|+|+---
T Consensus       251 ~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~al~---~~~rlIlvGD  300 (615)
T PRK10875        251 PGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLIDALP---PHARVIFLGD  300 (615)
T ss_pred             CCccchhhccccCCCCCeEEEChHhcccHHHHHHHHHhcc---cCCEEEEecc
Confidence                       11   289999975  3445566666654   5678776554

>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=90.02  E-value=0.76  Score=38.74  Aligned_cols=48  Identities=17%  Similarity=0.285  Sum_probs=27.6

Q ss_pred             HHHHhcCceEEEEEeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           69 LRVRLRRKKVLVVIDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        69 l~~~l~~k~~LLVLDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      +-+.+..++=+++||+.-.   ..   .+..++..+.  ..|..||++|.+.....
T Consensus       107 la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~--~~~~tii~~sh~~~~~~  160 (173)
T cd03246         107 LARALYGNPRILVLDEPNSHLDVEGERALNQAIAALK--AAGATRIVIAHRPETLA  160 (173)
T ss_pred             HHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHH--hCCCEEEEEeCCHHHHH
Confidence            4445556677899999743   22   2222322222  23667888888876554

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

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=90.01  E-value=3.5  Score=42.30  Aligned_cols=144  Identities=18%  Similarity=0.122  Sum_probs=78.8

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||.||-+++..-.-+     ++. +.+.            +++....+.      +++...+.+.+.-.-++++|
T Consensus       709 ppGcGKT~la~a~a~~~~~~-----fis-vKGP------------ElL~KyIGa------SEq~vR~lF~rA~~a~PCiL  764 (952)
T KOG0735|consen  709 PPGCGKTLLASAIASNSNLR-----FIS-VKGP------------ELLSKYIGA------SEQNVRDLFERAQSAKPCIL  764 (952)
T ss_pred             CCCCcHHHHHHHHHhhCCee-----EEE-ecCH------------HHHHHHhcc------cHHHHHHHHHHhhccCCeEE
Confidence            48999999999998743322     233 4332            233333222      34444555555556799999


Q ss_pred             EEeCCCCh-------------hhhhHhhCCCCCC--CCCCeEEE-EecchhHHhhC----CCCCeeecCCCChhhhHHHH
Q 040234           81 VIDDAAHP-------------DHLRRLVGEPDWF--GPGSRIII-TTRNEHLLKLH----PVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        81 VLDdv~~~-------------~~~~~l~~~l~~~--~~gs~IIv-TTR~~~v~~~~----~~~~~~~l~~L~~~ea~~L~  140 (377)
                      .+|..++.             ..++.++..+...  -.|--|+. |||-.-+-..+    +-.+.+.-+.-++.+-.++|
T Consensus       765 FFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il  844 (952)
T KOG0735|consen  765 FFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEIL  844 (952)
T ss_pred             EeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHH
Confidence            99998753             1355666555432  23444554 55543221111    22444555556677777888


Q ss_pred             HHHhcCCCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          141 CLKAFDTHKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      ......-..+.   ....+-++.+.+|  ..-|
T Consensus       845 ~~ls~s~~~~~---~vdl~~~a~~T~g--~tgA  872 (952)
T KOG0735|consen  845 QVLSNSLLKDT---DVDLECLAQKTDG--FTGA  872 (952)
T ss_pred             HHHhhccCCcc---ccchHHHhhhcCC--Cchh
Confidence            76663211111   2234567777787  5544

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=90.01  E-value=0.99  Score=38.36  Aligned_cols=25  Identities=20%  Similarity=0.230  Sum_probs=17.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      .|+|||||++.++.-.+. ..+.+.+
T Consensus        34 nGsGKSTLl~~l~Gl~~p-~~G~i~~   58 (177)
T cd03222          34 NGTGKTTAVKILAGQLIP-NGDNDEW   58 (177)
T ss_pred             CCChHHHHHHHHHcCCCC-CCcEEEE
Confidence            699999999999974322 2344444

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=90.00  E-value=0.93  Score=44.70  Aligned_cols=45  Identities=24%  Similarity=0.322  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+|+..+...+.+..++.+-+..+++..+   .+.+++..++.
T Consensus       170 ~GvGKs~L~~~~~~~~~~~~~dv~V~~lIGERgr---Ev~efi~~~~~  214 (494)
T CHL00060        170 AGVGKTVLIMELINNIAKAHGGVSVFGGVGERTR---EGNDLYMEMKE  214 (494)
T ss_pred             CCCChhHHHHHHHHHHHHhcCCeEEEEEeccCch---HHHHHHHHHHh
Confidence            6999999999988864333234444444665432   44455555544

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=89.91  E-value=0.17  Score=39.04  Aligned_cols=21  Identities=29%  Similarity=0.401  Sum_probs=17.1

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      .+|+|||+||..++..+.+++
T Consensus         6 ~~G~GKS~l~~~l~~~l~~~~   26 (107)
T PF00910_consen    6 PPGIGKSTLAKELAKDLLKHI   26 (107)
T ss_pred             CCCCCHHHHHHHHHHHHHHHh
Confidence            379999999999998666544

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

>PRK00625 shikimate kinase; Provisional

Probab=89.86  E-value=0.22  Score=42.23  Aligned_cols=18  Identities=22%  Similarity=0.521  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      |+|+||||+++.+++++.
T Consensus         8 ~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          8 LPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            689999999999998664

>PRK11823 DNA repair protein RadA; Provisional

Probab=89.76  E-value=0.7  Score=45.47  Aligned_cols=27  Identities=22%  Similarity=0.263  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||||+.+++.....+-..++|+.
T Consensus        89 pG~GKTtL~lq~a~~~a~~g~~vlYvs  115 (446)
T PRK11823         89 PGIGKSTLLLQVAARLAAAGGKVLYVS  115 (446)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            699999999999986543323345554

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=89.72  E-value=0.83  Score=40.25  Aligned_cols=106  Identities=17%  Similarity=0.184  Sum_probs=52.2

Q ss_pred             CCCCcHHHHHHHHHchhcc---cc-ccceEEecchhhc-ccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcC
Q 040234            1 MGGLGKTTLARVVYDLISH---EF-DGSSFLADVREKC-DKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRR   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~---~f-~~~~w~~~~~~~~-~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~   75 (377)
                      .+|+|||||.+.+++-+..   .| +.++-+.|.+..- ......-++  .+..++...  ......+.....+++   -
T Consensus       145 pP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~--~~g~R~dVl--d~cpk~~gmmmaIrs---m  217 (308)
T COG3854         145 PPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQH--GRGRRMDVL--DPCPKAEGMMMAIRS---M  217 (308)
T ss_pred             CCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchh--hhhhhhhhc--ccchHHHHHHHHHHh---c
Confidence            4799999999999984332   34 3445554443321 000000000  011111000  000111222333332   2


Q ss_pred             ceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhH
Q 040234           76 KKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHL  116 (377)
Q Consensus        76 k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v  116 (377)
                      .+=++|+|.+-..++..+++..+   ..|-++|.|..--.+
T Consensus       218 ~PEViIvDEIGt~~d~~A~~ta~---~~GVkli~TaHG~~i  255 (308)
T COG3854         218 SPEVIIVDEIGTEEDALAILTAL---HAGVKLITTAHGNGI  255 (308)
T ss_pred             CCcEEEEeccccHHHHHHHHHHH---hcCcEEEEeeccccH
Confidence            46689999998876666555553   457778777764433

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=89.65  E-value=0.63  Score=49.55  Aligned_cols=125  Identities=18%  Similarity=0.236  Sum_probs=63.7

Q ss_pred             CCCcHHHHHHHHHchhccc-c---ccceEEecchhhc--ccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcC
Q 040234            2 GGLGKTTLARVVYDLISHE-F---DGSSFLADVREKC--DKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRR   75 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-f---~~~~w~~~~~~~~--~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~   75 (377)
                      +|.||||+.+.++-....+ +   +.-+++. +....  ..+..-..+...+...+....     ...+......+.+..
T Consensus       231 pGsGKTtfl~~lA~~~~~~~~~~~~vpi~~~-l~~~~~~~~~~~q~~~~~~l~~~~~~~~-----~~~~~~~~~~e~l~~  304 (824)
T COG5635         231 PGSGKTTFLQRLALWLAQRTLEPEDVPIFLL-LNAFALARKFEKQLSLIDYLAEELFSQG-----IAKQLIEAHQELLKT  304 (824)
T ss_pred             CCCCceehHHHHHHHhccCcCCcccCceeee-chhHHHhhhhHhhccHHHHHHHHHhccC-----CcchhhHHHHHHHhc
Confidence            6999999999988732222 1   2223332 22110  000000023333333322221     112222333678889


Q ss_pred             ceEEEEEeCCCChh---------hhhHhhCCCCCCCCCCeEEEEecchhHHhhCCCCCeeecCCCChhhh
Q 040234           76 KKVLVVIDDAAHPD---------HLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLEALTYDEA  136 (377)
Q Consensus        76 k~~LLVLDdv~~~~---------~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~~~l~~L~~~ea  136 (377)
                      .+.|+++|.++...         .+..+.+.    -+.+++|+|+|....-....+-...++..+.++.-
T Consensus       305 g~~llLlDGlDe~~~~~~~~~~~~i~~f~~~----~~~~~~iltcR~~~~~~~~~~f~~~ei~~~~~~~i  370 (824)
T COG5635         305 GKLLLLLDGLDELEPKNQRALIREINKFLQE----YPDAQVLLTCRPDTYKEEFKGFAVFEIYKFLDLQI  370 (824)
T ss_pred             cchhhHhhccchhhhhhHHHHHHHHHHHhhh----ccCCeEEEEeccchhhhhhhhhhhccchhhhHHHH
Confidence            99999999987632         23444444    56889999998654433332333344555554433

>TIGR00416 sms DNA repair protein RadA

Probab=89.64  E-value=0.77  Score=45.23  Aligned_cols=27  Identities=22%  Similarity=0.257  Sum_probs=19.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||||+.+++......-..++|+.
T Consensus       103 pGsGKTTL~lq~a~~~a~~g~kvlYvs  129 (454)
T TIGR00416       103 PGIGKSTLLLQVACQLAKNQMKVLYVS  129 (454)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            699999999999876544323345554

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)).

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=89.58  E-value=1.1  Score=43.70  Aligned_cols=78  Identities=17%  Similarity=0.187  Sum_probs=39.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-----cCccch----------hhhH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-----NNIRNV----------YDGI   66 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~----------~~~~   66 (377)
                      .|+|||||++.+++....  + .+.+..+++..+   .+.++.+.++..-.....     ....+.          -..+
T Consensus       171 sG~GKSTLL~~I~~~~~~--d-v~Vi~lIGER~r---Ev~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~A~tiA  244 (444)
T PRK08972        171 SGVGKSVLLGMMTRGTTA--D-VIVVGLVGERGR---EVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCETATTIA  244 (444)
T ss_pred             CCCChhHHHHHhccCCCC--C-EEEEEEEcCChH---HHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            699999999999874332  2 233333554331   334444443322100000     000000          0123


Q ss_pred             HHHHHHhcCceEEEEEeCCCC
Q 040234           67 NMLRVRLRRKKVLVVIDDAAH   87 (377)
Q Consensus        67 ~~l~~~l~~k~~LLVLDdv~~   87 (377)
                      +.++.  +++++||++||+-.
T Consensus       245 Eyfrd--~G~~VLl~~DslTR  263 (444)
T PRK08972        245 EYFRD--QGLNVLLLMDSLTR  263 (444)
T ss_pred             HHHHH--cCCCEEEEEcChHH
Confidence            33443  57899999999854

>PTZ00088 adenylate kinase 1; Provisional

Probab=89.58  E-value=1.3  Score=39.44  Aligned_cols=17  Identities=29%  Similarity=0.409  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        14 ~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088         14 APGVGKGTFAEILSKKE   30 (229)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999999854

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

Probab=89.55  E-value=0.7  Score=47.10  Aligned_cols=127  Identities=18%  Similarity=0.178  Sum_probs=63.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhh-hHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYD-GINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~-~~~~l~~~l~~k~~L   79 (377)
                      ++|+|||+|++.+++.+...|-.   +. +++..    +-.++        -++...-..+... ..+.+++ .+.++=|
T Consensus       358 PPGVGKTSLgkSIA~al~RkfvR---~s-LGGvr----DEAEI--------RGHRRTYIGamPGrIiQ~mkk-a~~~NPv  420 (782)
T COG0466         358 PPGVGKTSLGKSIAKALGRKFVR---IS-LGGVR----DEAEI--------RGHRRTYIGAMPGKIIQGMKK-AGVKNPV  420 (782)
T ss_pred             CCCCCchhHHHHHHHHhCCCEEE---Ee-cCccc----cHHHh--------ccccccccccCChHHHHHHHH-hCCcCCe
Confidence            58999999999999977766632   11 33322    22221        1221111111111 1122222 2456778


Q ss_pred             EEEeCCCChh---------h-hhHhhCCCCCC---------CCCCeEE-EEecch-h-H-HhhCCCCCeeecCCCChhhh
Q 040234           80 VVIDDAAHPD---------H-LRRLVGEPDWF---------GPGSRII-ITTRNE-H-L-LKLHPVKKVYKLEALTYDEA  136 (377)
Q Consensus        80 LVLDdv~~~~---------~-~~~l~~~l~~~---------~~gs~II-vTTR~~-~-v-~~~~~~~~~~~l~~L~~~ea  136 (377)
                      ++||.++...         . ++-|-|.....         -.=|.|+ |||-+. . + +..+....++++.+.+++|=
T Consensus       421 ~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EK  500 (782)
T COG0466         421 FLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEK  500 (782)
T ss_pred             EEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhcceeeeeecCCChHHH
Confidence            9999986421         1 12111111000         0113333 444332 2 2 22234467899999999998


Q ss_pred             HHHHHHHh
Q 040234          137 FRLLCLKA  144 (377)
Q Consensus       137 ~~L~~~~~  144 (377)
                      .++-.++.
T Consensus       501 l~IAk~~L  508 (782)
T COG0466         501 LEIAKRHL  508 (782)
T ss_pred             HHHHHHhc
Confidence            87766654

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=89.54  E-value=4.7  Score=37.12  Aligned_cols=57  Identities=12%  Similarity=0.061  Sum_probs=33.9

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecc-hhHHhhC-CCCCeeecCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRN-EHLLKLH-PVKKVYKLEAL  131 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~-~~v~~~~-~~~~~~~l~~L  131 (377)
                      ++.-++|+|+++.  .+..+.|+..+..-.+++.+|++|.+ ..+...+ +....+.+.++
T Consensus        94 ~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~  154 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPME  154 (290)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccch
Confidence            4455889999986  45566666655443556666665555 4444332 33556666654

>PRK12678 transcription termination factor Rho; Provisional

Probab=89.52  E-value=0.6  Score=46.77  Aligned_cols=32  Identities=22%  Similarity=0.216  Sum_probs=21.8

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhh
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREK   33 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~   33 (377)
                      +|+|||+|++.+++.+....+ ..+++..+++-
T Consensus       425 p~aGKTtLL~~IAn~i~~n~~~~~~ivvLIgER  457 (672)
T PRK12678        425 PKAGKTTILQNIANAITTNNPECHLMVVLVDER  457 (672)
T ss_pred             CCCCHHHHHHHHHHHHhhcCCCeEEEEEEEeCc
Confidence            689999999999996654433 33445545543

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=89.52  E-value=0.21  Score=41.96  Aligned_cols=21  Identities=24%  Similarity=0.351  Sum_probs=17.8

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      ++|+||||||..+.+++....
T Consensus        31 LSGsGKSTiA~ale~~L~~~G   51 (197)
T COG0529          31 LSGSGKSTIANALEEKLFAKG   51 (197)
T ss_pred             CCCCCHHHHHHHHHHHHHHcC
Confidence            589999999999999776653

>PRK13947 shikimate kinase; Provisional

Probab=89.47  E-value=0.24  Score=41.61  Aligned_cols=20  Identities=35%  Similarity=0.421  Sum_probs=16.9

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      |+|+||||+|+.+++++.-.
T Consensus         9 ~~GsGKst~a~~La~~lg~~   28 (171)
T PRK13947          9 FMGTGKTTVGKRVATTLSFG   28 (171)
T ss_pred             CCCCCHHHHHHHHHHHhCCC
Confidence            68999999999999976443

>PRK14974 cell division protein FtsY; Provisional

Probab=89.38  E-value=1.4  Score=41.54  Aligned_cols=20  Identities=25%  Similarity=0.317  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      +.|+||||++..++..++.+
T Consensus       148 ~~GvGKTTtiakLA~~l~~~  167 (336)
T PRK14974        148 VNGTGKTTTIAKLAYYLKKN  167 (336)
T ss_pred             CCCCCHHHHHHHHHHHHHHc
Confidence            47999999999888865543

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=89.38  E-value=1.4  Score=39.80  Aligned_cols=116  Identities=16%  Similarity=0.193  Sum_probs=61.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhc--ccccCHHHHHHHHHHHHhhccc------cCccchhhhHHHHHHHh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKC--DKEGSVISLQKQLLSDLLKLAD------NNIRNVYDGINMLRVRL   73 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~--~~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~~~l~~~l   73 (377)
                      +|+|||||++.+..-.+-. .+.+++. ..+..  ... ...+...+++...+....      .+.+.-+...-.+.+.|
T Consensus        48 SG~GKSTlgr~i~~L~~pt-~G~i~f~-g~~i~~~~~~-~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQRi~IARAL  124 (268)
T COG4608          48 SGCGKSTLGRLILGLEEPT-SGEILFE-GKDITKLSKE-ERRERVLELLEKVGLPEEFLYRYPHELSGGQRQRIGIARAL  124 (268)
T ss_pred             CCCCHHHHHHHHHcCcCCC-CceEEEc-Ccchhhcchh-HHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhhHHHHHHH
Confidence            7999999999999843322 2334433 11100  000 233444555555432211      11112222233456777


Q ss_pred             cCceEEEEEeCCCCh------hhhhHhhCCCCCCCCCCeEEEEecchhHHhhCC
Q 040234           74 RRKKVLVVIDDAAHP------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHP  121 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~  121 (377)
                      .-++-|+|.|..-+.      .+.-.++..+.. ..|-..|..|.+-.+++.+.
T Consensus       125 al~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~-~~~lt~lFIsHDL~vv~~is  177 (268)
T COG4608         125 ALNPKLIVADEPVSALDVSVQAQILNLLKDLQE-ELGLTYLFISHDLSVVRYIS  177 (268)
T ss_pred             hhCCcEEEecCchhhcchhHHHHHHHHHHHHHH-HhCCeEEEEEEEHHhhhhhc
Confidence            889999999996542      222223222221 23667888888887777654

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

Probab=89.22  E-value=0.75  Score=41.29  Aligned_cols=51  Identities=18%  Similarity=0.272  Sum_probs=33.7

Q ss_pred             HHHHHHHhcCceEEEEEeCC----CC--hhhhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           66 INMLRVRLRRKKVLVVIDDA----AH--PDHLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        66 ~~~l~~~l~~k~~LLVLDdv----~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      .-.+-+.|.+++=||+||.-    +.  ...+-.++..+..  .|..||++|.+-....
T Consensus       147 RV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~--eg~tIl~vtHDL~~v~  203 (254)
T COG1121         147 RVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQ--EGKTVLMVTHDLGLVM  203 (254)
T ss_pred             HHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHH--CCCEEEEEeCCcHHhH
Confidence            34566778899999999984    22  2234445444443  3888999999865443

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=89.18  E-value=0.52  Score=43.23  Aligned_cols=25  Identities=24%  Similarity=0.205  Sum_probs=19.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSF   26 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w   26 (377)
                      +|+|||||...+.+.++......+.
T Consensus       113 pGsGKTTLl~~l~~~l~~~~~~~VI  137 (290)
T PRK10463        113 PGSGKTTLLTETLMRLKDSVPCAVI  137 (290)
T ss_pred             CCCCHHHHHHHHHHHhccCCCEEEE
Confidence            6999999999999987766544444

>PRK05922 type III secretion system ATPase; Validated

Probab=89.18  E-value=0.69  Score=45.00  Aligned_cols=16  Identities=25%  Similarity=0.283  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||||.+.++...
T Consensus       166 nG~GKSTLL~~Ia~~~  181 (434)
T PRK05922        166 PGSGKSSLLSTIAKGS  181 (434)
T ss_pred             CCCChHHHHHHHhccC
Confidence            5999999999998754

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

Probab=89.16  E-value=4.7  Score=36.64  Aligned_cols=101  Identities=16%  Similarity=0.156  Sum_probs=58.3

Q ss_pred             ceE-EEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecc--hhHHhhCCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           76 KKV-LVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRN--EHLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        76 k~~-LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~--~~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +.| ++||-.++.  .+.-..|+.....-.+.+|+|+...+  +-+...-+..-.+.+...+++|....+....-+..-.
T Consensus       126 r~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~  205 (351)
T KOG2035|consen  126 RPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQ  205 (351)
T ss_pred             cceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhccc
Confidence            344 666666665  23333343332222456777764332  1112211234557888999999999998877443333


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      .|  .+.+.+|+++++| -+--|+.++-+
T Consensus       206 lp--~~~l~rIa~kS~~-nLRrAllmlE~  231 (351)
T KOG2035|consen  206 LP--KELLKRIAEKSNR-NLRRALLMLEA  231 (351)
T ss_pred             Cc--HHHHHHHHHHhcc-cHHHHHHHHHH
Confidence            33  6789999999988 24555544433

>PRK00131 aroK shikimate kinase; Reviewed

Probab=89.16  E-value=0.26  Score=41.33  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+++++.
T Consensus        12 ~~GsGKstla~~La~~l~   29 (175)
T PRK00131         12 FMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            589999999999999763

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=89.16  E-value=0.48  Score=45.30  Aligned_cols=85  Identities=22%  Similarity=0.208  Sum_probs=47.4

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEe-cchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLA-DVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~-~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      .|+||||++..+.+.+.+..+ ..+... +..+..-.  ....+..  ..+     .....+.....+.++..|+..+=.
T Consensus       158 TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~~--~~~~~~~--~~q-----~evg~~~~~~~~~l~~aLR~~PD~  228 (372)
T TIGR02525       158 TGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYILG--SPDDLLP--PAQ-----SQIGRDVDSFANGIRLALRRAPKI  228 (372)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhccC--CCceeec--ccc-----cccCCCccCHHHHHHHhhccCCCE
Confidence            599999999999886654333 333322 11110000  0000000  000     000112335667888899999999


Q ss_pred             EEEeCCCChhhhhHhh
Q 040234           80 VVIDDAAHPDHLRRLV   95 (377)
Q Consensus        80 LVLDdv~~~~~~~~l~   95 (377)
                      |+++.+.+.+.+...+
T Consensus       229 I~vGEiRd~et~~~al  244 (372)
T TIGR02525       229 IGVGEIRDLETFQAAV  244 (372)
T ss_pred             EeeCCCCCHHHHHHHH
Confidence            9999999988776543

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases

Probab=89.11  E-value=0.31  Score=41.70  Aligned_cols=19  Identities=37%  Similarity=0.653  Sum_probs=16.4

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus         8 GG~GKTt~a~~la~~la~~   26 (195)
T PF01656_consen    8 GGVGKTTIAANLAQALARK   26 (195)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCccHHHHHHHHHhccccc
Confidence            8999999999999966553

These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....

>CHL00206 ycf2 Ycf2; Provisional

Probab=88.99  E-value=3.3  Score=47.29  Aligned_cols=68  Identities=12%  Similarity=0.073  Sum_probs=35.9

Q ss_pred             cCceEEEEEeCCCChh-------hhhHhhCCCCCC-----CCCCeEEEEecchhHHhhC-----CCCCeeecCCCChhhh
Q 040234           74 RRKKVLVVIDDAAHPD-------HLRRLVGEPDWF-----GPGSRIIITTRNEHLLKLH-----PVKKVYKLEALTYDEA  136 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~~-------~~~~l~~~l~~~-----~~gs~IIvTTR~~~v~~~~-----~~~~~~~l~~L~~~ea  136 (377)
                      +..+++|-+|+++...       .+..|+..+...     ..+--||.+|-.+.+.+..     .-.+.+.++.++..+-
T Consensus      1730 k~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R 1809 (2281)
T CHL00206       1730 AMSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQ 1809 (2281)
T ss_pred             HCCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhH
Confidence            3468999999987632       133443333211     1233455556544432221     2356778887776555


Q ss_pred             HHHHH
Q 040234          137 FRLLC  141 (377)
Q Consensus       137 ~~L~~  141 (377)
                      .+.|.
T Consensus      1810 ~kiL~ 1814 (2281)
T CHL00206       1810 RKHFF 1814 (2281)
T ss_pred             HHHHH
Confidence            55443

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=88.79  E-value=1.4  Score=43.42  Aligned_cols=79  Identities=15%  Similarity=0.097  Sum_probs=39.7

Q ss_pred             CCCcHHHHHHH-HHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-----cCccc----------hhhh
Q 040234            2 GGLGKTTLARV-VYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-----NNIRN----------VYDG   65 (377)
Q Consensus         2 gGiGKTtLA~~-v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~----------~~~~   65 (377)
                      .|+|||+||.. +.++ + .-+..+.+..+++..+   .+.++...+...=.-...     ....+          .-..
T Consensus       150 ~g~GKt~Lal~~I~~q-~-~~dv~cV~~~IGer~r---ev~e~~~~l~~~~~l~~tvvV~atad~~~~~r~~ap~~a~ai  224 (485)
T CHL00059        150 RQTGKTAVATDTILNQ-K-GQNVICVYVAIGQKAS---SVAQVVTTLQERGAMEYTIVVAETADSPATLQYLAPYTGAAL  224 (485)
T ss_pred             CCCCHHHHHHHHHHhc-c-cCCeEEEEEEecCCch---HHHHHHHHhhcccchhceEEEEeCCCCCHHHHHHHHHHHhhH
Confidence            69999999754 5543 2 2244434444665432   444454444432100000     00000          0112


Q ss_pred             HHHHHHHhcCceEEEEEeCCCC
Q 040234           66 INMLRVRLRRKKVLVVIDDAAH   87 (377)
Q Consensus        66 ~~~l~~~l~~k~~LLVLDdv~~   87 (377)
                      ++.++.  ++++.|||+||+-.
T Consensus       225 AEyfr~--~G~~VLlv~DdlTr  244 (485)
T CHL00059        225 AEYFMY--RGRHTLIIYDDLSK  244 (485)
T ss_pred             HHHHHH--cCCCEEEEEcChhH
Confidence            334443  57899999999854

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=88.77  E-value=0.44  Score=44.18  Aligned_cols=83  Identities=18%  Similarity=0.183  Sum_probs=47.3

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+||||+++.+.+.+....+ .++...  -       +..++...--..+.-  . .........+.++..|+..+=.+
T Consensus       141 tGSGKTTll~al~~~i~~~~~~~ri~ti--E-------d~~El~~~~~~~v~~--~-~~~~~~~~~~~l~~aLR~~pD~i  208 (299)
T TIGR02782       141 TGSGKTTLANALLAEIAKNDPTDRVVII--E-------DTRELQCAAPNVVQL--R-TSDDAISMTRLLKATLRLRPDRI  208 (299)
T ss_pred             CCCCHHHHHHHHHHHhhccCCCceEEEE--C-------CchhhcCCCCCEEEE--E-ecCCCCCHHHHHHHHhcCCCCEE
Confidence            699999999999987765332 233222  1       111111000000000  0 00111256678888898888889


Q ss_pred             EEeCCCChhhhhHhhC
Q 040234           81 VIDDAAHPDHLRRLVG   96 (377)
Q Consensus        81 VLDdv~~~~~~~~l~~   96 (377)
                      |+..+.+.+.+..+..
T Consensus       209 ivGEiR~~ea~~~l~a  224 (299)
T TIGR02782       209 IVGEVRGGEALDLLKA  224 (299)
T ss_pred             EEeccCCHHHHHHHHH
Confidence            9999999887765443

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=88.75  E-value=3.8  Score=38.34  Aligned_cols=21  Identities=19%  Similarity=0.219  Sum_probs=17.3

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      .+|+|||+||+.++.++...|
T Consensus        72 ~pGtGKTtla~~lA~~l~~~~   92 (327)
T TIGR01650        72 YHGTGKSTHIEQIAARLNWPC   92 (327)
T ss_pred             CCCChHHHHHHHHHHHHCCCe
Confidence            379999999999999776443

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.

>TIGR01351 adk adenylate kinases

Probab=88.65  E-value=1.8  Score=37.80  Aligned_cols=17  Identities=29%  Similarity=0.276  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++.+.
T Consensus         7 ~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         7 PPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999998744

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.

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=88.62  E-value=1.2  Score=35.00  Aligned_cols=20  Identities=35%  Similarity=0.660  Sum_probs=16.5

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .||+|||+++..+++...++
T Consensus         7 kgG~GKTt~a~~la~~l~~~   26 (116)
T cd02034           7 KGGVGKTTIAALLARYLAEK   26 (116)
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            38999999999999866543

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>PHA02518 ParA-like protein; Provisional

Probab=88.60  E-value=0.35  Score=42.05  Aligned_cols=19  Identities=37%  Similarity=0.571  Sum_probs=15.8

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus        10 GGvGKTT~a~~la~~la~~   28 (211)
T PHA02518         10 GGAGKTTVATNLASWLHAD   28 (211)
T ss_pred             CCCCHHHHHHHHHHHHHhC
Confidence            8999999999998865543

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=88.59  E-value=0.84  Score=42.54  Aligned_cols=101  Identities=17%  Similarity=0.157  Sum_probs=52.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||||++.+...+..... .+.+.+..+......+...        +...........-...+.+...|+..+=.|+
T Consensus       153 tGsGKTTll~al~~~~~~~~~-iv~ied~~El~~~~~~~~~--------l~~~~~~~~~~~~~~~~~l~~~Lr~~pd~ii  223 (308)
T TIGR02788       153 TGSGKTTFLKSLVDEIPKDER-IITIEDTREIFLPHPNYVH--------LFYSKGGQGLAKVTPKDLLQSCLRMRPDRII  223 (308)
T ss_pred             CCCCHHHHHHHHHccCCcccc-EEEEcCccccCCCCCCEEE--------EEecCCCCCcCccCHHHHHHHHhcCCCCeEE
Confidence            599999999999986544322 2233322221100000000        0000000011122345677778888888899


Q ss_pred             EeCCCChhhhhHhhCCCCCCCCCCe-EEEEecchh
Q 040234           82 IDDAAHPDHLRRLVGEPDWFGPGSR-IIITTRNEH  115 (377)
Q Consensus        82 LDdv~~~~~~~~l~~~l~~~~~gs~-IIvTTR~~~  115 (377)
                      +|.+.+.+.+..+...    ..|.. ++.|+....
T Consensus       224 ~gE~r~~e~~~~l~a~----~~g~~~~i~T~Ha~~  254 (308)
T TIGR02788       224 LGELRGDEAFDFIRAV----NTGHPGSITTLHAGS  254 (308)
T ss_pred             EeccCCHHHHHHHHHH----hcCCCeEEEEEeCCC
Confidence            9999997766544433    22332 466665443

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.

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

Probab=88.56  E-value=0.31  Score=42.08  Aligned_cols=19  Identities=37%  Similarity=0.562  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||||+.+...+..
T Consensus         7 ~sgSGKTTla~~L~~~L~~   25 (194)
T PF00485_consen    7 PSGSGKTTLAKRLAQILNK   25 (194)
T ss_dssp             STTSSHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhCc
Confidence            3799999999999997654

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 ....

>PTZ00301 uridine kinase; Provisional

Probab=88.52  E-value=0.26  Score=43.22  Aligned_cols=20  Identities=20%  Similarity=0.340  Sum_probs=16.7

Q ss_pred             CCCcHHHHHHHHHchhcccc
Q 040234            2 GGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f   21 (377)
                      +|+||||||+.+.+++..++
T Consensus        12 SgSGKTTla~~l~~~l~~~~   31 (210)
T PTZ00301         12 SGSGKSSLSTNIVSELMAHC   31 (210)
T ss_pred             CcCCHHHHHHHHHHHHHhhc
Confidence            79999999999998775544

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=88.49  E-value=0.76  Score=43.00  Aligned_cols=14  Identities=29%  Similarity=0.159  Sum_probs=12.7

Q ss_pred             CCCcHHHHHHHHHc
Q 040234            2 GGLGKTTLARVVYD   15 (377)
Q Consensus         2 gGiGKTtLA~~v~~   15 (377)
                      +|+|||+|+..++.
T Consensus       105 ~g~GKT~l~~~~~~  118 (316)
T TIGR02239       105 FRTGKTQLCHTLAV  118 (316)
T ss_pred             CCCCcCHHHHHHHH
Confidence            69999999998886

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).

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=88.46  E-value=1  Score=44.02  Aligned_cols=16  Identities=31%  Similarity=0.432  Sum_probs=13.5

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||||++.++...
T Consensus       174 SGsGKTTLL~~Ia~l~  189 (450)
T PRK06002        174 SGVGKSTLLAMLARAD  189 (450)
T ss_pred             CCCCHHHHHHHHhCCC
Confidence            6999999999888743

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=88.43  E-value=2.5  Score=41.02  Aligned_cols=17  Identities=29%  Similarity=0.141  Sum_probs=14.4

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+||||++.+++...
T Consensus       231 ptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        231 PTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            47999999999999743

>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily

Probab=88.43  E-value=1.1  Score=37.55  Aligned_cols=18  Identities=33%  Similarity=0.514  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++....+
T Consensus         9 gG~GKTt~a~~LA~~la~   26 (169)
T cd02037           9 GGVGKSTVAVNLALALAK   26 (169)
T ss_pred             CcCChhHHHHHHHHHHHH
Confidence            899999999999985544

Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=88.38  E-value=1.5  Score=41.93  Aligned_cols=80  Identities=20%  Similarity=0.113  Sum_probs=38.6

Q ss_pred             CCCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ..|+||||++.+++.+...++. ..+.+... +.++ . ...+-++...+.++.. .....+..+....+ ..+.++. +
T Consensus       145 ptGvGKTTtiakLA~~~~~~~G~~~V~lit~-D~~R-~-ga~EqL~~~a~~~gv~-~~~~~~~~~l~~~l-~~l~~~D-l  218 (374)
T PRK14722        145 PTGVGKTTTTAKLAARCVMRFGASKVALLTT-DSYR-I-GGHEQLRIFGKILGVP-VHAVKDGGDLQLAL-AELRNKH-M  218 (374)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCCeEEEEec-cccc-c-cHHHHHHHHHHHcCCc-eEecCCcccHHHHH-HHhcCCC-E
Confidence            3799999999999986543332 23333312 1111 1 2233344444443322 11222223333333 3345554 5


Q ss_pred             EEEeCCC
Q 040234           80 VVIDDAA   86 (377)
Q Consensus        80 LVLDdv~   86 (377)
                      +++|.+-
T Consensus       219 VLIDTaG  225 (374)
T PRK14722        219 VLIDTIG  225 (374)
T ss_pred             EEEcCCC
Confidence            6689874

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=88.37  E-value=1.9  Score=36.54  Aligned_cols=58  Identities=16%  Similarity=0.282  Sum_probs=30.4

Q ss_pred             HHHHhcCc--eEEEEEeCCCC---hhhhhHhhCCCCCC-CCCCeEEEEecchhHHhhCCCCCeeec
Q 040234           69 LRVRLRRK--KVLVVIDDAAH---PDHLRRLVGEPDWF-GPGSRIIITTRNEHLLKLHPVKKVYKL  128 (377)
Q Consensus        69 l~~~l~~k--~~LLVLDdv~~---~~~~~~l~~~l~~~-~~gs~IIvTTR~~~v~~~~~~~~~~~l  128 (377)
                      +-+.+..+  +=+++||+.-.   ....+.+...+... ..|..||++|.+......  ....+.+
T Consensus        98 laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~~--~d~i~~l  161 (176)
T cd03238          98 LASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLSS--ADWIIDF  161 (176)
T ss_pred             HHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHh--CCEEEEE
Confidence            34445556  67888999743   22222222211111 246678888888766542  3344444

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=88.36  E-value=0.47  Score=41.77  Aligned_cols=32  Identities=25%  Similarity=0.389  Sum_probs=20.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREK   33 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~   33 (377)
                      ||+||||+|..++.++..+-...+.+.|.-++
T Consensus         9 GG~GKTtiaalll~~l~~~~~~~VLvVDaDpd   40 (255)
T COG3640           9 GGVGKTTIAALLLKRLLSKGGYNVLVVDADPD   40 (255)
T ss_pred             CCccHHHHHHHHHHHHHhcCCceEEEEeCCCC
Confidence            89999999999777554443233444444433

>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=88.36  E-value=0.33  Score=34.12  Aligned_cols=17  Identities=29%  Similarity=0.470  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ..|+||||+|+.+.++.
T Consensus         7 ~~gsGKst~~~~l~~~l   23 (69)
T cd02019           7 GSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            36999999999999875

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.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=88.34  E-value=2.5  Score=35.05  Aligned_cols=17  Identities=29%  Similarity=0.513  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.+.+..
T Consensus         6 ~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         6 VAGSGKSTIASALAHRL   22 (163)
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            47999999999999865

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=88.33  E-value=0.59  Score=40.00  Aligned_cols=33  Identities=18%  Similarity=0.272  Sum_probs=24.5

Q ss_pred             hhHHHHHHHhcCceEEEEEeCCCChhhhhHhhC
Q 040234           64 DGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVG   96 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv~~~~~~~~l~~   96 (377)
                      ...+.++..++..+=.++++.+.+.+.+..+..
T Consensus        88 ~~~~~l~~~lR~~pd~i~igEir~~ea~~~~~a  120 (186)
T cd01130          88 TMADLLRSALRMRPDRIIVGEVRGGEALDLLQA  120 (186)
T ss_pred             CHHHHHHHHhccCCCEEEEEccCcHHHHHHHHH
Confidence            455667777777788899999999877665543

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=88.16  E-value=0.91  Score=45.22  Aligned_cols=28  Identities=21%  Similarity=0.240  Sum_probs=20.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+|||||+.+++.....+-..++++.
T Consensus       271 ~~G~GKt~l~~~f~~~~~~~ge~~~y~s  298 (484)
T TIGR02655       271 ATGTGKTLLVSKFLENACANKERAILFA  298 (484)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            3799999999999986544434445543

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.

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=88.16  E-value=6.2  Score=40.91  Aligned_cols=63  Identities=22%  Similarity=0.247  Sum_probs=40.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|.|||-||++|+.+..-.|     +. |.+.            +++....++      +++...+.+.+.=..++++|
T Consensus       713 PPGTGKTLlAKAVATEcsL~F-----lS-VKGP------------ELLNMYVGq------SE~NVR~VFerAR~A~PCVI  768 (953)
T KOG0736|consen  713 PPGTGKTLLAKAVATECSLNF-----LS-VKGP------------ELLNMYVGQ------SEENVREVFERARSAAPCVI  768 (953)
T ss_pred             CCCCchHHHHHHHHhhceeeE-----Ee-ecCH------------HHHHHHhcc------hHHHHHHHHHHhhccCCeEE
Confidence            479999999999998554333     22 3332            223333332      34444555555556689999


Q ss_pred             EEeCCCC
Q 040234           81 VIDDAAH   87 (377)
Q Consensus        81 VLDdv~~   87 (377)
                      .+|.+++
T Consensus       769 FFDELDS  775 (953)
T KOG0736|consen  769 FFDELDS  775 (953)
T ss_pred             Eeccccc
Confidence            9999876

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=88.14  E-value=1.8  Score=37.19  Aligned_cols=45  Identities=18%  Similarity=0.370  Sum_probs=25.3

Q ss_pred             HHHHhcCceEEEEEeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchh
Q 040234           69 LRVRLRRKKVLVVIDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEH  115 (377)
Q Consensus        69 l~~~l~~k~~LLVLDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~  115 (377)
                      +-+.+..++=++++|+.-.   ..   .+..++..+.  ..+..||++|.+..
T Consensus       119 la~al~~~p~vlllDEP~~~LD~~~~~~l~~~l~~~~--~~~~tiiivtH~~~  169 (192)
T cd03232         119 IGVELAAKPSILFLDEPTSGLDSQAAYNIVRFLKKLA--DSGQAILCTIHQPS  169 (192)
T ss_pred             HHHHHhcCCcEEEEeCCCcCCCHHHHHHHHHHHHHHH--HcCCEEEEEEcCCh
Confidence            4455566777899999643   22   2222222221  23567888887754

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation

Probab=88.03  E-value=0.3  Score=37.19  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=18.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      ||+||||+|..++....++ ...+++.
T Consensus         9 gG~Gkst~~~~la~~~~~~-~~~vl~~   34 (104)
T cd02042           9 GGVGKTTTAVNLAAALARR-GKRVLLI   34 (104)
T ss_pred             CCcCHHHHHHHHHHHHHhC-CCcEEEE
Confidence            8999999999999865542 2334444

ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=88.02  E-value=5.1  Score=40.46  Aligned_cols=16  Identities=31%  Similarity=0.468  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||++|+.+.+..
T Consensus       228 ~GtGK~~lA~~ih~~s  243 (534)
T TIGR01817       228 SGTGKELIAKAIHYLS  243 (534)
T ss_pred             CCccHHHHHHHHHHhC
Confidence            6999999999999843

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=87.84  E-value=2.3  Score=42.58  Aligned_cols=53  Identities=6%  Similarity=-0.089  Sum_probs=31.5

Q ss_pred             CCCeeecCCCChhhhHHHHHHHhcCC------CCCchhHHHHHHHHHHHhCCCCchhhHH
Q 040234          122 VKKVYKLEALTYDEAFRLLCLKAFDT------HKPLEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       122 ~~~~~~l~~L~~~ea~~L~~~~~~~~------~~~~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      ....+...+.++.--.+.|.+.+-..      ....+...++.+.|++.++| ++--||.
T Consensus       204 ~i~~I~FNpIa~T~mkKaL~rI~~~E~~~~~~~~~~p~~~~~l~~I~~~s~G-DIRsAIn  262 (519)
T PF03215_consen  204 GITRIKFNPIAPTFMKKALKRILKKEARSSSGKNKVPDKQSVLDSIAESSNG-DIRSAIN  262 (519)
T ss_pred             CceEEEecCCCHHHHHHHHHHHHHHHhhhhcCCccCCChHHHHHHHHHhcCc-hHHHHHH
Confidence            45667788888877666666554322      11223334567788888855 2555553

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=87.84  E-value=1.9  Score=42.63  Aligned_cols=79  Identities=14%  Similarity=0.105  Sum_probs=39.3

Q ss_pred             CCCcHHHHH-HHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-----cCccc----------hhhh
Q 040234            2 GGLGKTTLA-RVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-----NNIRN----------VYDG   65 (377)
Q Consensus         2 gGiGKTtLA-~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~----------~~~~   65 (377)
                      .|+|||+|| ..+.++..  -+..+-+..+++..+   .+.++.+.+...=.....     ....+          .-..
T Consensus       171 ~g~GKT~Lal~~I~~q~~--~dv~~V~~~IGeR~r---ev~e~i~~l~~~~~l~~tvvV~atsd~p~~~r~~ap~~a~ai  245 (497)
T TIGR03324       171 RQTGKTAIAIDTILNQKG--RNVLCIYCAIGQRAS---AVAKVVANLREHGAMDYTIVVVTEGNDPPGLQYIAPYAATSI  245 (497)
T ss_pred             CCCCHHHHHHHHHHHhcC--CCcEEEEEEeccCcH---HHHHHHHHhhhcCCcceeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            499999997 46776432  233233333666532   444454444432100000     00000          1112


Q ss_pred             HHHHHHHhcCceEEEEEeCCCC
Q 040234           66 INMLRVRLRRKKVLVVIDDAAH   87 (377)
Q Consensus        66 ~~~l~~~l~~k~~LLVLDdv~~   87 (377)
                      ++.++.  ++++.|||+||+-.
T Consensus       246 AEyfrd--~G~~VLlv~DdlTr  265 (497)
T TIGR03324       246 GEHFME--QGRDVLIVYDDLTQ  265 (497)
T ss_pred             HHHHHh--CCCCEEEEEcChhH
Confidence            333332  57899999999854

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, 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 alpha subunit of this apparent second ATP synthase.

>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell

Probab=87.79  E-value=0.43  Score=40.18  Aligned_cols=20  Identities=30%  Similarity=0.398  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      -||+||||+|..++.....+
T Consensus         8 kgG~GKtt~a~~la~~l~~~   27 (179)
T cd02036           8 KGGVGKTTTTANLGTALAQL   27 (179)
T ss_pred             CCCCCHHHHHHHHHHHHHhC
Confidence            38999999999999866554

The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.

>PTZ00035 Rad51 protein; Provisional

Probab=87.70  E-value=1  Score=42.60  Aligned_cols=14  Identities=29%  Similarity=0.199  Sum_probs=12.6

Q ss_pred             CCCcHHHHHHHHHc
Q 040234            2 GGLGKTTLARVVYD   15 (377)
Q Consensus         2 gGiGKTtLA~~v~~   15 (377)
                      +|+|||+|+..++-
T Consensus       127 ~GsGKT~l~~~l~~  140 (337)
T PTZ00035        127 FRTGKTQLCHTLCV  140 (337)
T ss_pred             CCCchhHHHHHHHH
Confidence            69999999998875

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=87.58  E-value=2.2  Score=43.05  Aligned_cols=23  Identities=13%  Similarity=-0.161  Sum_probs=18.6

Q ss_pred             CCeeecCCCChhhhHHHHHHHhc
Q 040234          123 KKVYKLEALTYDEAFRLLCLKAF  145 (377)
Q Consensus       123 ~~~~~l~~L~~~ea~~L~~~~~~  145 (377)
                      ...+.+++|+.+|-.+++...+.
T Consensus       255 ~~~I~f~pL~~eei~~Il~~~a~  277 (531)
T TIGR02902       255 CVEIFFRPLLDEEIKEIAKNAAE  277 (531)
T ss_pred             hheeeCCCCCHHHHHHHHHHHHH
Confidence            35678899999999888888764

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.

>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=87.55  E-value=0.94  Score=38.43  Aligned_cols=28  Identities=21%  Similarity=0.080  Sum_probs=19.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+|||+||.+++......=..++|+.
T Consensus         7 ~~G~GKT~l~~~~~~~~~~~g~~v~~~s   34 (187)
T cd01124           7 GPGTGKTTFALQFLYAGLARGEPGLYVT   34 (187)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            3799999999998875433334455654

A related protein is found in archaea.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=87.51  E-value=0.83  Score=45.83  Aligned_cols=27  Identities=26%  Similarity=0.289  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhcccc-ccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEF-DGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f-~~~~w~~   28 (377)
                      +|+|||+||.+++.....++ ..++|+.
T Consensus        40 pGsGKT~l~~qf~~~~~~~~ge~~lyis   67 (509)
T PRK09302         40 AGTGKTLFALQFLVNGIKRFDEPGVFVT   67 (509)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCCEEEEE
Confidence            79999999999887544443 3455654

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=87.47  E-value=1.1  Score=37.08  Aligned_cols=106  Identities=22%  Similarity=0.284  Sum_probs=52.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|.|||||++.++..+.. ..+.+++... .... . ....    ....+.-.  .+.+.-+...-.+.+.+...+=+++
T Consensus        34 nGsGKStll~~l~g~~~~-~~G~i~~~~~-~~~~-~-~~~~----~~~~i~~~--~qlS~G~~~r~~l~~~l~~~~~i~i  103 (157)
T cd00267          34 NGSGKSTLLRAIAGLLKP-TSGEILIDGK-DIAK-L-PLEE----LRRRIGYV--PQLSGGQRQRVALARALLLNPDLLL  103 (157)
T ss_pred             CCCCHHHHHHHHhCCCCC-CccEEEECCE-Eccc-C-CHHH----HHhceEEE--eeCCHHHHHHHHHHHHHhcCCCEEE
Confidence            699999999999985532 3455555421 1100 0 0111    11111100  0011112223334555566678999


Q ss_pred             EeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchhHHhh
Q 040234           82 IDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEHLLKL  119 (377)
Q Consensus        82 LDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~  119 (377)
                      ||+...   ..   .+..+...+.  ..+..+|++|.+......
T Consensus       104 lDEp~~~lD~~~~~~l~~~l~~~~--~~~~tii~~sh~~~~~~~  145 (157)
T cd00267         104 LDEPTSGLDPASRERLLELLRELA--EEGRTVIIVTHDPELAEL  145 (157)
T ss_pred             EeCCCcCCCHHHHHHHHHHHHHHH--HCCCEEEEEeCCHHHHHH
Confidence            999753   22   2222222222  224678888888766554

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=87.46  E-value=1.8  Score=41.98  Aligned_cols=17  Identities=29%  Similarity=0.485  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||+..++...+
T Consensus       146 sG~GKTtLl~~I~~~~~  162 (411)
T TIGR03496       146 SGVGKSTLLGMMARYTE  162 (411)
T ss_pred             CCCCHHHHHHHHhcCCC
Confidence            69999999998887443

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.

>PF13245 AAA_19: Part of AAA domain

Probab=87.42  E-value=1.1  Score=32.18  Aligned_cols=28  Identities=21%  Similarity=0.183  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHc-hh--ccccccceEEe
Q 040234            1 MGGLGKTTLARVVYD-LI--SHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~-~~--~~~f~~~~w~~   28 (377)
                      .+|.|||+++.+... -+  +......+.+.
T Consensus        18 ~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~   48 (76)
T PF13245_consen   18 PPGTGKTTTLAARIAELLAARADPGKRVLVL   48 (76)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhcCCCCeEEEE
Confidence            379999965554444 33  22234455554

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=87.41  E-value=0.4  Score=40.55  Aligned_cols=18  Identities=22%  Similarity=0.468  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+..+..
T Consensus        10 ~~gsGKst~a~~l~~~~~   27 (175)
T cd00227          10 GSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CCCCCHHHHHHHHHHhhC
Confidence            479999999999988643

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=87.39  E-value=0.52  Score=41.38  Aligned_cols=47  Identities=21%  Similarity=0.285  Sum_probs=27.4

Q ss_pred             cCceEEEEEeCCCCh---hh----hhHhhCCCCCCC-CCCeEEEEecchhHHhhC
Q 040234           74 RRKKVLVVIDDAAHP---DH----LRRLVGEPDWFG-PGSRIIITTRNEHLLKLH  120 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~---~~----~~~l~~~l~~~~-~gs~IIvTTR~~~v~~~~  120 (377)
                      ..++-|++||..-..   .+    ...+...+...+ .+..+|+||....++...
T Consensus       106 ~~~~slvllDE~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH~~~l~~~~  160 (213)
T cd03281         106 ATRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRS  160 (213)
T ss_pred             CCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcChHHHHHhh
Confidence            467899999998541   11    122222222111 235799999988776543

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

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=87.27  E-value=1.9  Score=39.36  Aligned_cols=20  Identities=25%  Similarity=0.429  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+||||++..++...+..
T Consensus        80 ~~G~GKTTt~akLA~~l~~~   99 (272)
T TIGR00064        80 VNGVGKTTTIAKLANKLKKQ   99 (272)
T ss_pred             CCCCcHHHHHHHHHHHHHhc
Confidence            47999999999999866544

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.

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=87.26  E-value=6.1  Score=40.11  Aligned_cols=139  Identities=16%  Similarity=0.072  Sum_probs=67.8

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCc-eEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRK-KVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k-~~L   79 (377)
                      ++|.|||-||+.|+++...+    ++..          +..+++    +.+.+.      +...+.+.+.+..+.+ +.+
T Consensus       226 ppg~Gkt~l~~aVa~e~~a~----~~~i----------~~peli----~k~~gE------te~~LR~~f~~a~k~~~psi  281 (693)
T KOG0730|consen  226 PPGTGKTFLVRAVANEYGAF----LFLI----------NGPELI----SKFPGE------TESNLRKAFAEALKFQVPSI  281 (693)
T ss_pred             CCCCChHHHHHHHHHHhCce----eEec----------ccHHHH----Hhcccc------hHHHHHHHHHHHhccCCCee
Confidence            47999999999999966522    2222          111222    221221      3334455555566666 788


Q ss_pred             EEEeCCCCh---------------hhhhHhhCCCCCCCCCCeEEEEecchhH----HhhCCCCCeeecCCCChhhhHHHH
Q 040234           80 VVIDDAAHP---------------DHLRRLVGEPDWFGPGSRIIITTRNEHL----LKLHPVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        80 LVLDdv~~~---------------~~~~~l~~~l~~~~~gs~IIvTTR~~~v----~~~~~~~~~~~l~~L~~~ea~~L~  140 (377)
                      +.+|+++..               .++..|...... ..+.-||-|||.+.-    .++-.-.+.+.+.--+..+=.+++
T Consensus       282 i~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~~-~~~vivl~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl  360 (693)
T KOG0730|consen  282 IFIDELDALCPKREGADDVESRVVSQLLTLLDGLKP-DAKVIVLAATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDIL  360 (693)
T ss_pred             EeHHhHhhhCCcccccchHHHHHHHHHHHHHhhCcC-cCcEEEEEecCCccccChhhhcCCCcceeeecCCCchhHHHHH
Confidence            888886542               133344444321 122234445665432    111112344556666655555555


Q ss_pred             HHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          141 CLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      +...-.-...   .......|+..+.|
T Consensus       361 ~~l~k~~~~~---~~~~l~~iA~~thG  384 (693)
T KOG0730|consen  361 RVLTKKMNLL---SDVDLEDIAVSTHG  384 (693)
T ss_pred             HHHHHhcCCc---chhhHHHHHHHccc
Confidence            5444221111   12334456666665

>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

Probab=87.14  E-value=0.43  Score=42.88  Aligned_cols=32  Identities=31%  Similarity=0.353  Sum_probs=27.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREK   33 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~   33 (377)
                      ||+||||+|..++.-+...|.....=+||-..
T Consensus        11 GGtGKTTva~~la~~l~~~~~~~l~DcDVe~P   42 (284)
T COG1149          11 GGTGKTTVAANLAVLLGDKYKLVLADCDVEAP   42 (284)
T ss_pred             CCCChhhHHHHHHHHhccccceEEEecCCCCC
Confidence            89999999999999888888887777766554

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=87.13  E-value=1.4  Score=39.81  Aligned_cols=46  Identities=22%  Similarity=0.176  Sum_probs=29.6

Q ss_pred             CCCcHHHHHHHHHchhcccc-ccceEEecchhhcccccCHHHHHHHHHHHHhhc
Q 040234            2 GGLGKTTLARVVYDLISHEF-DGSSFLADVREKCDKEGSVISLQKQLLSDLLKL   54 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f-~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~   54 (377)
                      +|+|||++|.+++.....+- ..++|+. .- .     +..++...++....+.
T Consensus        28 pg~GKT~~~l~ia~~~a~~~~~~vly~S-lE-m-----~~~~l~~R~la~~s~v   74 (259)
T PF03796_consen   28 PGVGKTAFALQIALNAALNGGYPVLYFS-LE-M-----SEEELAARLLARLSGV   74 (259)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTSSEEEEEE-SS-S------HHHHHHHHHHHHHTS
T ss_pred             ccCCchHHHHHHHHHHHHhcCCeEEEEc-CC-C-----CHHHHHHHHHHHhhcc
Confidence            79999999999998654432 3444444 21 1     5567777777776443

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK06936 type III secretion system ATPase; Provisional

Probab=87.13  E-value=1.9  Score=42.11  Aligned_cols=17  Identities=29%  Similarity=0.311  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||.+.+++...
T Consensus       171 sG~GKStLl~~Ia~~~~  187 (439)
T PRK06936        171 AGGGKSTLLASLIRSAE  187 (439)
T ss_pred             CCCChHHHHHHHhcCCC
Confidence            69999999999998544

>PRK06217 hypothetical protein; Validated

Probab=86.99  E-value=0.42  Score=40.80  Aligned_cols=17  Identities=29%  Similarity=0.448  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||||+++.++.
T Consensus         9 ~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          9 ASGSGTTTLGAALAERL   25 (183)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999999864

>PRK13233 nifH nitrogenase reductase; Reviewed

Probab=86.95  E-value=0.47  Score=43.35  Aligned_cols=18  Identities=28%  Similarity=0.484  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+.+
T Consensus        11 GGVGKTT~a~nLA~~La~   28 (275)
T PRK13233         11 GGIGKSTTTQNTAAAMAY   28 (275)
T ss_pred             CCCcHHHHHHHHHHHHHH
Confidence            899999999998886653

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=86.90  E-value=0.9  Score=42.95  Aligned_cols=15  Identities=27%  Similarity=0.142  Sum_probs=12.9

Q ss_pred             CCCCcHHHHHHHHHc
Q 040234            1 MGGLGKTTLARVVYD   15 (377)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (377)
                      .+|+|||+||..++-
T Consensus       131 ~~g~GKT~l~~~l~~  145 (342)
T PLN03186        131 EFRTGKTQLCHTLCV  145 (342)
T ss_pred             CCCCCccHHHHHHHH
Confidence            379999999998885

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=86.85  E-value=0.78  Score=39.99  Aligned_cols=45  Identities=13%  Similarity=0.124  Sum_probs=28.1

Q ss_pred             cCceEEEEEeCCCC---hhh----hhHhhCCCCCCCCCCeEEEEecchhHHhhC
Q 040234           74 RRKKVLVVIDDAAH---PDH----LRRLVGEPDWFGPGSRIIITTRNEHLLKLH  120 (377)
Q Consensus        74 ~~k~~LLVLDdv~~---~~~----~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~  120 (377)
                      ..++-|++||....   ..+    ...+...+.  ..+..+|++|....++...
T Consensus       106 ~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~--~~~~~~i~~TH~~~l~~~~  157 (204)
T cd03282         106 ADGDSLVLIDELGRGTSSADGFAISLAILECLI--KKESTVFFATHFRDIAAIL  157 (204)
T ss_pred             cCCCcEEEeccccCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHHh
Confidence            35678999999732   211    122222222  2377899999998877654

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

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=86.70  E-value=1.9  Score=42.87  Aligned_cols=14  Identities=36%  Similarity=0.544  Sum_probs=11.9

Q ss_pred             cCceEEEEEeCCCC
Q 040234           74 RRKKVLVVIDDAAH   87 (377)
Q Consensus        74 ~~k~~LLVLDdv~~   87 (377)
                      ++++.|||+||+-.
T Consensus       252 ~G~~VLli~DdlTr  265 (502)
T PRK09281        252 NGKDALIVYDDLSK  265 (502)
T ss_pred             cCCCEEEEecCchH
Confidence            37899999999865

>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=86.69  E-value=1.8  Score=41.40  Aligned_cols=79  Identities=18%  Similarity=0.205  Sum_probs=39.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcccc--CccchhhhH---------HHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN--NIRNVYDGI---------NMLR   70 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~---------~~l~   70 (377)
                      +|+|||||.-.+++.-+  ++..+ +.-+++.. +  .+.+.+++.+..-+.....  ...+.+...         -.+-
T Consensus       172 sGVGKStLLgMiar~t~--aDv~V-iaLIGERG-R--EVrEFIE~~Lg~egl~rsViVvATSD~s~l~R~~aa~~At~IA  245 (441)
T COG1157         172 SGVGKSTLLGMIARNTE--ADVNV-IALIGERG-R--EVREFIEKDLGEEGLKRSVVVVATSDESALMRLKAAFTATTIA  245 (441)
T ss_pred             CCCcHHHHHHHHhcccc--CCEEE-EEEeeccc-h--hHHHHHHHhcchhhccceEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            69999999999998333  33222 22133322 1  4445544444332221111  011111111         1233


Q ss_pred             HHh--cCceEEEEEeCCC
Q 040234           71 VRL--RRKKVLVVIDDAA   86 (377)
Q Consensus        71 ~~l--~~k~~LLVLDdv~   86 (377)
                      +++  +++++||++|.+-
T Consensus       246 EyFRDqG~~VLL~mDSlT  263 (441)
T COG1157         246 EYFRDQGKRVLLIMDSLT  263 (441)
T ss_pred             HHHHhCCCeEEEEeecHH
Confidence            344  4689999999974

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=86.66  E-value=0.43  Score=39.09  Aligned_cols=16  Identities=25%  Similarity=0.532  Sum_probs=14.4

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      ++|+||||+|+.+..+
T Consensus         7 ~~GsGKST~a~~l~~~   22 (150)
T cd02021           7 VSGSGKSTVGKALAER   22 (150)
T ss_pred             CCCCCHHHHHHHHHhh
Confidence            4799999999999886

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=86.64  E-value=1.2  Score=40.63  Aligned_cols=94  Identities=20%  Similarity=0.259  Sum_probs=52.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEE-ecchhhcccccCHHHHHHHHHHHHhhccccCc-cchhhhHHHHHHHhcCceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFL-ADVREKCDKEGSVISLQKQLLSDLLKLADNNI-RNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~-~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~-~~~~~~~~~l~~~l~~k~~L   79 (377)
                      .|+||||++..+...+... ...+.. .+..+..     +        ... ....... .......+.++..|+..+=.
T Consensus       136 tGSGKTT~l~all~~i~~~-~~~iv~iEd~~E~~-----l--------~~~-~~~~~~~~~~~~~~~~~l~~~LR~~pD~  200 (270)
T PF00437_consen  136 TGSGKTTLLNALLEEIPPE-DERIVTIEDPPELR-----L--------PGP-NQIQIQTRRDEISYEDLLKSALRQDPDV  200 (270)
T ss_dssp             TTSSHHHHHHHHHHHCHTT-TSEEEEEESSS-S---------------SCS-SEEEEEEETTTBSHHHHHHHHTTS--SE
T ss_pred             CccccchHHHHHhhhcccc-ccceEEecccccee-----e--------ccc-ceEEEEeecCcccHHHHHHHHhcCCCCc
Confidence            6999999999999866655 333332 2111110     0        000 0000011 23445677888889988889


Q ss_pred             EEEeCCCChhhhhHhhCCCCCCCCCCeE-EEEecch
Q 040234           80 VVIDDAAHPDHLRRLVGEPDWFGPGSRI-IITTRNE  114 (377)
Q Consensus        80 LVLDdv~~~~~~~~l~~~l~~~~~gs~I-IvTTR~~  114 (377)
                      ++++.+.+.+.+..+...    ..|..+ +-|....
T Consensus       201 iiigEiR~~e~~~~~~a~----~tGh~~~~tT~Ha~  232 (270)
T PF00437_consen  201 IIIGEIRDPEAAEAIQAA----NTGHLGSLTTLHAN  232 (270)
T ss_dssp             EEESCE-SCHHHHHHHHH----HTT-EEEEEEEE-S
T ss_pred             ccccccCCHhHHHHHHhh----ccCCceeeeeeecC
Confidence            999999998877765443    456666 5555543

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit

Probab=86.62  E-value=1.9  Score=42.85  Aligned_cols=14  Identities=29%  Similarity=0.539  Sum_probs=11.9

Q ss_pred             cCceEEEEEeCCCC
Q 040234           74 RRKKVLVVIDDAAH   87 (377)
Q Consensus        74 ~~k~~LLVLDdv~~   87 (377)
                      ++++.|||+||+-.
T Consensus       251 ~G~~VLlv~Ddltr  264 (501)
T TIGR00962       251 NGKHALIIYDDLSK  264 (501)
T ss_pred             cCCCEEEEecchHH
Confidence            47899999999854

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. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=86.60  E-value=5.1  Score=34.98  Aligned_cols=50  Identities=14%  Similarity=0.108  Sum_probs=28.1

Q ss_pred             HHHHhcCceEEEEEeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchhHHhhC
Q 040234           69 LRVRLRRKKVLVVIDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEHLLKLH  120 (377)
Q Consensus        69 l~~~l~~k~~LLVLDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~  120 (377)
                      +.+.+..++=+++||+.-+   .+   .+..++..+.  ..+..||++|.+.......
T Consensus       148 laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~--~~~~tiii~sH~~~~~~~~  203 (214)
T PRK13543        148 LARLWLSPAPLWLLDEPYANLDLEGITLVNRMISAHL--RGGGAALVTTHGAYAAPPV  203 (214)
T ss_pred             HHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHH--hCCCEEEEEecChhhhhhh
Confidence            3344455667999999743   22   2333332222  2356788888887655443

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=86.54  E-value=1.5  Score=41.03  Aligned_cols=17  Identities=29%  Similarity=0.454  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||.+.++....
T Consensus        78 sG~GKTtLl~~Ia~~~~   94 (326)
T cd01136          78 SGVGKSTLLGMIARGTT   94 (326)
T ss_pred             CCCChHHHHHHHhCCCC
Confidence            69999999999998544

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.

>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon

Probab=86.49  E-value=0.75  Score=41.11  Aligned_cols=27  Identities=26%  Similarity=0.267  Sum_probs=19.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      ||+|||||+..++..+...=..++-|.
T Consensus        11 GGvG~TTltAnLA~aL~~~G~~VlaID   37 (243)
T PF06564_consen   11 GGVGKTTLTANLAWALARLGESVLAID   37 (243)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            899999999999986555433444343

It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=86.38  E-value=0.44  Score=37.85  Aligned_cols=15  Identities=40%  Similarity=0.547  Sum_probs=13.3

Q ss_pred             CCcHHHHHHHHHchh
Q 040234            3 GLGKTTLARVVYDLI   17 (377)
Q Consensus         3 GiGKTtLA~~v~~~~   17 (377)
                      |+|||||++.+++.+
T Consensus        25 GaGKTtf~r~l~~~l   39 (123)
T PF02367_consen   25 GAGKTTFVRGLARAL   39 (123)
T ss_dssp             TSSHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHc
Confidence            899999999999843

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=86.35  E-value=1.1  Score=40.66  Aligned_cols=27  Identities=22%  Similarity=0.153  Sum_probs=23.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||++|.+++.+...+...++|+.
T Consensus        32 pGsGKT~f~~qfl~~~~~~ge~vlyvs   58 (260)
T COG0467          32 PGTGKTIFALQFLYEGAREGEPVLYVS   58 (260)
T ss_pred             CCCcHHHHHHHHHHHHHhcCCcEEEEE
Confidence            799999999999998777777777776

>cd03111 CpaE_like This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster

Probab=86.34  E-value=0.68  Score=35.63  Aligned_cols=29  Identities=34%  Similarity=0.479  Sum_probs=21.0

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecc
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADV   30 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~   30 (377)
                      ||+||||+|..++......+...+++.+.
T Consensus         9 gg~gkt~~~~~la~~~~~~~~~~~~l~d~   37 (106)
T cd03111           9 GGVGATTLAANLAVALAKEAGRRVLLVDL   37 (106)
T ss_pred             CCCcHHHHHHHHHHHHHhcCCCcEEEEEC
Confidence            89999999999998776653444444433

The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.

>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2

Probab=86.23  E-value=0.47  Score=39.43  Aligned_cols=20  Identities=25%  Similarity=0.497  Sum_probs=17.0

Q ss_pred             CCCcHHHHHHHHHchhcccc
Q 040234            2 GGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f   21 (377)
                      .|+||||+++.++.++.-.|
T Consensus         1 ~GsGKStvg~~lA~~L~~~f   20 (158)
T PF01202_consen    1 MGSGKSTVGKLLAKRLGRPF   20 (158)
T ss_dssp             TTSSHHHHHHHHHHHHTSEE
T ss_pred             CCCcHHHHHHHHHHHhCCCc
Confidence            48999999999999776554

7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....

>PRK06696 uridine kinase; Validated

Probab=86.14  E-value=0.43  Score=42.20  Aligned_cols=19  Identities=32%  Similarity=0.370  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||||+.+++.+..
T Consensus        30 ~sgsGKSTlA~~L~~~l~~   48 (223)
T PRK06696         30 ITASGKTTFADELAEEIKK   48 (223)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3799999999999987654

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=86.10  E-value=2.1  Score=41.82  Aligned_cols=17  Identities=24%  Similarity=0.399  Sum_probs=14.3

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||++.+++...
T Consensus       167 sG~GKTtLL~~I~~~~~  183 (442)
T PRK08927        167 SGVGKSVLLSMLARNAD  183 (442)
T ss_pred             CCCCHHHHHHHHHhccC
Confidence            69999999999997543

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=86.07  E-value=2.2  Score=36.31  Aligned_cols=18  Identities=28%  Similarity=0.512  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+...+.
T Consensus        26 ~~GsGKstla~~l~~~l~   43 (184)
T TIGR00455        26 LSGSGKSTIANALEKKLE   43 (184)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            369999999999998654

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>PRK08149 ATP synthase SpaL; Validated

Probab=86.04  E-value=1.1  Score=43.45  Aligned_cols=78  Identities=18%  Similarity=0.202  Sum_probs=39.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc-----ccCccc----------hhhhH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA-----DNNIRN----------VYDGI   66 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~-----~~~~~~----------~~~~~   66 (377)
                      .|+|||||+..++.....  +..+ +..++...   ..+..+....+.......     .....+          .-..+
T Consensus       160 sG~GKTTLl~~i~~~~~~--dv~v-~g~Ig~rg---~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~~~a~tiA  233 (428)
T PRK08149        160 AGCGKTSLMNMLIEHSEA--DVFV-IGLIGERG---REVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAALVATTVA  233 (428)
T ss_pred             CCCChhHHHHHHhcCCCC--CeEE-EEEEeeCC---ccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHHHHHHHHH
Confidence            699999999999873322  1111 22232221   155555555554321110     000010          11123


Q ss_pred             HHHHHHhcCceEEEEEeCCCC
Q 040234           67 NMLRVRLRRKKVLVVIDDAAH   87 (377)
Q Consensus        67 ~~l~~~l~~k~~LLVLDdv~~   87 (377)
                      +.++.  ++++.||++||+-.
T Consensus       234 E~fr~--~G~~Vll~~DslTr  252 (428)
T PRK08149        234 EYFRD--QGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHH--cCCCEEEEccchHH
Confidence            33443  58899999999854

>PRK13849 putative crown gall tumor protein VirC1; Provisional

Probab=86.03  E-value=0.6  Score=41.58  Aligned_cols=28  Identities=25%  Similarity=0.306  Sum_probs=19.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecc
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADV   30 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~   30 (377)
                      ||+||||+|..++...... ...+.+.|.
T Consensus        11 GGvGKTT~a~nLA~~la~~-G~~VlliD~   38 (231)
T PRK13849         11 GGAGKTTALMGLCAALASD-GKRVALFEA   38 (231)
T ss_pred             CCccHHHHHHHHHHHHHhC-CCcEEEEeC
Confidence            8999999999999855443 223444444

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=86.03  E-value=2.5  Score=41.29  Aligned_cols=18  Identities=28%  Similarity=0.231  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+||||++..++....
T Consensus       229 ptGvGKTTt~~kLA~~~~  246 (424)
T PRK05703        229 PTGVGKTTTLAKLAARYA  246 (424)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999887554

>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=86.02  E-value=0.53  Score=38.58  Aligned_cols=17  Identities=41%  Similarity=0.618  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++..+
T Consensus         7 ~~GsGKstla~~la~~l   23 (154)
T cd00464           7 MMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            57999999999999865

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.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=86.01  E-value=2  Score=40.79  Aligned_cols=28  Identities=32%  Similarity=0.283  Sum_probs=21.6

Q ss_pred             CCCCcHHHHHHHHHchh--ccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLI--SHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~--~~~f~~~~w~~   28 (377)
                      .+|.|||.||..++.++  .......++++
T Consensus         9 ~aGTGKTvla~~l~~~l~~~~~~~~~~~l~   38 (352)
T PF09848_consen    9 GAGTGKTVLALNLAKELQNSEEGKKVLYLC   38 (352)
T ss_pred             cCCcCHHHHHHHHHHHhhccccCCceEEEE
Confidence            37999999999999987  55555556555

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=86.00  E-value=8.8  Score=36.11  Aligned_cols=15  Identities=33%  Similarity=0.359  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHch
Q 040234            2 GGLGKTTLARVVYDL   16 (377)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (377)
                      .|+||+++|+.+.+.
T Consensus        31 ~GtGK~~lAr~iH~~   45 (329)
T TIGR02974        31 RGTGKELIAARLHYL   45 (329)
T ss_pred             CCChHHHHHHHHHHh
Confidence            699999999999873

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

>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=85.97  E-value=2.6  Score=37.20  Aligned_cols=17  Identities=47%  Similarity=0.604  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+||||||+.+...+.
T Consensus         8 sGSGKTTla~~L~~~l~   24 (220)
T cd02025           8 VAVGKSTTARVLQALLS   24 (220)
T ss_pred             CCCCHHHHHHHHHHHHh
Confidence            69999999999998664

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=85.94  E-value=2.3  Score=40.10  Aligned_cols=40  Identities=15%  Similarity=0.263  Sum_probs=24.0

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQL   47 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i   47 (377)
                      .|+|||+|++++++....  +..+++. +++...   .+.+++.++
T Consensus       166 ~G~GKT~L~~~Iak~~~~--dvvVyv~-iGERg~---Ev~e~l~ef  205 (369)
T cd01134         166 FGCGKTVIQQSLSKYSNS--DIVIYVG-CGERGN---EMTEVLEEF  205 (369)
T ss_pred             CCCChHHHHHHHHhCCCC--CEEEEEE-eCCChH---HHHHHHHHH
Confidence            699999999999985322  2344433 555321   445555554

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.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=85.90  E-value=4.6  Score=34.93  Aligned_cols=17  Identities=24%  Similarity=0.305  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||++.++...+
T Consensus        42 nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          42 PGSGCSTLLKALANRTE   58 (202)
T ss_pred             CCCCHHHHHHHhcccCC
Confidence            69999999999998543

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=85.87  E-value=1.3  Score=45.32  Aligned_cols=21  Identities=29%  Similarity=0.588  Sum_probs=17.3

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      ++|+|||++|+.+++.+...|
T Consensus       446 PPGVGKTSI~kSIA~ALnRkF  466 (906)
T KOG2004|consen  446 PPGVGKTSIAKSIARALNRKF  466 (906)
T ss_pred             CCCCCcccHHHHHHHHhCCce
Confidence            589999999999999665444

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=85.86  E-value=0.48  Score=41.04  Aligned_cols=18  Identities=39%  Similarity=0.567  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      |=|+||||||+.++++++
T Consensus        12 ~IG~GKSTLa~~La~~l~   29 (216)
T COG1428          12 MIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             ccccCHHHHHHHHHHHhC
Confidence            348999999999998765

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.81  E-value=3.3  Score=39.85  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+||||.+..++....
T Consensus       183 tGvGKTTT~aKLA~~~~  199 (388)
T PRK12723        183 TGVGKTTTIAKLAAIYG  199 (388)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999988554

>PTZ00185 ATPase alpha subunit; Provisional

Probab=85.80  E-value=3.3  Score=41.16  Aligned_cols=14  Identities=36%  Similarity=0.563  Sum_probs=12.0

Q ss_pred             cCceEEEEEeCCCC
Q 040234           74 RRKKVLVVIDDAAH   87 (377)
Q Consensus        74 ~~k~~LLVLDdv~~   87 (377)
                      +++..|+|+||+-.
T Consensus       287 ~GkdVLiv~DDLTr  300 (574)
T PTZ00185        287 RGRHCLCVYDDLSK  300 (574)
T ss_pred             cCCCEEEEEcCchH
Confidence            57899999999854

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=85.78  E-value=4.2  Score=35.09  Aligned_cols=49  Identities=18%  Similarity=0.288  Sum_probs=28.7

Q ss_pred             HHHHHhcCceEEEEEeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchhHHh
Q 040234           68 MLRVRLRRKKVLVVIDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEHLLK  118 (377)
Q Consensus        68 ~l~~~l~~k~~LLVLDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~v~~  118 (377)
                      .+.+.+..++=+++||+.-.   ..   .+..++..+.  ..+..||++|.+.....
T Consensus       114 ~laral~~~p~illlDEPt~~LD~~~~~~l~~~L~~~~--~~~~tiii~sh~~~~~~  168 (200)
T cd03217         114 EILQLLLLEPDLAILDEPDSGLDIDALRLVAEVINKLR--EEGKSVLIITHYQRLLD  168 (200)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHH--HCCCEEEEEecCHHHHH
Confidence            34555667778999999743   22   2222222221  23567888888876655

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PRK13343 F0F1 ATP synthase subunit alpha; Provisional

Probab=85.77  E-value=2.1  Score=42.48  Aligned_cols=14  Identities=29%  Similarity=0.532  Sum_probs=12.0

Q ss_pred             cCceEEEEEeCCCC
Q 040234           74 RRKKVLVVIDDAAH   87 (377)
Q Consensus        74 ~~k~~LLVLDdv~~   87 (377)
                      ++++.|||+||+-.
T Consensus       252 ~G~~VLlv~DdlTr  265 (502)
T PRK13343        252 QGQDALIVYDDLSK  265 (502)
T ss_pred             CCCCEEEEecchHH
Confidence            57899999999854

>PRK14526 adenylate kinase; Provisional

Probab=85.74  E-value=1.8  Score=37.95  Aligned_cols=17  Identities=29%  Similarity=0.487  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++...
T Consensus         8 ~pGsGKsT~a~~La~~~   24 (211)
T PRK14526          8 PPGSGKGTIAKILSNEL   24 (211)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998744

>PRK13975 thymidylate kinase; Provisional

Probab=85.73  E-value=0.51  Score=40.56  Aligned_cols=19  Identities=32%  Similarity=0.532  Sum_probs=16.5

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      +.|+||||+|+.+++++..
T Consensus        10 ~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975         10 IDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             CCCCCHHHHHHHHHHHhCC
Confidence            4799999999999997754

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=85.68  E-value=3.9  Score=39.92  Aligned_cols=44  Identities=23%  Similarity=0.361  Sum_probs=25.1

Q ss_pred             cCceEEEEEeCCCC-hhhhhH---hhCCCCCCCCCCeEEEEecchhHHhh
Q 040234           74 RRKKVLVVIDDAAH-PDHLRR---LVGEPDWFGPGSRIIITTRNEHLLKL  119 (377)
Q Consensus        74 ~~k~~LLVLDdv~~-~~~~~~---l~~~l~~~~~gs~IIvTTR~~~v~~~  119 (377)
                      ++++.||++|++-. .+..+.   .....|.  .|--..+.|..+.+..+
T Consensus       244 ~G~~VLlilDslTr~a~A~reisl~~~e~p~--~G~~~~~~s~l~~L~ER  291 (432)
T PRK06793        244 QGNNVLLMMDSVTRFADARRSVDIAVKELPI--GGKTLLMESYMKKLLER  291 (432)
T ss_pred             cCCcEEEEecchHHHHHHHHHHHHHhcCCCC--CCeeeeeeccchhHHHH
Confidence            47899999999865 222333   2333332  25555665555555444

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=85.59  E-value=0.91  Score=38.87  Aligned_cols=29  Identities=24%  Similarity=0.373  Sum_probs=24.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecc
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADV   30 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~   30 (377)
                      .|+|||+|..+.++.++++|+..+.-.|+
T Consensus        22 ~GSGKTaLie~~~~~L~~~~~~aVI~~Di   50 (202)
T COG0378          22 PGSGKTALIEKTLRALKDEYKIAVITGDI   50 (202)
T ss_pred             CCcCHHHHHHHHHHHHHhhCCeEEEecee
Confidence            69999999999999999999877655444

>PRK06547 hypothetical protein; Provisional

Probab=85.57  E-value=0.52  Score=39.90  Aligned_cols=17  Identities=41%  Similarity=0.393  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+||||||..+++..
T Consensus        23 ~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         23 RSGSGKTTLAGALAART   39 (172)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999853

>PRK13231 nitrogenase reductase-like protein; Reviewed

Probab=85.57  E-value=0.5  Score=42.87  Aligned_cols=27  Identities=22%  Similarity=0.388  Sum_probs=19.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecc
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADV   30 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~   30 (377)
                      ||+||||+|..++..+.+.-  ++.+.|.
T Consensus        11 GGvGKTT~a~nLA~~La~~G--rVLliD~   37 (264)
T PRK13231         11 GGIGKSTTVSNMAAAYSNDH--RVLVIGC   37 (264)
T ss_pred             CCCcHHHHHHHHhcccCCCC--EEEEEeE
Confidence            89999999999999665542  4444434

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=85.55  E-value=13  Score=33.26  Aligned_cols=116  Identities=18%  Similarity=0.279  Sum_probs=59.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh----cCc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL----RRK   76 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l----~~k   76 (377)
                      .+|.|||-||+.+++..     . +|+..++..        ++....    .+.          ....+|+.+    ..-
T Consensus       189 ppgtGktLlaraVahht-----~-c~firvsgs--------elvqk~----ige----------gsrmvrelfvmareha  240 (404)
T KOG0728|consen  189 PPGTGKTLLARAVAHHT-----D-CTFIRVSGS--------ELVQKY----IGE----------GSRMVRELFVMAREHA  240 (404)
T ss_pred             CCCCchhHHHHHHHhhc-----c-eEEEEechH--------HHHHHH----hhh----------hHHHHHHHHHHHHhcC
Confidence            47999999999999732     2 333335443        111111    111          123333332    234


Q ss_pred             eEEEEEeCCCCh------------hh----hhHhhCCCCCC--CCCCeEEEEecchhHHhh-----CCCCCeeecCCCCh
Q 040234           77 KVLVVIDDAAHP------------DH----LRRLVGEPDWF--GPGSRIIITTRNEHLLKL-----HPVKKVYKLEALTY  133 (377)
Q Consensus        77 ~~LLVLDdv~~~------------~~----~~~l~~~l~~~--~~gs~IIvTTR~~~v~~~-----~~~~~~~~l~~L~~  133 (377)
                      +-++.+|.+++.            .+    .-.++..+...  .+.-+||..|..-++...     -...+.++.++-++
T Consensus       241 psiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p~e  320 (404)
T KOG0728|consen  241 PSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNE  320 (404)
T ss_pred             CceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCCCH
Confidence            678888887642            11    11233333221  345577765544333221     13356778888777


Q ss_pred             hhhHHHHHHHh
Q 040234          134 DEAFRLLCLKA  144 (377)
Q Consensus       134 ~ea~~L~~~~~  144 (377)
                      +.-.+++.-+.
T Consensus       321 ~ar~~ilkihs  331 (404)
T KOG0728|consen  321 EARLDILKIHS  331 (404)
T ss_pred             HHHHHHHHHhh
Confidence            77777776544

>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein

Probab=85.54  E-value=0.65  Score=42.23  Aligned_cols=17  Identities=29%  Similarity=0.493  Sum_probs=14.3

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      ||+||||+|..++..+.
T Consensus         9 GGVGKTT~~~nLA~~La   25 (268)
T TIGR01281         9 GGIGKSTTSSNLSVAFA   25 (268)
T ss_pred             CcCcHHHHHHHHHHHHH
Confidence            89999999988887544

The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit.

>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=85.54  E-value=0.48  Score=43.33  Aligned_cols=17  Identities=29%  Similarity=0.411  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ..|+|||++++...++.
T Consensus        41 ~~GtGKT~li~~~l~~l   57 (272)
T PF12775_consen   41 PSGTGKTSLIQNFLSSL   57 (272)
T ss_dssp             STTSSHHHHHHHHHHCS
T ss_pred             CCCCchhHHHHhhhccC
Confidence            37999999999988744

>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []

Probab=85.47  E-value=0.48  Score=39.39  Aligned_cols=16  Identities=44%  Similarity=0.513  Sum_probs=13.5

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      -|+||||+|..+.+-.
T Consensus         8 iGCGKTTva~aL~~LF   23 (168)
T PF08303_consen    8 IGCGKTTVALALSNLF   23 (168)
T ss_pred             CCcCHHHHHHHHHHHc
Confidence            4999999999998743

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>PRK13946 shikimate kinase; Provisional

Probab=85.46  E-value=0.57  Score=40.04  Aligned_cols=18  Identities=28%  Similarity=0.540  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      |.|+||||+|+.+++++.
T Consensus        18 ~~GsGKsti~~~LA~~Lg   35 (184)
T PRK13946         18 LMGAGKSTVGRRLATMLG   35 (184)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            589999999999999763

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=85.42  E-value=1.7  Score=42.76  Aligned_cols=16  Identities=25%  Similarity=0.270  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||+|+..+++..
T Consensus       150 ~G~GKs~L~~~ia~~~  165 (458)
T TIGR01041       150 SGLPHNELAAQIARQA  165 (458)
T ss_pred             CCCCHHHHHHHHHHhh
Confidence            6999999999999843

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK13949 shikimate kinase; Provisional

Probab=85.42  E-value=0.58  Score=39.45  Aligned_cols=18  Identities=33%  Similarity=0.436  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+|||||++.+++...
T Consensus         9 ~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          9 YMGAGKTTLGKALARELG   26 (169)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            579999999999998664

>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=85.31  E-value=0.49  Score=39.86  Aligned_cols=18  Identities=39%  Similarity=0.584  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      .|+|||||++.+++.++.
T Consensus         8 pG~GKTTll~k~i~~l~~   25 (168)
T PF03266_consen    8 PGVGKTTLLKKVIEELKK   25 (168)
T ss_dssp             TTSSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhhc
Confidence            799999999999986643

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.

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=85.29  E-value=0.61  Score=40.78  Aligned_cols=19  Identities=37%  Similarity=0.536  Sum_probs=17.1

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      +|+||||+|+.+...++..
T Consensus        17 SgSGKTTva~~l~~~~~~~   35 (218)
T COG0572          17 SGSGKTTVAKELSEQLGVE   35 (218)
T ss_pred             CCCCHHHHHHHHHHHhCcC
Confidence            6999999999999988766

>PRK00889 adenylylsulfate kinase; Provisional

Probab=85.23  E-value=0.7  Score=39.01  Aligned_cols=19  Identities=37%  Similarity=0.643  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||+|+.++.....
T Consensus        12 ~~GsGKST~a~~la~~l~~   30 (175)
T PRK00889         12 LSGAGKTTIARALAEKLRE   30 (175)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            4799999999999986643

>PRK13948 shikimate kinase; Provisional

Probab=85.17  E-value=0.6  Score=39.89  Aligned_cols=19  Identities=16%  Similarity=0.216  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      |.|+||||+++.+++++..
T Consensus        18 ~~GsGKSTvg~~La~~lg~   36 (182)
T PRK13948         18 FMGTGKSRIGWELSRALML   36 (182)
T ss_pred             CCCCCHHHHHHHHHHHcCC
Confidence            5799999999999987643

>PRK10037 cell division protein; Provisional

Probab=85.13  E-value=0.69  Score=41.63  Aligned_cols=28  Identities=18%  Similarity=0.299  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecc
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADV   30 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~   30 (377)
                      ||+||||+|..++..+..+=. ++.+.|.
T Consensus        11 GGvGKTT~a~nLA~~La~~G~-rVLlID~   38 (250)
T PRK10037         11 GGVGTTSITAALAWSLQMLGE-NVLVIDA   38 (250)
T ss_pred             CCccHHHHHHHHHHHHHhcCC-cEEEEeC
Confidence            899999999999985554322 3444433

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=85.07  E-value=2.1  Score=41.60  Aligned_cols=17  Identities=29%  Similarity=0.452  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||++.++...+
T Consensus       149 sG~GKTtLl~~I~~~~~  165 (418)
T TIGR03498       149 SGVGKSTLLSMLARNTD  165 (418)
T ss_pred             CCCChHHHHHHHhCCCC
Confidence            69999999998887543

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.

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=85.04  E-value=0.53  Score=34.73  Aligned_cols=18  Identities=44%  Similarity=0.667  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      +|+||||++..++..+++
T Consensus         8 ~G~Gktt~~~~l~~~l~~   25 (99)
T cd01983           8 GGVGKTTLAANLAAALAK   25 (99)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            699999999999996654

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>TIGR01969 minD_arch cell division ATPase MinD, archaeal

Probab=85.03  E-value=0.69  Score=41.38  Aligned_cols=18  Identities=33%  Similarity=0.473  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+..
T Consensus        10 GGvGKTt~a~~LA~~la~   27 (251)
T TIGR01969        10 GGTGKTTITANLGVALAK   27 (251)
T ss_pred             CCCcHHHHHHHHHHHHHH
Confidence            899999999999985543

This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=85.03  E-value=0.6  Score=39.07  Aligned_cols=17  Identities=29%  Similarity=0.458  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||||+.++.+.
T Consensus         3 ~sGsGKSTla~~la~~l   19 (163)
T PRK11545          3 VSGSGKSAVASEVAHQL   19 (163)
T ss_pred             CCCCcHHHHHHHHHHHh
Confidence            47999999999999866

>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=85.02  E-value=0.77  Score=39.09  Aligned_cols=18  Identities=33%  Similarity=0.486  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      +|+||||||..+...+..
T Consensus         8 sgsGKttla~~l~~~l~~   25 (179)
T cd02028           8 SGSGKTTFAKKLSNQLRV   25 (179)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            799999999999986653

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK05973 replicative DNA helicase; Provisional

Probab=84.93  E-value=1.4  Score=39.32  Aligned_cols=27  Identities=22%  Similarity=0.118  Sum_probs=18.4

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||+||.+++.....+-..++++.
T Consensus        73 PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         73 PGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            799999999999875433323344443

>PRK04040 adenylate kinase; Provisional

Probab=84.82  E-value=0.59  Score=40.15  Aligned_cols=18  Identities=28%  Similarity=0.482  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+++.+.+++.
T Consensus        10 ~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040         10 VPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             CCCCCHHHHHHHHHHHhc
Confidence            589999999999998774

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=84.79  E-value=1.6  Score=36.70  Aligned_cols=19  Identities=21%  Similarity=0.218  Sum_probs=12.1

Q ss_pred             CCCcHHH-HHHHHHchhccc
Q 040234            2 GGLGKTT-LARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTt-LA~~v~~~~~~~   20 (377)
                      .|+|||+ ++..+++.....
T Consensus        33 ~GsGKT~~~~~~~~~~~~~~   52 (201)
T smart00487       33 TGSGKTLAALLPALEALKRG   52 (201)
T ss_pred             CCCchhHHHHHHHHHHhccc
Confidence            6999999 445555544443

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=84.78  E-value=1  Score=42.77  Aligned_cols=23  Identities=26%  Similarity=0.235  Sum_probs=20.1

Q ss_pred             CCCCcHHHHHHHHHchhcccccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDG   23 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~   23 (377)
                      ++|.|||++|..+.+.++++.+.
T Consensus        18 ~PGTGKTtfaLelL~~l~~~~~v   40 (484)
T PF07088_consen   18 EPGTGKTTFALELLNSLKDHGNV   40 (484)
T ss_pred             CCCCCceeeehhhHHHHhccCCe
Confidence            58999999999999988887653

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=84.76  E-value=1  Score=43.21  Aligned_cols=58  Identities=17%  Similarity=0.183  Sum_probs=34.2

Q ss_pred             HHHHHHHhcCceEEEEEeCCCC-hhh------hhHhhCCCCCCCCCCeEEEEecchhHHhhCCCCCe
Q 040234           66 INMLRVRLRRKKVLVVIDDAAH-PDH------LRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKV  125 (377)
Q Consensus        66 ~~~l~~~l~~k~~LLVLDdv~~-~~~------~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~  125 (377)
                      ...+-+.++.+.-+++.|.... .+.      ...+...-  ...|..+++.|+.+++.+.+..+..
T Consensus       515 R~KLAkllaerpn~~~iDEF~AhLD~~TA~rVArkisela--Re~giTlivvThrpEv~~AL~PD~l  579 (593)
T COG2401         515 RAKLAKLLAERPNVLLIDEFAAHLDELTAVRVARKISELA--REAGITLIVVTHRPEVGNALRPDTL  579 (593)
T ss_pred             HHHHHHHHhcCCCcEEhhhhhhhcCHHHHHHHHHHHHHHH--HHhCCeEEEEecCHHHHhccCCcee
Confidence            4456677788888999998643 221      11221110  0246677777777888777654433

>PRK03846 adenylylsulfate kinase; Provisional

Probab=84.75  E-value=0.81  Score=39.56  Aligned_cols=20  Identities=25%  Similarity=0.428  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+||||||+.+...+...
T Consensus        32 ~~GsGKSTla~~l~~~l~~~   51 (198)
T PRK03846         32 LSGSGKSTVAGALEEALHEL   51 (198)
T ss_pred             CCCCCHHHHHHHHHHHHHhC
Confidence            36999999999999866443

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=84.73  E-value=2.2  Score=39.94  Aligned_cols=82  Identities=18%  Similarity=0.200  Sum_probs=46.2

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .|+||||+++.+...+....+ .++...  -       +..++.   +.. .........+.....+.++..|+.++=.+
T Consensus       153 tGSGKTTll~aL~~~i~~~~~~~rivti--E-------d~~El~---~~~-~n~v~l~~~~~~~~~~lv~~aLR~~PD~I  219 (323)
T PRK13833        153 TGSGKTTLANAVIAEIVASAPEDRLVIL--E-------DTAEIQ---CAA-ENAVALHTSDTVDMARLLKSTMRLRPDRI  219 (323)
T ss_pred             CCCCHHHHHHHHHHHHhcCCCCceEEEe--c-------CCcccc---cCC-CCEEEeccCCCcCHHHHHHHHhCCCCCEE
Confidence            599999999999886643322 233221  1       111111   000 00000001122345677888888888899


Q ss_pred             EEeCCCChhhhhHhhC
Q 040234           81 VIDDAAHPDHLRRLVG   96 (377)
Q Consensus        81 VLDdv~~~~~~~~l~~   96 (377)
                      |+..+.+.+.+..+..
T Consensus       220 ivGEiRg~ea~~~l~a  235 (323)
T PRK13833        220 IVGEVRDGAALTLLKA  235 (323)
T ss_pred             EEeecCCHHHHHHHHH
Confidence            9999999887765543

>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=84.71  E-value=0.89  Score=40.65  Aligned_cols=20  Identities=25%  Similarity=0.416  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      |+|+||||+++.+.+-....
T Consensus         4 paGSGKTT~~~~~~~~~~~~   23 (238)
T PF03029_consen    4 PAGSGKTTFCKGLSEWLESN   23 (238)
T ss_dssp             STTSSHHHHHHHHHHHHTTT
T ss_pred             CCCCCHHHHHHHHHHHHHhc
Confidence            68999999999999844433

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=84.66  E-value=0.73  Score=41.82  Aligned_cols=18  Identities=28%  Similarity=0.577  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+..
T Consensus        10 GGvGKTT~~~nLA~~La~   27 (270)
T cd02040          10 GGIGKSTTTQNLSAALAE   27 (270)
T ss_pred             CcCCHHHHHHHHHHHHHh
Confidence            899999999999985543

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=84.65  E-value=4.2  Score=34.95  Aligned_cols=46  Identities=15%  Similarity=0.293  Sum_probs=26.1

Q ss_pred             HHHHHhcCceEEEEEeCCCC---hh---hhhHhhCCCCCCCCCCeEEEEecchh
Q 040234           68 MLRVRLRRKKVLVVIDDAAH---PD---HLRRLVGEPDWFGPGSRIIITTRNEH  115 (377)
Q Consensus        68 ~l~~~l~~k~~LLVLDdv~~---~~---~~~~l~~~l~~~~~gs~IIvTTR~~~  115 (377)
                      .+-+.+..++=+++||+.-.   ..   .+..++..+.  ..+..||++|.+..
T Consensus       121 ~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~--~~~~tiii~sh~~~  172 (194)
T cd03213         121 SIALELVSNPSLLFLDEPTSGLDSSSALQVMSLLRRLA--DTGRTIICSIHQPS  172 (194)
T ss_pred             HHHHHHHcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHH--hCCCEEEEEecCch
Confidence            34455566777999999743   22   2222222222  23667888888753

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=84.63  E-value=0.66  Score=38.94  Aligned_cols=18  Identities=28%  Similarity=0.398  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.+++++.
T Consensus        10 ~~GsGKst~~~~la~~lg   27 (171)
T PRK03731         10 ARGCGKTTVGMALAQALG   27 (171)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999998763

>PRK07667 uridine kinase; Provisional

Probab=84.61  E-value=0.86  Score=39.27  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||||..+...+..
T Consensus        25 ~~gsGKStla~~L~~~l~~   43 (193)
T PRK07667         25 LSRSGKTTFVANLKENMKQ   43 (193)
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            4799999999999986654

>PRK05480 uridine/cytidine kinase; Provisional

Probab=84.61  E-value=0.61  Score=40.67  Aligned_cols=17  Identities=41%  Similarity=0.663  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+||||||+.++..+
T Consensus        14 ~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480         14 GSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            37999999999999866

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=84.59  E-value=3.8  Score=37.49  Aligned_cols=84  Identities=21%  Similarity=0.256  Sum_probs=52.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      +.|+|||+-++++++...     ..|+...++.+    ....++..+.......   ......+....+...+.+..-++
T Consensus       102 ~~g~gKt~a~~~y~~s~p-----~~~l~~~~p~~----~a~~~i~~i~~~~~~~---~~~~~~d~~~~~~~~l~~~~~~i  169 (297)
T COG2842         102 YAGLGKTQAAKNYAPSNP-----NALLIEADPSY----TALVLILIICAAAFGA---TDGTINDLTERLMIRLRDTVRLI  169 (297)
T ss_pred             cccchhHHHHHhhcccCc-----cceeecCChhh----HHHHHHHHHHHHHhcc---cchhHHHHHHHHHHHHccCccee
Confidence            479999999999998543     24444344444    4444444444443332   22344556667777778888899


Q ss_pred             EEeCCCC--hhhhhHhhC
Q 040234           81 VIDDAAH--PDHLRRLVG   96 (377)
Q Consensus        81 VLDdv~~--~~~~~~l~~   96 (377)
                      +.|+++.  ...++.+..
T Consensus       170 ivDEA~~L~~~ale~lr~  187 (297)
T COG2842         170 IVDEADRLPYRALEELRR  187 (297)
T ss_pred             eeehhhccChHHHHHHHH
Confidence            9999987  334444443

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=84.51  E-value=2.5  Score=40.14  Aligned_cols=21  Identities=38%  Similarity=0.411  Sum_probs=17.3

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      ++|.|||-||+.|+.+-...|
T Consensus       253 PPGTGKTlLAKAvATEc~tTF  273 (491)
T KOG0738|consen  253 PPGTGKTLLAKAVATECGTTF  273 (491)
T ss_pred             CCCCcHHHHHHHHHHhhcCeE
Confidence            489999999999998765443

>PRK05595 replicative DNA helicase; Provisional

Probab=84.49  E-value=3.1  Score=40.94  Aligned_cols=43  Identities=23%  Similarity=0.233  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHHHchh--ccccccceEEecchhhcccccCHHHHHHHHHHHHh
Q 040234            2 GGLGKTTLARVVYDLI--SHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLL   52 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~--~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~   52 (377)
                      +|+|||++|..++...  ++..+ ++++. + +.     +..++..+++....
T Consensus       210 pg~GKT~~al~ia~~~a~~~g~~-vl~fS-l-Em-----s~~~l~~R~~a~~~  254 (444)
T PRK05595        210 PSMGKTTFALNIAEYAALREGKS-VAIFS-L-EM-----SKEQLAYKLLCSEA  254 (444)
T ss_pred             CCCChHHHHHHHHHHHHHHcCCc-EEEEe-c-CC-----CHHHHHHHHHHHhc
Confidence            6999999999998743  33333 33332 2 11     56677777776654

>PF02223 Thymidylate_kin: Thymidylate kinase; InterPro: IPR018094 Thymidylate kinase (2

Probab=84.48  E-value=1.3  Score=37.71  Aligned_cols=22  Identities=27%  Similarity=0.359  Sum_probs=18.0

Q ss_pred             CCCCcHHHHHHHHHchhccccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFD   22 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~   22 (377)
                      +-|+||||+++.+++.++....
T Consensus         4 iDGsGKtT~~~~L~~~l~~~~~   25 (186)
T PF02223_consen    4 IDGSGKTTQIRLLAEALKEKGY   25 (186)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTE
T ss_pred             CCCCCHHHHHHHHHHHHHHcCC
Confidence            3699999999999997766543

7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process; PDB: 2PLR_B 1NMX_A 1NN0_A 2XX3_A 1NN3_A 1E9F_A 1E2Q_A 1E2D_A 1E9A_A 1E99_A ....

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=84.44  E-value=2.4  Score=44.60  Aligned_cols=19  Identities=21%  Similarity=0.347  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|.||||++..+....+.
T Consensus       376 ~aGTGKTtll~~i~~~~~~  394 (744)
T TIGR02768       376 RAGTGKSTMLKAAREAWEA  394 (744)
T ss_pred             cCCCCHHHHHHHHHHHHHh
Confidence            3799999999998875443

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>TIGR00665 DnaB replicative DNA helicase

Probab=84.36  E-value=3.2  Score=40.71  Aligned_cols=43  Identities=21%  Similarity=0.236  Sum_probs=26.7

Q ss_pred             CCCcHHHHHHHHHchhcccc-ccceEEecchhhcccccCHHHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEF-DGSSFLADVREKCDKEGSVISLQKQLLSDL   51 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f-~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l   51 (377)
                      +|+|||++|.+++.....+- ..++|+. +-.      +..++..+++...
T Consensus       204 pg~GKT~~~l~~a~~~a~~~g~~vl~~S-lEm------~~~~i~~R~~~~~  247 (434)
T TIGR00665       204 PSMGKTAFALNIAENAAIKEGKPVAFFS-LEM------SAEQLAMRMLSSE  247 (434)
T ss_pred             CCCChHHHHHHHHHHHHHhCCCeEEEEe-CcC------CHHHHHHHHHHHh
Confidence            79999999999987543221 2334443 211      5667777776654

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>cd02032 Bchl_like This family of proteins contains bchL and chlL

Probab=84.34  E-value=0.77  Score=41.71  Aligned_cols=19  Identities=26%  Similarity=0.490  Sum_probs=15.8

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus         9 GGvGKTT~a~nLA~~la~~   27 (267)
T cd02032           9 GGIGKSTTSSNLSVALAKR   27 (267)
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            8999999999988865544

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.

>TIGR00235 udk uridine kinase

Probab=84.34  E-value=0.62  Score=40.63  Aligned_cols=18  Identities=44%  Similarity=0.715  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+||||||+.++....
T Consensus        14 ~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235        14 GSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CCCCCHHHHHHHHHHHhc
Confidence            479999999999998544

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

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=84.22  E-value=1.9  Score=42.02  Aligned_cols=17  Identities=29%  Similarity=0.483  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||++.++....
T Consensus       164 sG~GKSTLL~~I~~~~~  180 (433)
T PRK07594        164 PGVGKSTLLAMLCNAPD  180 (433)
T ss_pred             CCCCccHHHHHhcCCCC
Confidence            69999999999987443

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=84.13  E-value=2.2  Score=41.77  Aligned_cols=16  Identities=19%  Similarity=0.283  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||+|+..+++..
T Consensus       150 sGvGKs~L~~~i~~~~  165 (466)
T TIGR01040       150 AGLPHNEIAAQICRQA  165 (466)
T ss_pred             CCCCHHHHHHHHHHhh
Confidence            6999999999998744

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=84.12  E-value=2.6  Score=42.05  Aligned_cols=19  Identities=26%  Similarity=0.211  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||++..++.....
T Consensus       358 PtGvGKTTtaakLAa~la~  376 (559)
T PRK12727        358 PTGAGKTTTIAKLAQRFAA  376 (559)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3799999999999875543

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=84.03  E-value=0.66  Score=39.25  Aligned_cols=18  Identities=28%  Similarity=0.313  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+|||||++.++..+.
T Consensus         9 ~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         9 PSGAGKDTLLDYARARLA   26 (179)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999988653

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.

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=83.81  E-value=0.82  Score=41.87  Aligned_cols=19  Identities=26%  Similarity=0.494  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+...
T Consensus        10 GGVGKTT~a~nLA~~La~~   28 (279)
T PRK13230         10 GGIGKSTTVCNIAAALAES   28 (279)
T ss_pred             CCCcHHHHHHHHHHHHHhC
Confidence            8999999999998855443

>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=83.81  E-value=0.76  Score=37.18  Aligned_cols=17  Identities=29%  Similarity=0.509  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ..|+||||+|+.++.+.
T Consensus         7 ~~GsGKst~a~~la~~~   23 (147)
T cd02020           7 PAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999865

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=83.77  E-value=0.66  Score=39.82  Aligned_cols=16  Identities=38%  Similarity=0.590  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+||||||+.++...
T Consensus         8 sgsGKTtla~~l~~~~   23 (187)
T cd02024           8 TNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CCCCHHHHHHHHHHHc
Confidence            6999999999999865

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=83.75  E-value=5.8  Score=38.04  Aligned_cols=17  Identities=29%  Similarity=0.151  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+||||++..++....
T Consensus       215 tGvGKTTt~akLA~~l~  231 (407)
T PRK12726        215 TGVGKTTTLVKLGWQLL  231 (407)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999987553

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

Probab=83.74  E-value=0.96  Score=36.55  Aligned_cols=39  Identities=15%  Similarity=0.202  Sum_probs=21.9

Q ss_pred             ceEEEEEeCCCCh--hhhhHhhCCCCCC-CCCCeEEEEecch
Q 040234           76 KKVLVVIDDAAHP--DHLRRLVGEPDWF-GPGSRIIITTRNE  114 (377)
Q Consensus        76 k~~LLVLDdv~~~--~~~~~l~~~l~~~-~~gs~IIvTTR~~  114 (377)
                      +.-.|+|+|++..  +....+...+... ....|+|.||+..
T Consensus        69 ~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~  110 (138)
T PF14532_consen   69 KGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQD  110 (138)
T ss_dssp             TTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-
T ss_pred             CCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCC
Confidence            4456789999873  2222222222111 4567999999854

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=83.51  E-value=18  Score=33.98  Aligned_cols=14  Identities=29%  Similarity=0.299  Sum_probs=12.8

Q ss_pred             CCCcHHHHHHHHHc
Q 040234            2 GGLGKTTLARVVYD   15 (377)
Q Consensus         2 gGiGKTtLA~~v~~   15 (377)
                      .|+||+++|+.+..
T Consensus        38 ~GtGK~~lA~~iH~   51 (326)
T PRK11608         38 RGTGKELIASRLHY   51 (326)
T ss_pred             CCCcHHHHHHHHHH
Confidence            69999999999886

>PRK13764 ATPase; Provisional

Probab=83.46  E-value=1.7  Score=44.19  Aligned_cols=77  Identities=12%  Similarity=0.141  Sum_probs=40.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+||||+++.+++.+..+-.....+.+..+..     ...    ...++    .....+..   ......|+.++=.++
T Consensus       266 TGSGKTTll~AL~~~i~~~~riV~TiEDp~El~-----~~~----~i~q~----~~~~~~~~---~~~~~lLR~rPD~Ii  329 (602)
T PRK13764        266 PGAGKSTFAQALAEFYADMGKIVKTMESPRDLQ-----VPP----EITQY----SKLEGSME---ETADILLLVRPDYTI  329 (602)
T ss_pred             CCCCHHHHHHHHHHHHhhCCCEEEEECCCcccc-----CCC----cceEE----eeccccHH---HHHHHHHhhCCCEEE
Confidence            699999999999986654322222333222211     000    00010    00001111   222233677788999


Q ss_pred             EeCCCChhhhhHh
Q 040234           82 IDDAAHPDHLRRL   94 (377)
Q Consensus        82 LDdv~~~~~~~~l   94 (377)
                      +|.+.+.+.++.+
T Consensus       330 vGEiRd~Et~~~~  342 (602)
T PRK13764        330 YDEMRKTEDFKIF  342 (602)
T ss_pred             ECCCCCHHHHHHH
Confidence            9999998887754

>cd03110 Fer4_NifH_child This protein family's function is unkown

Probab=83.46  E-value=0.7  Score=39.10  Aligned_cols=16  Identities=44%  Similarity=0.723  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      ||+||||+|..++...
T Consensus         9 gG~GKSt~a~nLA~~l   24 (179)
T cd03110           9 GGTGKTTVTAALAALL   24 (179)
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            8999999999999866

It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=83.42  E-value=0.82  Score=37.01  Aligned_cols=20  Identities=25%  Similarity=0.446  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      +.|+|||||++.+.+....+
T Consensus         7 psGsGKstl~~~L~~~~~~~   26 (137)
T cd00071           7 PSGVGKSTLLKRLLEEFDPN   26 (137)
T ss_pred             CCCCCHHHHHHHHHhcCCcc
Confidence            47999999999999865444

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.

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=83.42  E-value=0.79  Score=38.54  Aligned_cols=21  Identities=29%  Similarity=0.518  Sum_probs=18.0

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      |.|+||||+.+.+++++.-+|
T Consensus        10 ~mGaGKSTIGr~LAk~L~~~F   30 (172)
T COG0703          10 FMGAGKSTIGRALAKALNLPF   30 (172)
T ss_pred             CCCCCHhHHHHHHHHHcCCCc
Confidence            579999999999999776665

>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=83.41  E-value=0.69  Score=43.03  Aligned_cols=19  Identities=37%  Similarity=0.576  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|...+-...++
T Consensus        10 GGVGKTT~aaA~A~~~A~~   28 (305)
T PF02374_consen   10 GGVGKTTVAAALALALARR   28 (305)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHHHHHhhC
Confidence            8999999998888754443

...

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=83.40  E-value=0.69  Score=37.26  Aligned_cols=16  Identities=38%  Similarity=0.401  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      -|+|||||++.+++.+
T Consensus        31 lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150        31 LGAGKTTLVQGLLQGL   46 (133)
T ss_pred             CCCCHHHHHHHHHHHc
Confidence            4899999999999854

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.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=83.40  E-value=0.78  Score=38.76  Aligned_cols=18  Identities=28%  Similarity=0.416  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||||+.+++...
T Consensus        12 ~~GaGKStl~~~La~~l~   29 (172)
T PRK05057         12 PMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCCcCHHHHHHHHHHHcC
Confidence            579999999999998653

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=83.39  E-value=0.77  Score=43.63  Aligned_cols=48  Identities=21%  Similarity=0.356  Sum_probs=28.8

Q ss_pred             hhHHHHHHHhcCceEEEEEeCCCChh-----hhhHhhCCCCCCCCCCeEEEEecch
Q 040234           64 DGINMLRVRLRRKKVLVVIDDAAHPD-----HLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv~~~~-----~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      +.+..+-..+....+||.+|...-.+     .++.|...+.  ..| .|||.|-++
T Consensus       181 Dpl~~vA~eIa~ea~lLCFDEfQVTDVADAmiL~rLf~~Lf--~~G-vVlvATSNR  233 (467)
T KOG2383|consen  181 DPLPVVADEIAEEAILLCFDEFQVTDVADAMILKRLFEHLF--KNG-VVLVATSNR  233 (467)
T ss_pred             CccHHHHHHHhhhceeeeechhhhhhHHHHHHHHHHHHHHH--hCC-eEEEEeCCC
Confidence            44556666777789999999964322     3455555543  235 455555443

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=83.31  E-value=3.7  Score=38.48  Aligned_cols=32  Identities=19%  Similarity=0.382  Sum_probs=25.4

Q ss_pred             hhHHHHHHHhcCceEEEEEeCCCChhhhhHhh
Q 040234           64 DGINMLRVRLRRKKVLVVIDDAAHPDHLRRLV   95 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv~~~~~~~~l~   95 (377)
                      ...+.++..|+.++=.||+..+.+.+.+..+.
T Consensus       207 ~~~~ll~~aLR~~PD~IivGEiR~~Ea~~~l~  238 (319)
T PRK13894        207 NMTALLKTTLRMRPDRILVGEVRGPEALDLLM  238 (319)
T ss_pred             CHHHHHHHHhcCCCCEEEEeccCCHHHHHHHH
Confidence            45677888888888889999999988776543

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=83.25  E-value=0.73  Score=38.21  Aligned_cols=18  Identities=39%  Similarity=0.577  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+++...
T Consensus         8 ~pGsG~TTva~~lAe~~g   25 (179)
T COG1102           8 LPGSGKTTVARELAEHLG   25 (179)
T ss_pred             CCCCChhHHHHHHHHHhC
Confidence            489999999999998553

>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional

Probab=83.24  E-value=0.91  Score=41.31  Aligned_cols=28  Identities=18%  Similarity=0.279  Sum_probs=19.0

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecc
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADV   30 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~   30 (377)
                      ||+||||+|..++..+..+ ..++.+.|.
T Consensus        11 GGVGKTT~~~nLA~~la~~-G~kVLliD~   38 (270)
T PRK13185         11 GGIGKSTTSSNLSAAFAKL-GKKVLQIGC   38 (270)
T ss_pred             CCCCHHHHHHHHHHHHHHC-CCeEEEEec
Confidence            8999999999998855433 223444434

>PRK10646 ADP-binding protein; Provisional

Probab=83.23  E-value=0.7  Score=38.18  Aligned_cols=15  Identities=40%  Similarity=0.607  Sum_probs=13.5

Q ss_pred             CCcHHHHHHHHHchh
Q 040234            3 GLGKTTLARVVYDLI   17 (377)
Q Consensus         3 GiGKTtLA~~v~~~~   17 (377)
                      |+||||+++.+++.+
T Consensus        38 GaGKTtf~rgl~~~L   52 (153)
T PRK10646         38 GAGKTTFSRGFLQAL   52 (153)
T ss_pred             CCCHHHHHHHHHHHc
Confidence            899999999999844

>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]

Probab=83.18  E-value=1.7  Score=37.98  Aligned_cols=28  Identities=21%  Similarity=0.214  Sum_probs=21.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +-|+||||+++.+++.++.+.-.+++..
T Consensus        11 iDGaGKTT~~~~L~~~l~~~g~~v~~tr   38 (208)
T COG0125          11 IDGAGKTTQAELLKERLEERGIKVVLTR   38 (208)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3599999999999998877755555543

>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ

Probab=83.03  E-value=0.98  Score=40.30  Aligned_cols=19  Identities=37%  Similarity=0.504  Sum_probs=16.0

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++.....+
T Consensus        11 GGvGKTt~a~nla~~la~~   29 (246)
T TIGR03371        11 GGVGKTTLTANLASALKLL   29 (246)
T ss_pred             CCccHHHHHHHHHHHHHhC
Confidence            8999999999999866543

Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria

Probab=83.01  E-value=7.9  Score=33.80  Aligned_cols=14  Identities=29%  Similarity=0.553  Sum_probs=12.8

Q ss_pred             CCCcHHHHHHHHHc
Q 040234            2 GGLGKTTLARVVYD   15 (377)
Q Consensus         2 gGiGKTtLA~~v~~   15 (377)
                      .|+|||+++..+..
T Consensus         9 tGsGKSs~~N~ilg   22 (212)
T PF04548_consen    9 TGSGKSSLGNSILG   22 (212)
T ss_dssp             TTSSHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHhc
Confidence            69999999999986

The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....

>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]

Probab=82.91  E-value=0.84  Score=37.25  Aligned_cols=20  Identities=25%  Similarity=0.527  Sum_probs=17.4

Q ss_pred             CCCcHHHHHHHHHchhcccc
Q 040234            2 GGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f   21 (377)
                      +|+||||++..+++++.-.|
T Consensus         4 sG~GKStvg~~lA~~lg~~f   23 (161)
T COG3265           4 SGSGKSTVGSALAERLGAKF   23 (161)
T ss_pred             CccCHHHHHHHHHHHcCCce
Confidence            69999999999999887554

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=82.86  E-value=3.5  Score=40.05  Aligned_cols=17  Identities=29%  Similarity=0.450  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||++.++...+
T Consensus       146 sG~GKTtLl~~i~~~~~  162 (413)
T TIGR03497       146 SGVGKSTLLGMIARNAK  162 (413)
T ss_pred             CCCCHHHHHHHHhCCCC
Confidence            69999999998887543

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.

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

Probab=82.85  E-value=4.4  Score=39.89  Aligned_cols=24  Identities=25%  Similarity=0.306  Sum_probs=19.7

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .|.|||.+|..++.+++..   .++++
T Consensus        64 TGaGKT~va~~~~~~~~~~---~Lvlv   87 (442)
T COG1061          64 TGAGKTVVAAEAIAELKRS---TLVLV   87 (442)
T ss_pred             CCCCHHHHHHHHHHHhcCC---EEEEE
Confidence            6999999999999987776   55555

>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]

Probab=82.83  E-value=1.5  Score=41.31  Aligned_cols=95  Identities=22%  Similarity=0.234  Sum_probs=52.7

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc-------ccCcc--------chhhhH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA-------DNNIR--------NVYDGI   66 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~-------~~~~~--------~~~~~~   66 (377)
                      +|+|||.|.+++.+.+.........+.-+++..+   .-.++..++.+.-....       ..++.        .--..+
T Consensus       156 AGVGKTVl~~ELI~Nia~~h~g~SVFaGvGERtR---EGndLy~Em~es~vl~ktalv~gQMNEpPGaR~RValtGlT~A  232 (468)
T COG0055         156 AGVGKTVLIQELINNIAKEHGGYSVFAGVGERTR---EGNDLYHEMKESGVLDKTALVFGQMNEPPGARMRVALTGLTMA  232 (468)
T ss_pred             CCccceeeHHHHHHHHHHHcCCeEEEEecccccc---chHHHHHHHHhcCCCCceeEEEeecCCCCcceeeehhhhhhHH
Confidence            6999999999999977766665544454666543   22344444444311000       00110        111223


Q ss_pred             HHHHHHhcCceEEEEEeCCCC----hhhhhHhhCCCCC
Q 040234           67 NMLRVRLRRKKVLVVIDDAAH----PDHLRRLVGEPDW  100 (377)
Q Consensus        67 ~~l~~~l~~k~~LLVLDdv~~----~~~~~~l~~~l~~  100 (377)
                      +.+|.. .++..||.+||+-.    ..++..++...|.
T Consensus       233 EyfRD~-~gqdVLlFIDNIfRftQAGsEVSalLGr~PS  269 (468)
T COG0055         233 EYFRDE-EGQDVLLFIDNIFRFTQAGSEVSALLGRMPS  269 (468)
T ss_pred             HHhhcc-cCCeEEEEehhhhHHhhcchHHHHHhccCcc
Confidence            334432 46799999999854    3445666655543

>PRK09099 type III secretion system ATPase; Provisional

Probab=82.78  E-value=3.1  Score=40.68  Aligned_cols=17  Identities=29%  Similarity=0.382  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|+|||||++.++....
T Consensus       172 sG~GKTtLl~~ia~~~~  188 (441)
T PRK09099        172 AGVGKSTLMGMFARGTQ  188 (441)
T ss_pred             CCCCHHHHHHHHhCCCC
Confidence            69999999999987443

>COG1485 Predicted ATPase [General function prediction only]

Probab=82.78  E-value=2.9  Score=39.20  Aligned_cols=90  Identities=19%  Similarity=0.223  Sum_probs=46.4

Q ss_pred             CCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEEE
Q 040234            3 GLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVVI   82 (377)
Q Consensus         3 GiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLVL   82 (377)
                      |.|||-|.-..|+.+..+=..++             ...+.+..+-+.+....     ...+....+-..+...-.+|.+
T Consensus        75 GrGKT~LMD~Fy~~lp~~~k~R~-------------HFh~FM~~vH~~l~~l~-----g~~dpl~~iA~~~~~~~~vLCf  136 (367)
T COG1485          75 GRGKTMLMDLFYESLPGERKRRL-------------HFHRFMARVHQRLHTLQ-----GQTDPLPPIADELAAETRVLCF  136 (367)
T ss_pred             CccHHHHHHHHHhhCCccccccc-------------cHHHHHHHHHHHHHHHc-----CCCCccHHHHHHHHhcCCEEEe
Confidence            78999999999984432211111             11122222222222211     1113455566667777789999


Q ss_pred             eCC--CChh---hhhHhhCCCCCCCCCCeEEEEec
Q 040234           83 DDA--AHPD---HLRRLVGEPDWFGPGSRIIITTR  112 (377)
Q Consensus        83 Ddv--~~~~---~~~~l~~~l~~~~~gs~IIvTTR  112 (377)
                      |..  .|..   .+..|...+-  ..|..++.||.
T Consensus       137 DEF~VtDI~DAMiL~rL~~~Lf--~~GV~lvaTSN  169 (367)
T COG1485         137 DEFEVTDIADAMILGRLLEALF--ARGVVLVATSN  169 (367)
T ss_pred             eeeeecChHHHHHHHHHHHHHH--HCCcEEEEeCC
Confidence            984  4432   3444544443  34655555553

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=82.72  E-value=0.65  Score=39.74  Aligned_cols=52  Identities=17%  Similarity=0.128  Sum_probs=29.6

Q ss_pred             HHHHHhcC--ceEEEEEeCCCC---hh---h-hhHhhCCCCCCCCCCeEEEEecchhHHhhC
Q 040234           68 MLRVRLRR--KKVLVVIDDAAH---PD---H-LRRLVGEPDWFGPGSRIIITTRNEHLLKLH  120 (377)
Q Consensus        68 ~l~~~l~~--k~~LLVLDdv~~---~~---~-~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~  120 (377)
                      .+...+..  ++-|+++|..-.   ..   . ...+...+.. ..++.+|++|....+....
T Consensus        68 ~l~~~l~~~~~~~llllDEp~~g~d~~~~~~~~~~~l~~l~~-~~~~~iii~TH~~~l~~~~  128 (185)
T smart00534       68 ETANILKNATENSLVLLDELGRGTSTYDGVAIAAAVLEYLLE-KIGALTLFATHYHELTKLA  128 (185)
T ss_pred             HHHHHHHhCCCCeEEEEecCCCCCCHHHHHHHHHHHHHHHHh-cCCCeEEEEecHHHHHHHh
Confidence            34444443  788999999743   11   1 1222222211 1367899999988765543

>PRK14532 adenylate kinase; Provisional

Probab=82.71  E-value=0.82  Score=39.06  Aligned_cols=17  Identities=24%  Similarity=0.124  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         8 ~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          8 PPAAGKGTQAKRLVEER   24 (188)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            48999999999999754

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=82.67  E-value=0.79  Score=38.95  Aligned_cols=17  Identities=24%  Similarity=0.200  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.+++..
T Consensus        11 ~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360        11 GPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999754

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=82.65  E-value=3  Score=41.53  Aligned_cols=31  Identities=13%  Similarity=0.142  Sum_probs=25.1

Q ss_pred             hhHHHHHHHhcCceEEEEEeCCCChhhhhHh
Q 040234           64 DGINMLRVRLRRKKVLVVIDDAAHPDHLRRL   94 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv~~~~~~~~l   94 (377)
                      ...+.++..|+..+=.+++.++.+.+.....
T Consensus       299 ~f~~~lr~~LR~dPDvI~vGEiRd~eta~~a  329 (486)
T TIGR02533       299 TFAAGLRAILRQDPDIIMVGEIRDLETAQIA  329 (486)
T ss_pred             cHHHHHHHHHhcCCCEEEEeCCCCHHHHHHH
Confidence            4567888899999999999999998765443

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>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=82.65  E-value=1.9  Score=36.84  Aligned_cols=19  Identities=32%  Similarity=0.536  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      +.|+||||+++.+++.+..
T Consensus         8 ~~GsGKtT~~~~L~~~l~~   26 (200)
T cd01672           8 IDGAGKTTLIELLAERLEA   26 (200)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3699999999999987643

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=82.54  E-value=0.67  Score=40.97  Aligned_cols=44  Identities=14%  Similarity=0.109  Sum_probs=27.1

Q ss_pred             CceEEEEEeCCCC----hh--h-hhHhhCCCCCCCCCCeEEEEecchhHHhh
Q 040234           75 RKKVLVVIDDAAH----PD--H-LRRLVGEPDWFGPGSRIIITTRNEHLLKL  119 (377)
Q Consensus        75 ~k~~LLVLDdv~~----~~--~-~~~l~~~l~~~~~gs~IIvTTR~~~v~~~  119 (377)
                      +++-|++||....    .+  . ...+...+.. ..++.+|++|....++..
T Consensus       109 ~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~-~~~~~~i~~TH~~~l~~~  159 (222)
T cd03287         109 TSRSLVILDELGRGTSTHDGIAIAYATLHYLLE-EKKCLVLFVTHYPSLGEI  159 (222)
T ss_pred             CCCeEEEEccCCCCCChhhHHHHHHHHHHHHHh-ccCCeEEEEcccHHHHHH
Confidence            5689999999632    11  1 1223333322 247889999999877554

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

>PRK04196 V-type ATP synthase subunit B; Provisional

Probab=82.38  E-value=3.9  Score=40.28  Aligned_cols=45  Identities=13%  Similarity=0.070  Sum_probs=25.2

Q ss_pred             CCCcHHHHHHHHHchhcc---ccccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISH---EFDGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~---~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      .|+|||+|+..+++....   +-+..+-+..+++..+   .+.+++..+..
T Consensus       152 ~G~GKs~L~~~ia~~~~~d~~~~~~v~V~~~iGeRgr---Ev~e~~~~~~~  199 (460)
T PRK04196        152 SGLPHNELAAQIARQAKVLGEEENFAVVFAAMGITFE---EANFFMEDFEE  199 (460)
T ss_pred             CCCCccHHHHHHHHhhhhccCCCceEEEEEEeccccH---HHHHHHHHHHh
Confidence            699999999999984321   1112333333555431   44555555544

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=82.37  E-value=0.81  Score=37.41  Aligned_cols=16  Identities=38%  Similarity=0.457  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+||||||.+++...
T Consensus        16 PG~GKstl~~~lae~~   31 (176)
T KOG3347|consen   16 PGTGKSTLAERLAEKT   31 (176)
T ss_pred             CCCCchhHHHHHHHHh
Confidence            7999999999999743

>PRK09165 replicative DNA helicase; Provisional

Probab=82.35  E-value=4.1  Score=40.69  Aligned_cols=17  Identities=29%  Similarity=0.241  Sum_probs=14.3

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+|||+||..++..+.
T Consensus       226 pg~GKT~~al~ia~~~a  242 (497)
T PRK09165        226 PSMGKTALATNIAFNAA  242 (497)
T ss_pred             CCCChHHHHHHHHHHHH
Confidence            79999999999887553

>COG3910 Predicted ATPase [General function prediction only]

Probab=82.27  E-value=7  Score=33.51  Aligned_cols=63  Identities=21%  Similarity=0.396  Sum_probs=36.1

Q ss_pred             hhhHHHHHHHhcCceEEEEEeCCCCh----hhhhHhh--CCCCCCCCCCeEEEEecchhHHhhCCCCCeeecC
Q 040234           63 YDGINMLRVRLRRKKVLVVIDDAAHP----DHLRRLV--GEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLE  129 (377)
Q Consensus        63 ~~~~~~l~~~l~~k~~LLVLDdv~~~----~~~~~l~--~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~~~l~  129 (377)
                      +.....+.+++.++- +-|||.-+..    .|++-+.  ..+.  ..|+.||+.|.++-+.. ++.+..++..
T Consensus       134 Esf~~i~~~rf~~~G-iYiLDEPEa~LSp~RQlella~l~~la--~sGaQ~IiATHSPiLlA-iP~A~I~~~~  202 (233)
T COG3910         134 ESFLAIFHNRFNGQG-IYILDEPEAALSPSRQLELLAILRDLA--DSGAQIIIATHSPILLA-IPGAEIYEIS  202 (233)
T ss_pred             hHHHHHHHHHhccCc-eEEecCccccCCHHHHHHHHHHHHHHH--hcCCeEEEEecChhhee-CCCcEEEEEe
Confidence            344555666666554 6788987642    2332221  1111  45789999999985433 5556665543

>TIGR01287 nifH nitrogenase iron protein

Probab=82.26  E-value=1  Score=41.10  Aligned_cols=18  Identities=28%  Similarity=0.595  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+..
T Consensus         9 GGVGKTT~a~nLA~~La~   26 (275)
T TIGR01287         9 GGIGKSTTTQNIAAALAE   26 (275)
T ss_pred             CcCcHHHHHHHHHHHHHH
Confidence            899999999999985543

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=82.22  E-value=2.6  Score=44.65  Aligned_cols=73  Identities=18%  Similarity=0.241  Sum_probs=44.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceE-E
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKV-L   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~-L   79 (377)
                      +.|+|||.||+.++.-+-+..+.-+-+. ++          +.+.  ..++.+.++.-  --.+....+.+.++.++| +
T Consensus       599 pdgvGKt~lAkaLA~~~Fgse~~~IriD-ms----------e~~e--vskligsp~gy--vG~e~gg~LteavrrrP~sV  663 (898)
T KOG1051|consen  599 PDGVGKTELAKALAEYVFGSEENFIRLD-MS----------EFQE--VSKLIGSPPGY--VGKEEGGQLTEAVKRRPYSV  663 (898)
T ss_pred             CCchhHHHHHHHHHHHHcCCccceEEec-hh----------hhhh--hhhccCCCccc--ccchhHHHHHHHHhcCCceE
Confidence            3699999999999997766655545443 33          3333  23322221111  112234467777888876 6


Q ss_pred             EEEeCCCCh
Q 040234           80 VVIDDAAHP   88 (377)
Q Consensus        80 LVLDdv~~~   88 (377)
                      ++||||+..
T Consensus       664 VLfdeIEkA  672 (898)
T KOG1051|consen  664 VLFEEIEKA  672 (898)
T ss_pred             EEEechhhc
Confidence            778999764

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=82.22  E-value=5.4  Score=40.17  Aligned_cols=15  Identities=33%  Similarity=0.428  Sum_probs=13.3

Q ss_pred             CCCCcHHHHHHHHHc
Q 040234            1 MGGLGKTTLARVVYD   15 (377)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (377)
                      ..|+|||||++.+..
T Consensus       369 ~SGsGKSTLl~lL~g  383 (529)
T TIGR02868       369 PSGSGKSTLLMLLTG  383 (529)
T ss_pred             CCCCCHHHHHHHHhc
Confidence            369999999999986

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.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=82.20  E-value=18  Score=36.30  Aligned_cols=16  Identities=31%  Similarity=0.466  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||++|+.+.+.-
T Consensus       219 ~GtGK~~~A~~ih~~s  234 (509)
T PRK05022        219 TGVGKELVARAIHAAS  234 (509)
T ss_pred             CCccHHHHHHHHHHhC
Confidence            6999999999999843

>PRK14529 adenylate kinase; Provisional

Probab=82.14  E-value=4.4  Score=35.80  Aligned_cols=84  Identities=14%  Similarity=0.143  Sum_probs=42.5

Q ss_pred             CCCCcHHHHHHHHHchhccc-cccceEEe-cchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCc-e
Q 040234            1 MGGLGKTTLARVVYDLISHE-FDGSSFLA-DVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRK-K   77 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-f~~~~w~~-~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k-~   77 (377)
                      ++|+||||+|+.++.+..-. .+.+-.+. .+....    ......+.++.+      ......+-....+.+.+.+. .
T Consensus         8 ~PGsGK~T~a~~La~~~~~~~is~gdllr~~i~~~t----~lg~~i~~~i~~------G~lvpdei~~~lv~~~l~~~~~   77 (223)
T PRK14529          8 PNGSGKGTQGALVKKKYDLAHIESGAIFREHIGGGT----ELGKKAKEYIDR------GDLVPDDITIPMILETLKQDGK   77 (223)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCcccchhhhhhccCCC----hHHHHHHHHHhc------cCcchHHHHHHHHHHHHhccCC
Confidence            47999999999999865322 22222211 111111    233333333322      12223344556666666432 4


Q ss_pred             EEEEEeCCC-ChhhhhHh
Q 040234           78 VLVVIDDAA-HPDHLRRL   94 (377)
Q Consensus        78 ~LLVLDdv~-~~~~~~~l   94 (377)
                      --+|||..- +.+|.+.|
T Consensus        78 ~g~iLDGfPRt~~Qa~~l   95 (223)
T PRK14529         78 NGWLLDGFPRNKVQAEKL   95 (223)
T ss_pred             CcEEEeCCCCCHHHHHHH
Confidence            468999974 44554443

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=82.13  E-value=1.3  Score=41.37  Aligned_cols=22  Identities=32%  Similarity=0.391  Sum_probs=17.0

Q ss_pred             CCCCcHHHHHHHHHchhccccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFD   22 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~   22 (377)
                      .||+||||+|...+-...+...
T Consensus        10 KGGVGKTT~aaA~A~~lA~~g~   31 (322)
T COG0003          10 KGGVGKTTIAAATAVKLAESGK   31 (322)
T ss_pred             CCcccHHHHHHHHHHHHHHcCC
Confidence            3999999999998776555543

>TIGR01968 minD_bact septum site-determining protein MinD

Probab=82.09  E-value=1.1  Score=40.36  Aligned_cols=18  Identities=33%  Similarity=0.508  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+..
T Consensus        11 GGvGKTt~a~~lA~~la~   28 (261)
T TIGR01968        11 GGVGKTTTTANLGTALAR   28 (261)
T ss_pred             CCccHHHHHHHHHHHHHH
Confidence            899999999999985543

This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.

>PRK13235 nifH nitrogenase reductase; Reviewed

Probab=82.07  E-value=1.1  Score=40.96  Aligned_cols=18  Identities=28%  Similarity=0.499  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+.+
T Consensus        10 GGVGKTT~~~nLA~~La~   27 (274)
T PRK13235         10 GGIGKSTTTQNTVAGLAE   27 (274)
T ss_pred             CCccHHHHHHHHHHHHHH
Confidence            899999999998885543

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=81.99  E-value=1.1  Score=40.94  Aligned_cols=18  Identities=33%  Similarity=0.584  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+.+
T Consensus        10 GGVGKTT~a~nLA~~La~   27 (273)
T PRK13232         10 GGIGKSTTTQNLTAALST   27 (273)
T ss_pred             CCCcHHHHHHHHHHHHHh
Confidence            899999999999885543

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=81.94  E-value=4.8  Score=41.05  Aligned_cols=105  Identities=21%  Similarity=0.250  Sum_probs=52.5

Q ss_pred             CCCcHHH-HHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccC---------ccchhhh-----
Q 040234            2 GGLGKTT-LARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNN---------IRNVYDG-----   65 (377)
Q Consensus         2 gGiGKTt-LA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~---------~~~~~~~-----   65 (377)
                      .|+|||| ||+.++..   -|. .++.-  +.+..  -+....+.+.+...+++.....         ..+.+..     
T Consensus       380 TGSGKTTQl~QyL~ed---GY~~~GmIG--cTQPR--RvAAiSVAkrVa~EM~~~lG~~VGYsIRFEdvT~~~T~IkymT  452 (1042)
T KOG0924|consen  380 TGSGKTTQLAQYLYED---GYADNGMIG--CTQPR--RVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSEDTKIKYMT  452 (1042)
T ss_pred             CCCCchhhhHHHHHhc---ccccCCeee--ecCch--HHHHHHHHHHHHHHhCCccccccceEEEeeecCCCceeEEEec
Confidence            5999998 77777762   222 23322  22321  1155566677777764332211         0111110     


Q ss_pred             -HHHHHHHhcC----ceEEEEEeCCCC----hhhhhHhhCCCCCCCCCCeEEEEecc
Q 040234           66 -INMLRVRLRR----KKVLVVIDDAAH----PDHLRRLVGEPDWFGPGSRIIITTRN  113 (377)
Q Consensus        66 -~~~l~~~l~~----k~~LLVLDdv~~----~~~~~~l~~~l~~~~~gs~IIvTTR~  113 (377)
                       --.||+.|.+    |=-.+|+|.+-.    .+.+--|+.........-|+||||-.
T Consensus       453 DGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~larRrdlKliVtSAT  509 (1042)
T KOG0924|consen  453 DGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARRRDLKLIVTSAT  509 (1042)
T ss_pred             cchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHHhhccceEEEeecc
Confidence             1235555554    445889999854    23222222211111446799999865

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=81.90  E-value=4.6  Score=39.44  Aligned_cols=43  Identities=28%  Similarity=0.317  Sum_probs=27.2

Q ss_pred             CCCcHHHHHHHHHchhc--cccccceEEecchhhcccccCHHHHHHHHHHHHh
Q 040234            2 GGLGKTTLARVVYDLIS--HEFDGSSFLADVREKCDKEGSVISLQKQLLSDLL   52 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~--~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~   52 (377)
                      +|+|||++|..++....  ...+ ++|+. + +.     +..++..+++....
T Consensus       203 pg~GKT~~al~ia~~~a~~~g~~-v~~fS-l-Em-----~~~~l~~Rl~~~~~  247 (421)
T TIGR03600       203 PSMGKTTLALNIAENVALREGKP-VLFFS-L-EM-----SAEQLGERLLASKS  247 (421)
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCc-EEEEE-C-CC-----CHHHHHHHHHHHHc
Confidence            79999999999996443  3333 33433 2 11     56677777776543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=81.86  E-value=0.89  Score=39.22  Aligned_cols=17  Identities=35%  Similarity=0.495  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+||||||+.+...+
T Consensus         7 ~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           7 GSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            37999999999998865

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.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=81.85  E-value=0.92  Score=39.28  Aligned_cols=17  Identities=24%  Similarity=0.417  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        11 ~~G~GKst~a~~l~~~~   27 (197)
T PRK12339         11 IPGVGKTSISGYIARHR   27 (197)
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            47999999999999864

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=81.83  E-value=1.1  Score=39.60  Aligned_cols=45  Identities=13%  Similarity=0.083  Sum_probs=25.6

Q ss_pred             cCceEEEEEeCC---CChhh----hhHhhCCCCCCCCCCeEEEEecchhHHhh
Q 040234           74 RRKKVLVVIDDA---AHPDH----LRRLVGEPDWFGPGSRIIITTRNEHLLKL  119 (377)
Q Consensus        74 ~~k~~LLVLDdv---~~~~~----~~~l~~~l~~~~~gs~IIvTTR~~~v~~~  119 (377)
                      ...+-|++||..   -+..+    ...+...+.. ..++.+|+||....+...
T Consensus       107 ~~~~sLvLLDEp~~gT~~lD~~~~~~~il~~l~~-~~~~~vlisTH~~el~~~  158 (222)
T cd03285         107 ATENSLIIIDELGRGTSTYDGFGLAWAIAEYIAT-QIKCFCLFATHFHELTAL  158 (222)
T ss_pred             CCCCeEEEEecCcCCCChHHHHHHHHHHHHHHHh-cCCCeEEEEechHHHHHH
Confidence            356789999998   33211    1111122211 246789999987666543

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

>PRK06761 hypothetical protein; Provisional

Probab=81.72  E-value=0.98  Score=41.39  Aligned_cols=20  Identities=35%  Similarity=0.733  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+||||+|+.+++++...
T Consensus        11 ~~GsGKTTla~~L~~~L~~~   30 (282)
T PRK06761         11 LPGFGKSTTAKMLNDILSQN   30 (282)
T ss_pred             CCCCCHHHHHHHHHHhcCcC
Confidence            47999999999999976543

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=81.68  E-value=5.2  Score=40.23  Aligned_cols=48  Identities=19%  Similarity=0.346  Sum_probs=32.8

Q ss_pred             HHHHhcCceEEEEEeCCCC------hhhhhHhhCCCCCCCCCCeEEEEecchhHHhhCC
Q 040234           69 LRVRLRRKKVLVVIDDAAH------PDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHP  121 (377)
Q Consensus        69 l~~~l~~k~~LLVLDdv~~------~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~  121 (377)
                      |.+.|-.++=+|+||.--+      ...++.++..    -+| .|||.|.++.....+.
T Consensus       164 LA~aL~~~pDlLLLDEPTNHLD~~~i~WLe~~L~~----~~g-tviiVSHDR~FLd~V~  217 (530)
T COG0488         164 LARALLEEPDLLLLDEPTNHLDLESIEWLEDYLKR----YPG-TVIVVSHDRYFLDNVA  217 (530)
T ss_pred             HHHHHhcCCCEEEEcCCCcccCHHHHHHHHHHHHh----CCC-cEEEEeCCHHHHHHHh
Confidence            4455566788999999654      2334555544    445 7999999998776653

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=81.46  E-value=0.84  Score=39.90  Aligned_cols=18  Identities=28%  Similarity=0.586  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||++..++..+.+
T Consensus         9 GGvGKTt~~~nLA~~la~   26 (212)
T cd02117           9 GGIGKSTTSQNLSAALAE   26 (212)
T ss_pred             CcCcHHHHHHHHHHHHHH
Confidence            899999999988885544

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>PRK14530 adenylate kinase; Provisional

Probab=81.28  E-value=1  Score=39.49  Aligned_cols=17  Identities=24%  Similarity=0.235  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        11 ~pGsGKsT~~~~La~~~   27 (215)
T PRK14530         11 APGAGKGTQSSNLAEEF   27 (215)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999855

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=81.19  E-value=3.7  Score=40.22  Aligned_cols=16  Identities=31%  Similarity=0.480  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||||++.+....
T Consensus       172 sG~GKStLl~~I~~~~  187 (440)
T TIGR01026       172 SGVGKSTLLGMIARNT  187 (440)
T ss_pred             CCCCHHHHHHHHhCCC
Confidence            6999999999988754

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.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=81.13  E-value=2.3  Score=37.13  Aligned_cols=17  Identities=29%  Similarity=0.301  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|.|||+++..+...+
T Consensus        25 pPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   25 PPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHh
Confidence            47999998887777755

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=80.93  E-value=1.1  Score=38.40  Aligned_cols=17  Identities=24%  Similarity=0.239  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+|||||++.++...
T Consensus        10 ~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078         10 PSGSGKDSLLAALRQRE   26 (186)
T ss_pred             CCCCCHHHHHHHHhccC
Confidence            47999999999998754

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=80.87  E-value=5.1  Score=39.30  Aligned_cols=15  Identities=27%  Similarity=0.521  Sum_probs=13.1

Q ss_pred             CCCcHHHHHHHHHch
Q 040234            2 GGLGKTTLARVVYDL   16 (377)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (377)
                      .|+|||||++.++..
T Consensus       177 sG~GKSTLl~~I~g~  191 (451)
T PRK05688        177 TGVGKSVLLGMMTRF  191 (451)
T ss_pred             CCCCHHHHHHHHhCC
Confidence            699999999998874

>COG0802 Predicted ATPase or kinase [General function prediction only]

Probab=80.81  E-value=0.95  Score=37.01  Aligned_cols=15  Identities=47%  Similarity=0.567  Sum_probs=13.3

Q ss_pred             CCcHHHHHHHHHchh
Q 040234            3 GLGKTTLARVVYDLI   17 (377)
Q Consensus         3 GiGKTtLA~~v~~~~   17 (377)
                      |.|||||++.+++-+
T Consensus        35 GAGKTtf~rgi~~~L   49 (149)
T COG0802          35 GAGKTTLVRGIAKGL   49 (149)
T ss_pred             cCChHHHHHHHHHHc
Confidence            899999999999843

>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase

Probab=80.70  E-value=1.3  Score=38.53  Aligned_cols=18  Identities=22%  Similarity=0.124  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++.....
T Consensus        45 gG~GkSt~a~nLA~~la~   62 (207)
T TIGR03018        45 PGEGKSFTAINLAISLAQ   62 (207)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            899999999999986543

Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=80.63  E-value=13  Score=37.01  Aligned_cols=17  Identities=47%  Similarity=0.417  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|.|||-||+.++.+-
T Consensus       345 PPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  345 PPGTGKTLLARAVAGEA  361 (752)
T ss_pred             CCCCchhHHHHHhhccc
Confidence            47999999999999743

>PRK04182 cytidylate kinase; Provisional

Probab=80.60  E-value=1.1  Score=37.60  Aligned_cols=18  Identities=39%  Similarity=0.545  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.+++++.
T Consensus         8 ~~GsGKstia~~la~~lg   25 (180)
T PRK04182          8 PPGSGKTTVARLLAEKLG   25 (180)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999998653

>PRK15453 phosphoribulokinase; Provisional

Probab=80.45  E-value=6.2  Score=36.17  Aligned_cols=17  Identities=29%  Similarity=0.495  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+||||+|+.+++.++
T Consensus        14 SGsGKTTva~~l~~if~   30 (290)
T PRK15453         14 SGAGTTTVKRAFEKIFR   30 (290)
T ss_pred             CCCCHHHHHHHHHHHHh
Confidence            79999999999997554

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=80.44  E-value=5.9  Score=41.55  Aligned_cols=32  Identities=13%  Similarity=0.193  Sum_probs=20.9

Q ss_pred             eEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEe
Q 040234           77 KVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITT  111 (377)
Q Consensus        77 ~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTT  111 (377)
                      .-+||+|.+.-  ...+..++..++   .+++||+.-
T Consensus       417 ~~llIvDEaSMvd~~~~~~Ll~~~~---~~~rlilvG  450 (720)
T TIGR01448       417 CDLLIVDESSMMDTWLALSLLAALP---DHARLLLVG  450 (720)
T ss_pred             CCEEEEeccccCCHHHHHHHHHhCC---CCCEEEEEC
Confidence            45999999865  344556665543   467877654

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=80.43  E-value=2.1  Score=41.75  Aligned_cols=16  Identities=31%  Similarity=0.491  Sum_probs=13.7

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||||++.++...
T Consensus       166 sG~GKStLl~~i~~~~  181 (434)
T PRK08472        166 SGVGKSTLMGMIVKGC  181 (434)
T ss_pred             CCCCHHHHHHHHhhcc
Confidence            6999999999998743

>PRK08506 replicative DNA helicase; Provisional

Probab=80.39  E-value=5.9  Score=39.33  Aligned_cols=44  Identities=23%  Similarity=0.206  Sum_probs=27.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLL   52 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~   52 (377)
                      +|+|||++|..++.....+-..++++. +-      .+..++..+++....
T Consensus       201 pg~GKT~fal~ia~~~~~~g~~V~~fS-lE------Ms~~ql~~Rlla~~s  244 (472)
T PRK08506        201 PSMGKTTLCLNMALKALNQDKGVAFFS-LE------MPAEQLMLRMLSAKT  244 (472)
T ss_pred             CCCChHHHHHHHHHHHHhcCCcEEEEe-Cc------CCHHHHHHHHHHHhc
Confidence            799999999999885532212233332 21      166777777777654

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

Probab=80.23  E-value=22  Score=35.57  Aligned_cols=56  Identities=5%  Similarity=-0.181  Sum_probs=32.5

Q ss_pred             CCCCeeecCCCChhhhHHHHHHHhcCCCCC-c---hhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKP-L---EEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       121 ~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~-~---~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      +....+...|..+.--.+.+.+..-....+ .   -........|+..++| ++--||..+
T Consensus       257 ~ri~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k~~~~~~v~~i~~~s~G-DIRsAInsL  316 (634)
T KOG1970|consen  257 PRISNISFNPIAPTIMKKFLKRICRIEANKKSGIKVPDTAEVELICQGSGG-DIRSAINSL  316 (634)
T ss_pred             cCcceEeecCCcHHHHHHHHHHHHHHhcccccCCcCchhHHHHHHHHhcCc-cHHHHHhHh
Confidence            344566777777776666665543221111 1   1235567888999988 566666543

>PRK06820 type III secretion system ATPase; Validated

Probab=80.14  E-value=4.7  Score=39.40  Aligned_cols=16  Identities=31%  Similarity=0.445  Sum_probs=13.5

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||||++.++...
T Consensus       172 sG~GKStLl~~I~~~~  187 (440)
T PRK06820        172 AGVGKSTLLGMLCADS  187 (440)
T ss_pred             CCCChHHHHHHHhccC
Confidence            6999999999888743

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=80.11  E-value=3.7  Score=40.23  Aligned_cols=16  Identities=31%  Similarity=0.490  Sum_probs=13.7

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||||++.+....
T Consensus       167 sG~GKStLl~~I~~~~  182 (438)
T PRK07721        167 SGVGKSTLMGMIARNT  182 (438)
T ss_pred             CCCCHHHHHHHHhccc
Confidence            6999999999888744

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=80.11  E-value=5.9  Score=41.33  Aligned_cols=46  Identities=24%  Similarity=0.277  Sum_probs=26.1

Q ss_pred             HHHHHhcCceEEEEEeCCCCh------hh-hhHhhCCCCCCCCCCeEEEEecchhH
Q 040234           68 MLRVRLRRKKVLVVIDDAAHP------DH-LRRLVGEPDWFGPGSRIIITTRNEHL  116 (377)
Q Consensus        68 ~l~~~l~~k~~LLVLDdv~~~------~~-~~~l~~~l~~~~~gs~IIvTTR~~~v  116 (377)
                      .+-+.+-.++-+|+||.+-+.      .. .+.+....   ...+.|+||=|...+
T Consensus       619 alARaLl~~P~ILlLDEaTSaLD~~sE~~I~~~L~~~~---~~~T~I~IaHRl~ti  671 (709)
T COG2274         619 ALARALLSKPKILLLDEATSALDPETEAIILQNLLQIL---QGRTVIIIAHRLSTI  671 (709)
T ss_pred             HHHHHhccCCCEEEEeCcccccCHhHHHHHHHHHHHHh---cCCeEEEEEccchHh
Confidence            355666778889999997541      11 23333321   234566666665544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	377
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-26
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	3e-25
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	4e-25
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	1e-10

>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 =  110 bits (276), Expect = 2e-26
 Identities = 69/451 (15%), Positives = 144/451 (31%), Gaps = 133/451 (29%)

Query: 1   MGGLGKTTLARVVY--DLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDL---LKLA 55
           + G GKT +A  V     +  + D   F  +++  C+   +V+ + ++LL  +       
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLK-NCNSPETVLEMLQKLLYQIDPNWTSR 216

Query: 56  DNNIRNVYDGINMLRVRLRR-------KKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRII 108
            ++  N+   I+ ++  LRR       +  L+V+ +  +           + F    +I+
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW-------NAFNLSCKIL 269

Query: 109 ITTRNEHLLKLHPVKKVYKL------EALTYDEAFRLLCLKAFDTHKPLEEYVELAESVV 162
           +TTR + +           +        LT DE   LL LK  D         +L   V+
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL-LKYLDC-----RPQDLPREVL 323

Query: 163 RICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLF------FSVGLQN 216
                               +   L++  + ++  L  +  + ++            L  
Sbjct: 324 TT------------------NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV 365

Query: 217 MPPSDKYGNMHSPQREY----SIVVPGSEIPE------WFEYQNNEGSSITISTPPKTYK 266
           + P++         R+     S+  P + IP       WF+   ++   +          
Sbjct: 366 LEPAE--------YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV--------- 408

Query: 267 NSKLVGYVVCCVFRVPKYSLPYYHPLW--------PQYPVHELSINRKGTTSGLCS---- 314
            +KL  Y    V + PK S      ++         +Y +H   ++         S    
Sbjct: 409 -NKLHKY--SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI 465

Query: 315 -------IY------LRKQFGQAMSDHLF--LYY-----QNRERISKVTFDSPSGLV--- 351
                   Y      L K         LF  ++      + + R     +++   ++   
Sbjct: 466 PPYLDQYFYSHIGHHL-KNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL 524

Query: 352 --LKR-----CGVHPIYVHQGDKLTKQLIPF 375
             LK      C   P Y    ++L   ++ F
Sbjct: 525 QQLKFYKPYICDNDPKY----ERLVNAILDF 551

>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 =  106 bits (265), Expect = 3e-25
 Identities = 27/175 (15%), Positives = 57/175 (32%), Gaps = 16/175 (9%)

Query: 1   MGGLGKTTLARVVY----DLISHEFDGSSFL----ADVREKCDKEGSVISLQKQLLSDLL 52
             G GK+ +A         LI   +D   +L       +   D    ++ + K     L 
Sbjct: 160 RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLN 219

Query: 53  KLADNNIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTR 112
             +  ++ +V     +    + R   L V DD    + +R             R ++TTR
Sbjct: 220 FPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIR------WAQELRLRCLVTTR 273

Query: 113 NEHLLK-LHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICH 166
           +  +        +  ++ +L  DE +  L           E+  ++    + +  
Sbjct: 274 DVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVG-EKEEDVLNKTIELSS 327

>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 =  105 bits (264), Expect = 4e-25
 Identities = 34/176 (19%), Positives = 67/176 (38%), Gaps = 22/176 (12%)

Query: 1   MGGLGKTTLARVVY---DLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLK---L 54
           M G GK+ LA        L+   F G      V ++      ++   + L + L +    
Sbjct: 155 MAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSG--LLMKLQNLCTRLDQDESF 212

Query: 55  ADNNIRNVYDGINMLRVRL--RRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTR 112
           +     N+ +  + LR+ +  +  + L+++DD      L         F    +I++TTR
Sbjct: 213 SQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVL-------KAFDSQCQILLTTR 265

Query: 113 NEHLLKL--HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICH 166
           ++ +      P   V    +L  ++   +L L        L    E A S+++ C 
Sbjct: 266 DKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLP---EQAHSIIKECK 318

>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 = 62.2 bits (151), Expect = 1e-10
 Identities = 40/175 (22%), Positives = 72/175 (41%), Gaps = 20/175 (11%)

Query: 1   MGGLGKTTLARVV---YDLISHEFDGSSFLADVREKCDKEGSVISLQK--QLLSDLLKLA 55
           M G GK+ LA      + L+   F G      + +  DK G ++ LQ     L      +
Sbjct: 155 MAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK-QDKSGLLMKLQNLCMRLDQEESFS 213

Query: 56  DNNIRNVYDGINMLRVRLRRK--KVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRN 113
                N+ +  + LRV + RK  + L+++DD   P  L+        F    +I++TTR+
Sbjct: 214 QRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKA-------FDNQCQILLTTRD 266

Query: 114 EHLLK--LHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICH 166
           + +    + P   V     L  ++   +L L     +   E+    A S+++ C 
Sbjct: 267 KSVTDSVMGPKHVVPVESGLGREKGLEILSLF---VNMKKEDLPAEAHSIIKECK 318

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	377
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.96
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.93
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.91
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.89
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.22
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.09
2fna_A	357	Conserved hypothetical protein; structural genomic	99.01
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.89
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.89
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.89
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.85
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.78
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.68
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.37
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.21
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.11
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.1
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.07
3bos_A	242	Putative DNA replication factor; P-loop containing	98.0
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.96
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.87
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.85
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.84
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.67
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.6
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.58
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.55
3pvs_A	447	Replication-associated recombination protein A; ma	97.54
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.5
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.49
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.46
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.45
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.45
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.4
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.36
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.35
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.34
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.28
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.28
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.23
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.14
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.09
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.05
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.98
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.98
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.74
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.7
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	96.49
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.3
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.26
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.22
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.17
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.15
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.12
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.06
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.06
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.06
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.99
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.98
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.97
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	95.93
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.87
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.87
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.78
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.68
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.68
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	95.55
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.53
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.47
2cvh_A	220	DNA repair and recombination protein RADB; filamen	95.27
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	95.17
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	95.14
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.13
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.08
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	95.07
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.05
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	94.73
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.67
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	94.66
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	94.3
3co5_A	143	Putative two-component system transcriptional RES	94.28
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.18
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	93.94
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.48
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.43
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	93.39
3ice_A	422	Transcription termination factor RHO; transcriptio	93.21
3io5_A	333	Recombination and repair protein; storage dimer, i	93.17
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	93.17
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	93.14
2qgz_A	308	Helicase loader, putative primosome component; str	92.84
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	92.83
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	92.8
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	92.79
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	92.47
4a74_A	231	DNA repair and recombination protein RADA; hydrola	92.42
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	92.33
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	92.31
2z43_A	324	DNA repair and recombination protein RADA; archaea	92.15
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	92.12
1u94_A	356	RECA protein, recombinase A; homologous recombinat	91.87
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	91.8
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	91.65
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	91.65
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	91.43
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	91.3
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	90.95
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	90.74
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	90.64
3l0o_A	427	Transcription termination factor RHO; helicase, RH	90.58
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	90.35
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	90.04
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	89.89
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	89.85
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	89.85
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	89.74
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	89.71
2eyu_A	261	Twitching motility protein PILT; pilus retraction	89.68
2r6a_A	454	DNAB helicase, replicative helicase; replication,	89.28
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	89.22
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	89.21
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	88.82
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	88.82
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	88.71
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.54
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	88.51
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	88.22
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	87.96
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	87.89
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	87.88
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	87.86
1via_A	175	Shikimate kinase; structural genomics, transferase	87.78
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	87.5
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	87.36
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	87.3
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	87.21
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	87.16
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	87.08
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	87.07
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	86.97
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	86.72
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	86.68
3cwq_A	209	Para family chromosome partitioning protein; alpha	86.5
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	86.44
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	86.37
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	86.19
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	86.15
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	86.04
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	85.5
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	85.44
2ewv_A	372	Twitching motility protein PILT; pilus retraction	85.31
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	85.29
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	85.29
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	85.14
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	85.1
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	85.05
2vli_A	183	Antibiotic resistance protein; transferase, tunica	85.04
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	84.96
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	84.78
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	84.73
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	84.64
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	84.63
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	84.4
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	84.26
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	84.22
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	83.97
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	83.91
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	83.77
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	83.76
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	83.63
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	83.48
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	83.44
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	83.21
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	83.2
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	83.14
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	83.06
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	82.93
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	82.78
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	82.74
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	82.69
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	82.68
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	82.62
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	82.5
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	82.36
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	82.24
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	82.24
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	82.21
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	82.14
2xxa_A	433	Signal recognition particle protein; protein trans	82.01
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	81.98
2ph1_A	262	Nucleotide-binding protein; alpha-beta protein, st	81.84
3q9l_A	260	Septum site-determining protein MIND; ATPase, bact	81.83
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	81.79
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	81.74
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	81.71
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	81.63
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	81.55
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	81.49
3end_A	307	Light-independent protochlorophyllide reductase ir	81.35
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	81.24
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	81.21
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	81.0
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	81.0
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	80.99
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	80.9
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	80.88
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	80.7
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	80.54
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	80.46
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	80.45
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	80.43
1hyq_A	263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	80.27
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	80.19
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	80.14
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	80.14
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	80.11
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	80.09

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=99.96  E-value=3.4e-30  Score=257.52  Aligned_cols=207  Identities=16%  Similarity=0.154  Sum_probs=155.9

Q ss_pred             CCCCcHHHHHHHHHc----hhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-cCc-----cchhhhHHHHH
Q 040234            1 MGGLGKTTLARVVYD----LISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-NNI-----RNVYDGINMLR   70 (377)
Q Consensus         1 mgGiGKTtLA~~v~~----~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-~~~-----~~~~~~~~~l~   70 (377)
                      |||+||||||+++|+    +++.+|+.++|++ +++... . ++..++..++.+++.... ...     .+.+.+...++
T Consensus       160 ~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~-vs~~~~-~-~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~  236 (549)
T 2a5y_B          160 RAGSGKSVIASQALSKSDQLIGINYDSIVWLK-DSGTAP-K-STFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMIC  236 (549)
T ss_dssp             STTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE-CCCCST-T-HHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhhHHHhccCCcEEEEE-ECCCCC-C-CHHHHHHHHHHHHhcCcccccccccccccHHHHHHHHH
Confidence            799999999999995    7899999999996 776532 1 678999999999876422 111     23344688999


Q ss_pred             HHhcCc-eEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhCC-CCCeeecCCCChhhhHHHHHHHhcCCC
Q 040234           71 VRLRRK-KVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHP-VKKVYKLEALTYDEAFRLLCLKAFDTH  148 (377)
Q Consensus        71 ~~l~~k-~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~-~~~~~~l~~L~~~ea~~L~~~~~~~~~  148 (377)
                      +.|+++ |+||||||||+.+++ .+. .    .+||+||||||++.++..+. ....++|++|++++|++||.++++...
T Consensus       237 ~~L~~~kr~LlVLDdv~~~~~~-~~~-~----~~gs~ilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  310 (549)
T 2a5y_B          237 NALIDRPNTLFVFDDVVQEETI-RWA-Q----ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMP  310 (549)
T ss_dssp             HHHTTSTTEEEEEEEECCHHHH-HHH-H----HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC
T ss_pred             HHHcCCCcEEEEEECCCCchhh-ccc-c----cCCCEEEEEcCCHHHHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCC
Confidence            999996 999999999998865 222 1    37999999999999988775 446799999999999999999987653


Q ss_pred             CCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhhchhHHHHHHHHHhhccCchhHHHHHHHHHhhcccCCCCC
Q 040234          149 KPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSD  221 (377)
Q Consensus       149 ~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~~~~~~~~~~L~~~~~~~~~~~~~~~~l~~Sy~~L~~~~  221 (377)
                      . .+.+.+++++|+++|||  +|||++++|+.+..+. .++...+...... .....+.+++.+||+.||+..
T Consensus       311 ~-~~~~~~~~~~I~~~c~G--lPLAl~~~g~~l~~~~-w~~~~~l~~~l~~-~~~~~i~~~l~~Sy~~L~~~l  378 (549)
T 2a5y_B          311 V-GEKEEDVLNKTIELSSG--NPATLMMFFKSCEPKT-FEKMAQLNNKLES-RGLVGVECITPYSYKSLAMAL  378 (549)
T ss_dssp             ---CHHHHHHHHHHHHHTT--CHHHHHHHHTTCCSSS-HHHHHHHHHHHHH-HCSSTTCCCSSSSSSSHHHHH
T ss_pred             C-chhHHHHHHHHHHHhCC--ChHHHHHHHHHhccch-HHHHHHhHHHhhc-ccHHHHHHHHhcccccccHHH
Confidence            2 46778899999999999  9999999999987763 2333333221100 001235567778888876654

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=99.93  E-value=5.2e-26  Score=247.32  Aligned_cols=220  Identities=19%  Similarity=0.224  Sum_probs=163.8

Q ss_pred             CCCCcHHHHHHHHHch---hccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc---cCccchhhhHHHHHHHhc
Q 040234            1 MGGLGKTTLARVVYDL---ISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD---NNIRNVYDGINMLRVRLR   74 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~---~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~~l~~~l~   74 (377)
                      |||+||||||++++++   ...+|+.++||..+++....  .....+..++..+.....   ....+.+++.+.++..+.
T Consensus       155 ~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~  232 (1249)
T 3sfz_A          155 MAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKS--GLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLML  232 (1249)
T ss_dssp             STTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHH--HHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTS
T ss_pred             CCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCch--HHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHh
Confidence            7999999999999995   46778888866657764211  344556667666654321   223466778888899998


Q ss_pred             Cc--eEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhh-CCCCCeeecCC-CChhhhHHHHHHHhcCCCCC
Q 040234           75 RK--KVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKL-HPVKKVYKLEA-LTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k--~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~-~~~~~~~~l~~-L~~~ea~~L~~~~~~~~~~~  150 (377)
                      ++  |+||||||||+.++|+.+       .+|++||||||++.++.. ......+++++ |++++|++||...++...  
T Consensus       233 ~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~--  303 (1249)
T 3sfz_A          233 RKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKK--  303 (1249)
T ss_dssp             SSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCS--
T ss_pred             ccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCCh--
Confidence            77  999999999999888765       578999999999998854 45567899996 999999999999885432  


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHHhhhhchhHHHHHHHHHhhccC---------chhHHHHHHHHHhhcccCCCCC
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLC---------PFILFVYLLFFSVGLQNMPPSD  221 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~~~~~~~~~~L~~~~~~---------~~~~~~~~~~l~~Sy~~L~~~~  221 (377)
                       +..++.+++|+++|+|  +|||+.++|++++.+. .+|...+.++...         ......+.+++.+||+.|++..
T Consensus       304 -~~~~~~~~~i~~~~~g--lPLal~~~~~~l~~~~-~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~  379 (1249)
T 3sfz_A          304 -EDLPAEAHSIIKECKG--SPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDI  379 (1249)
T ss_dssp             -TTCCTHHHHHHHHTTT--CHHHHHHHHHHHHHSS-SCHHHHHHHHHSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTTT
T ss_pred             -hhCcHHHHHHHHHhCC--CHHHHHHHHHHhhcCh-hHHHHHHHHHhhhhhhhcccccccchHHHHHHHHHHHHhCCHHH
Confidence             2334678999999999  9999999999997644 2333333333211         1122479999999999999987


Q ss_pred             cccCCCCCCCceEE--EecCC-CCC
Q 040234          222 KYGNMHSPQREYSI--VVPGS-EIP  243 (377)
Q Consensus       222 ~~~~~~~~~~~~~~--~~pg~-~iP  243 (377)
                              +..|..  +||+. .||
T Consensus       380 --------~~~~~~l~~f~~~~~i~  396 (1249)
T 3sfz_A          380 --------KDYYTDLSILQKDVKVP  396 (1249)
T ss_dssp             --------HHHHHHGGGSCTTCCEE
T ss_pred             --------HHHHHHhCccCCCCeeC
Confidence                    666655  56665 666

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.91  E-value=1.2e-24  Score=223.56  Aligned_cols=190  Identities=16%  Similarity=0.079  Sum_probs=139.3

Q ss_pred             CCCCcHHHHHHHHHc--hhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcccc----------CccchhhhHHH
Q 040234            1 MGGLGKTTLARVVYD--LISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN----------NIRNVYDGINM   68 (377)
Q Consensus         1 mgGiGKTtLA~~v~~--~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~----------~~~~~~~~~~~   68 (377)
                      |||+||||||+++++  +++.+|+.+++|.++++.+    +...++..++..+......          .+.+.+.+.+.
T Consensus       158 mGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~----d~~~IL~~Ll~lL~~i~~~~~~~~d~~~~ip~~leeL~e~  233 (1221)
T 1vt4_I          158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN----SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE  233 (1221)
T ss_dssp             STTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSS----SHHHHHHHHHHHHHHHCSSSTTTSCCCSSHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCC----CHHHHHHHHHHHHhhcCcccccccccccCCCCCHHHHHHH
Confidence            799999999999997  6889999855555487765    6667777777654332100          01233455677


Q ss_pred             HHHHh---cCceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhCCCCCeeecC------CCChhhhHHH
Q 040234           69 LRVRL---RRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKLE------ALTYDEAFRL  139 (377)
Q Consensus        69 l~~~l---~~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~~~l~------~L~~~ea~~L  139 (377)
                      +++.|   .++|+||||||||+.++|+.+.       +||+||||||++.++..+.....+.++      +|+++||++|
T Consensus       234 Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eL  306 (1221)
T 1vt4_I          234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL  306 (1221)
T ss_dssp             HHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCSHHHHHHHHHSSCEEEECSSSSCCCHHHHHHH
T ss_pred             HHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccChHHHHhcCCCeEEEecCccccCCcCHHHHHHH
Confidence            77766   6899999999999999998863       689999999999887644333456676      9999999999


Q ss_pred             HHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhhch--hHHHHHHHHHhhccCchhHHHHHHHHHhhcccC
Q 040234          140 LCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSH--LLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNM  217 (377)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~~--~~~~~~~~L~~~~~~~~~~~~~~~~l~~Sy~~L  217 (377)
                      |.+.....   .   .++..+   .|+|  +|||+.++|++++.+  ....|...      .   ...+..++.+||+.|
T Consensus       307 F~~~~g~~---~---eeL~~e---ICgG--LPLALkLaGs~Lr~k~~s~eeW~~~------~---~~~I~aaLelSYd~L  366 (1221)
T 1vt4_I          307 LLKYLDCR---P---QDLPRE---VLTT--NPRRLSIIAESIRDGLATWDNWKHV------N---CDKLTTIIESSLNVL  366 (1221)
T ss_dssp             HHHHHCCC---T---TTHHHH---HCCC--CHHHHHHHHHHHHHSCSSHHHHHHC------S---CHHHHHHHHHHHHHS
T ss_pred             HHHHcCCC---H---HHHHHH---HhCC--CHHHHHHHHHHHhCCCCCHHHHhcC------C---hhHHHHHHHHHHHhC
Confidence            99985322   1   122333   3999  999999999999876  33334221      1   256899999999999


Q ss_pred             CCCC
Q 040234          218 PPSD  221 (377)
Q Consensus       218 ~~~~  221 (377)
                      ++..
T Consensus       367 p~ee  370 (1221)
T 1vt4_I          367 EPAE  370 (1221)
T ss_dssp             CTTH
T ss_pred             CHHH
Confidence            9864

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.89  E-value=3.2e-23  Score=209.09  Aligned_cols=217  Identities=18%  Similarity=0.187  Sum_probs=150.3

Q ss_pred             CCCCcHHHHHHHHHchh---ccccccceEEecchhhcccccCHHHHHHH---HHHHHhhcc---ccCccchhhhHHHHHH
Q 040234            1 MGGLGKTTLARVVYDLI---SHEFDGSSFLADVREKCDKEGSVISLQKQ---LLSDLLKLA---DNNIRNVYDGINMLRV   71 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~---~~~f~~~~w~~~~~~~~~~~~~~~~~~~~---i~~~l~~~~---~~~~~~~~~~~~~l~~   71 (377)
                      |||+||||||.+++++.   +.+|+.++||.++++.     +...++..   ++..+....   .....+.+...+.+++
T Consensus       155 ~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-----~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~  229 (591)
T 1z6t_A          155 MAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-----DKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRI  229 (591)
T ss_dssp             CTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-----CHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-----chHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHH
Confidence            79999999999999853   7889765555546654     22233333   333433111   1223455667788888


Q ss_pred             HhcC--ceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhCCCCCeeec---CCCChhhhHHHHHHHhcC
Q 040234           72 RLRR--KKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPVKKVYKL---EALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        72 ~l~~--k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~~~~~~l---~~L~~~ea~~L~~~~~~~  146 (377)
                      .+.+  +++||||||+|+.++++.+       .++++||||||++.++.... ...+++   ++|+.++|++||...++.
T Consensus       230 ~l~~~~~~~LLVLDdv~~~~~l~~l-------~~~~~ilvTsR~~~~~~~~~-~~~~~v~~l~~L~~~ea~~L~~~~~~~  301 (591)
T 1z6t_A          230 LMLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSVM-GPKYVVPVESSLGKEKGLEILSLFVNM  301 (591)
T ss_dssp             HHHHTCTTCEEEEEEECCHHHHHTT-------CSSCEEEEEESCGGGGTTCC-SCEEEEECCSSCCHHHHHHHHHHHHTS
T ss_pred             HHccCCCCeEEEEeCCCCHHHHHHh-------cCCCeEEEECCCcHHHHhcC-CCceEeecCCCCCHHHHHHHHHHHhCC
Confidence            8876  7899999999998777654       56899999999998876543 344555   589999999999999864


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhhchhHHHHHHHHHhhccC---------chhHHHHHHHHHhhcccC
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLC---------PFILFVYLLFFSVGLQNM  217 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~~~~~~~~~~L~~~~~~---------~~~~~~~~~~l~~Sy~~L  217 (377)
                      .   .....+.+.+|+++|+|  +|||+.++|+++..+.. +|...+.+....         ......+..++.+||+.|
T Consensus       302 ~---~~~~~~~~~~i~~~~~G--~PLal~~~a~~l~~~~~-~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L  375 (591)
T 1z6t_A          302 K---KADLPEQAHSIIKECKG--SPLVVSLIGALLRDFPN-RWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEML  375 (591)
T ss_dssp             C---GGGSCTHHHHHHHHHTT--CHHHHHHHHHHHHHSTT-CHHHHHHHHHSCCCCCSSCCCSSCCHHHHHHHHHHHHTS
T ss_pred             C---cccccHHHHHHHHHhCC--CcHHHHHHHHHHhcCch-hHHHHHHHHHHhHHHHhhhccccchHHHHHHHHHHHHhC
Confidence            2   22234578999999999  99999999999876531 233333322211         111246889999999999


Q ss_pred             CCCCcccCCCCCCCceEE--EecC-CCCCc
Q 040234          218 PPSDKYGNMHSPQREYSI--VVPG-SEIPE  244 (377)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~--~~pg-~~iP~  244 (377)
                      ++..        +..|..  +||+ ..||.
T Consensus       376 ~~~~--------~~~l~~la~f~~~~~i~~  397 (591)
T 1z6t_A          376 REDI--------KDYYTDLSILQKDVKVPT  397 (591)
T ss_dssp             CTTT--------HHHHHHGGGCCTTCCEEH
T ss_pred             CHHH--------HHHHHHccccCCCCccCH
Confidence            9987        555554  5654 56764

>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=99.22  E-value=3.5e-11  Score=115.25  Aligned_cols=171  Identities=15%  Similarity=0.122  Sum_probs=103.6

Q ss_pred             CCCCcHHHHHHHHHchhccc-----ccc-ceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhc
Q 040234            1 MGGLGKTTLARVVYDLISHE-----FDG-SSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLR   74 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-----f~~-~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~   74 (377)
                      ++|+|||+||+.++++....     +.. .+|+. +....    +...++..++.+++........+..+..+.+.+.+.
T Consensus        60 ~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~----~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~  134 (412)
T 1w5s_A           60 RVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN-AFNAP----NLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLY  134 (412)
T ss_dssp             CCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE-GGGCC----SHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEE-CCCCC----CHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHH
Confidence            58999999999999866543     222 34444 33332    677888888888754322112234455566666664


Q ss_pred             --CceEEEEEeCCCCh--------hhhhHhhCCCCCC---C--CCCeEEEEecchhHHhh---------CCCCCeeecCC
Q 040234           75 --RKKVLVVIDDAAHP--------DHLRRLVGEPDWF---G--PGSRIIITTRNEHLLKL---------HPVKKVYKLEA  130 (377)
Q Consensus        75 --~k~~LLVLDdv~~~--------~~~~~l~~~l~~~---~--~gs~IIvTTR~~~v~~~---------~~~~~~~~l~~  130 (377)
                        +++++|||||++..        +.+..+...+...   .  .+..+|+||+...+...         ......+.+++
T Consensus       135 ~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~  214 (412)
T 1w5s_A          135 VENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPA  214 (412)
T ss_dssp             HHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCC
T ss_pred             hcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCC
Confidence              67999999999763        3333332222110   1  33457878875543211         11123389999


Q ss_pred             CChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhC------CCCchhhHHHHH
Q 040234          131 LTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICH------CQKSTLNALMSV  178 (377)
Q Consensus       131 L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~------G~~lplal~~~~  178 (377)
                      |+.+++.++|..++...........+.+..|++.++      |  .|..+..+.
T Consensus       215 l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G--~p~~~~~l~  266 (412)
T 1w5s_A          215 YKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDG--SARRAIVAL  266 (412)
T ss_dssp             CCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCC--CHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCC--cHHHHHHHH
Confidence            999999999976542110111112457788999999      9  997655444

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.09  E-value=6.5e-10  Score=103.79  Aligned_cols=169  Identities=15%  Similarity=0.067  Sum_probs=99.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhc--ccccCHHHHHHHHHHHHhh---------------cccc--Cccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKC--DKEGSVISLQKQLLSDLLK---------------LADN--NIRN   61 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~--~~~~~~~~~~~~i~~~l~~---------------~~~~--~~~~   61 (377)
                      ++|+|||+|+++++++..     .+|+. +....  ....+...++..+...+..               ....  ...+
T Consensus        39 ~~G~GKT~Ll~~~~~~~~-----~~~~~-~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  112 (350)
T 2qen_A           39 IRRVGKSSLLRAFLNERP-----GILID-CRELYAERGHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLS  112 (350)
T ss_dssp             CTTSSHHHHHHHHHHHSS-----EEEEE-HHHHHHTTTCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCC
T ss_pred             CCcCCHHHHHHHHHHHcC-----cEEEE-eecccccccCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccch
Confidence            479999999999998652     45554 43321  0011334455555444321               0000  0123


Q ss_pred             hhhhHHHHHHHhcC-ceEEEEEeCCCChhh---------hhHhhCCCCCCCCCCeEEEEecchhHHhh----------C-
Q 040234           62 VYDGINMLRVRLRR-KKVLVVIDDAAHPDH---------LRRLVGEPDWFGPGSRIIITTRNEHLLKL----------H-  120 (377)
Q Consensus        62 ~~~~~~~l~~~l~~-k~~LLVLDdv~~~~~---------~~~l~~~l~~~~~gs~IIvTTR~~~v~~~----------~-  120 (377)
                      ..+..+.+.+.... ++.+|||||++..+.         +..+..... ..++.++|+|++...+...          . 
T Consensus       113 ~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~~-~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~  191 (350)
T 2qen_A          113 LREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAYD-SLPNLKIILTGSEVGLLHDFLKITDYESPLY  191 (350)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHHH-HCTTEEEEEEESSHHHHHHHHCTTCTTSTTT
T ss_pred             HHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHHH-hcCCeEEEEECCcHHHHHHHHhhcCCCCccc
Confidence            34444555554443 389999999976332         222221111 1246789999887643211          1 


Q ss_pred             -CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhh
Q 040234          121 -PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSY  180 (377)
Q Consensus       121 -~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~  180 (377)
                       .....+++.+|+.+|+.+++...........  ..+.+.+|++.+||  +|+++..++..
T Consensus       192 ~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~--~~~~~~~i~~~tgG--~P~~l~~~~~~  248 (350)
T 2qen_A          192 GRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV--PENEIEEAVELLDG--IPGWLVVFGVE  248 (350)
T ss_dssp             TCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC--CHHHHHHHHHHHTT--CHHHHHHHHHH
T ss_pred             cCccceeeCCCCCHHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHhCC--CHHHHHHHHHH
Confidence             1124789999999999999987653221111  13567899999999  99999888764

>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=99.01  E-value=1.3e-09  Score=102.05  Aligned_cols=100  Identities=14%  Similarity=0.006  Sum_probs=64.0

Q ss_pred             ceEEEEEeCCCChh-----hhhHhhCCCCCCCCCCeEEEEecchhHHh-h---------CC--CCCeeecCCCChhhhHH
Q 040234           76 KKVLVVIDDAAHPD-----HLRRLVGEPDWFGPGSRIIITTRNEHLLK-L---------HP--VKKVYKLEALTYDEAFR  138 (377)
Q Consensus        76 k~~LLVLDdv~~~~-----~~~~l~~~l~~~~~gs~IIvTTR~~~v~~-~---------~~--~~~~~~l~~L~~~ea~~  138 (377)
                      ++.+|||||++..+     ++..++..+....++.++|+|+|...... .         ..  ....+++.+|+.+++.+
T Consensus       137 ~~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~  216 (357)
T 2fna_A          137 DNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIE  216 (357)
T ss_dssp             SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHH
T ss_pred             CCeEEEEECHHHhhccCchhHHHHHHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHH
Confidence            48999999996632     22222111111124678999999765321 1         11  13578999999999999


Q ss_pred             HHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhh
Q 040234          139 LLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYT  181 (377)
Q Consensus       139 L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l  181 (377)
                      ++.............    ..+|++.+||  +|+.+..++..+
T Consensus       217 ~l~~~~~~~~~~~~~----~~~i~~~t~G--~P~~l~~~~~~~  253 (357)
T 2fna_A          217 FLRRGFQEADIDFKD----YEVVYEKIGG--IPGWLTYFGFIY  253 (357)
T ss_dssp             HHHHHHHHHTCCCCC----HHHHHHHHCS--CHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCc----HHHHHHHhCC--CHHHHHHHHHHH
Confidence            998764211111111    1789999999  999998887654

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.89  E-value=4.7e-09  Score=92.25  Aligned_cols=102  Identities=13%  Similarity=0.046  Sum_probs=68.7

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchhH-Hhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEHL-LKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~v-~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++.+|||||++.  .+.++.+...+.....+..+|+||+.... ... ......+++++++.++..+++...+......
T Consensus       125 ~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~  204 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA  204 (250)
T ss_dssp             SSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTCC
T ss_pred             CCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCCC
Confidence            4678999999965  44455554443333456788888876432 111 1224678999999999999998877432221


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHHhh
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSVSY  180 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~~~  180 (377)
                      .  .++..+.|++.++|  .|..+..+...
T Consensus       205 ~--~~~~~~~l~~~~~G--~~~~~~~~~~~  230 (250)
T 1njg_A          205 H--EPRALQLLARAAEG--SLRDALSLTDQ  230 (250)
T ss_dssp             B--CHHHHHHHHHHHTT--CHHHHHHHHHH
T ss_pred             C--CHHHHHHHHHHcCC--CHHHHHHHHHH
Confidence            1  14567899999999  99988765543

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.89  E-value=2.2e-08  Score=94.76  Aligned_cols=160  Identities=14%  Similarity=0.174  Sum_probs=99.1

Q ss_pred             CCCCcHHHHHHHHHchhccc------c-c-cceEEecchhhcccccCHHHHHHHHHHHHhhcccc-CccchhhhHHHHHH
Q 040234            1 MGGLGKTTLARVVYDLISHE------F-D-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN-NIRNVYDGINMLRV   71 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~------f-~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~~~l~~   71 (377)
                      ++|+|||+||+.++++....      + . ..+++. .....   .+...++..++.++.+.... ...+.....+.+.+
T Consensus        53 ~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~-~~~~~---~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~  128 (384)
T 2qby_B           53 LTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN-CREVG---GTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKN  128 (384)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEE-HHHHC---SCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEE-CccCC---CCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHH
Confidence            47999999999999976443      2 2 234443 33321   04456777777776433211 12234455677777


Q ss_pred             HhcCceEEEEEeCCCChh------h-hhHhhCCCCCCCCCCeEEEEecchhHHhhC------CCCCeeecCCCChhhhHH
Q 040234           72 RLRRKKVLVVIDDAAHPD------H-LRRLVGEPDWFGPGSRIIITTRNEHLLKLH------PVKKVYKLEALTYDEAFR  138 (377)
Q Consensus        72 ~l~~k~~LLVLDdv~~~~------~-~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~------~~~~~~~l~~L~~~ea~~  138 (377)
                      .+..++.+||||+++...      . +..+....    .+..+|+||+.......+      .....+++++++.++..+
T Consensus       129 ~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~----~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~  204 (384)
T 2qby_B          129 GTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD----ANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKF  204 (384)
T ss_dssp             HHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS----SCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHH
T ss_pred             HhccCCCEEEEECHHHhccCCCCceeHHHHhcCC----cceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHH
Confidence            787766699999997632      2 33444332    577889998865321111      112389999999999999


Q ss_pred             HHHHHhcC---CCCCchhHHHHHHHHHHHhC---CCCchhh
Q 040234          139 LLCLKAFD---THKPLEEYVELAESVVRICH---CQKSTLN  173 (377)
Q Consensus       139 L~~~~~~~---~~~~~~~~~~~~~~I~~~c~---G~~lpla  173 (377)
                      ++..++..   .....   ++..+.|++.++   |  .|..
T Consensus       205 il~~~~~~~~~~~~~~---~~~~~~i~~~~~~~~G--~~r~  240 (384)
T 2qby_B          205 ILSKYAEYGLIKGTYD---DEILSYIAAISAKEHG--DARK  240 (384)
T ss_dssp             HHHHHHHHTSCTTSCC---SHHHHHHHHHHHTTCC--CHHH
T ss_pred             HHHHHHHhhcccCCcC---HHHHHHHHHHHHhccC--CHHH
Confidence            99987531   12222   345667778887   8  7763

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.89  E-value=3.1e-09  Score=100.47  Aligned_cols=169  Identities=17%  Similarity=0.123  Sum_probs=96.6

Q ss_pred             CCCCcHHHHHHHHHchhccccc---cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhc--C
Q 040234            1 MGGLGKTTLARVVYDLISHEFD---GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLR--R   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~---~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~--~   75 (377)
                      ++|+||||||+.+++.....+.   ..+|+. .....    ....++..++.+++........+..+..+.+.+.+.  +
T Consensus        53 ~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~-~~~~~----~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~  127 (386)
T 2qby_A           53 LTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN-TRQID----TPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYG  127 (386)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE-HHHHC----SHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHhcCCceEEEEE-CCCCC----CHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccC
Confidence            4799999999999997765542   234444 43333    555666666665532211111233444555665554  3


Q ss_pred             ceEEEEEeCCCCh------hhhhHhhCCCCC-CCCCCeEEEEecchhHHhhCC-------CCCeeecCCCChhhhHHHHH
Q 040234           76 KKVLVVIDDAAHP------DHLRRLVGEPDW-FGPGSRIIITTRNEHLLKLHP-------VKKVYKLEALTYDEAFRLLC  141 (377)
Q Consensus        76 k~~LLVLDdv~~~------~~~~~l~~~l~~-~~~gs~IIvTTR~~~v~~~~~-------~~~~~~l~~L~~~ea~~L~~  141 (377)
                      ++.+||||+++..      +.+..+...+.. ...+..+|+||+.......+.       ....+.+++++.++..+++.
T Consensus       128 ~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~  207 (386)
T 2qby_A          128 SQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILT  207 (386)
T ss_dssp             SCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHH
T ss_pred             CeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHH
Confidence            4899999998652      233333222110 133556788887654322221       12579999999999999998


Q ss_pred             HHhcCCCCCchhHHHHHHHHHHHhC---CCCchhhHHH
Q 040234          142 LKAFDTHKPLEEYVELAESVVRICH---CQKSTLNALM  176 (377)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~I~~~c~---G~~lplal~~  176 (377)
                      ..+........-..+..+.|++.++   |  .|..+..
T Consensus       208 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~G--~~r~~~~  243 (386)
T 2qby_A          208 KRAQMAFKPGVLPDNVIKLCAALAAREHG--DARRALD  243 (386)
T ss_dssp             HHHHHHBCSSCSCHHHHHHHHHHHHHTTC--CHHHHHH
T ss_pred             HHHHhhccCCCCCHHHHHHHHHHHHHhcC--CHHHHHH
Confidence            8653111111112345666777776   9  8885443

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.85  E-value=8.2e-09  Score=97.63  Aligned_cols=163  Identities=13%  Similarity=0.057  Sum_probs=97.7

Q ss_pred             CCCCcHHHHHHHHHchhcccc-----c-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhc
Q 040234            1 MGGLGKTTLARVVYDLISHEF-----D-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLR   74 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f-----~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~   74 (377)
                      ++|+|||+||+.+++......     . ..+++. .....    +...++..++.+++........+..+..+.+.+.+.
T Consensus        52 ~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~-~~~~~----~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~  126 (387)
T 2v1u_A           52 LTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN-ARHRE----TPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLS  126 (387)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEE-TTTSC----SHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEE-CCcCC----CHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHh
Confidence            479999999999999664432     2 233444 33333    667788888888754322222334455566666663


Q ss_pred             --CceEEEEEeCCCChh-------hhhHhhCCCCCC--CCCCeEEEEecchhH--------HhhCCCCCeeecCCCChhh
Q 040234           75 --RKKVLVVIDDAAHPD-------HLRRLVGEPDWF--GPGSRIIITTRNEHL--------LKLHPVKKVYKLEALTYDE  135 (377)
Q Consensus        75 --~k~~LLVLDdv~~~~-------~~~~l~~~l~~~--~~gs~IIvTTR~~~v--------~~~~~~~~~~~l~~L~~~e  135 (377)
                        +++.+||||+++...       .+..+.......  ..+..+|.||+....        ..... ...+.+++++.++
T Consensus       127 ~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~r~~-~~~i~l~~l~~~~  205 (387)
T 2v1u_A          127 RLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLG-EVELVFPPYTAPQ  205 (387)
T ss_dssp             TSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHTTTT-SEECCBCCCCHHH
T ss_pred             ccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHhcCC-CeEEeeCCCCHHH
Confidence              468899999998632       122222221111  235577778776522        22111 2478999999999


Q ss_pred             hHHHHHHHhcC---CCCCchhHHHHHHHHHHHhC---CCCchhhH
Q 040234          136 AFRLLCLKAFD---THKPLEEYVELAESVVRICH---CQKSTLNA  174 (377)
Q Consensus       136 a~~L~~~~~~~---~~~~~~~~~~~~~~I~~~c~---G~~lplal  174 (377)
                      ..+++...+..   .....   ++..+.+++.++   |  .|..+
T Consensus       206 ~~~il~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~G--~~r~~  245 (387)
T 2v1u_A          206 LRDILETRAEEAFNPGVLD---PDVVPLCAALAAREHG--DARRA  245 (387)
T ss_dssp             HHHHHHHHHHHHBCTTTBC---SSHHHHHHHHHHSSSC--CHHHH
T ss_pred             HHHHHHHHHHhhccCCCCC---HHHHHHHHHHHHHhcc--CHHHH
Confidence            99999887532   21212   245677888887   9  88443

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.78  E-value=5.4e-08  Score=92.12  Aligned_cols=168  Identities=17%  Similarity=0.115  Sum_probs=101.6

Q ss_pred             CCCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhc--Cce
Q 040234            1 MGGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLR--RKK   77 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~--~k~   77 (377)
                      .+|+||||||+.+++....... ..+++. .....    +...++..++..++........+..+..+.+.+.+.  +++
T Consensus        52 ~~G~GKTtl~~~l~~~~~~~~~~~~~~i~-~~~~~----~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~  126 (389)
T 1fnn_A           52 RPGTGKTVTLRKLWELYKDKTTARFVYIN-GFIYR----NFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLY  126 (389)
T ss_dssp             CTTSSHHHHHHHHHHHHTTSCCCEEEEEE-TTTCC----SHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCHHHHHHHHHHHHhhhcCeeEEEEe-CccCC----CHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCe
Confidence            4799999999999987655421 233443 33332    566777888777643322122234445555555554  568


Q ss_pred             EEEEEeCCCCh--hhhhHhhCCCCCC-C---CCCeEEEEecchhHHhhCC-------CCCeeecCCCChhhhHHHHHHHh
Q 040234           78 VLVVIDDAAHP--DHLRRLVGEPDWF-G---PGSRIIITTRNEHLLKLHP-------VKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        78 ~LLVLDdv~~~--~~~~~l~~~l~~~-~---~gs~IIvTTR~~~v~~~~~-------~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      .+||||+++..  +.+..+...+... .   .+..||+||+.........       ....+.+++++.++..+++...+
T Consensus       127 ~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~  206 (389)
T 1fnn_A          127 MFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  206 (389)
T ss_dssp             EEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             EEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHH
Confidence            89999999763  3444443333211 1   3667888887654332221       12369999999999999998876


Q ss_pred             cCCCCCchhHHHHHHHHHHHh---------CCCCchhhHH
Q 040234          145 FDTHKPLEEYVELAESVVRIC---------HCQKSTLNAL  175 (377)
Q Consensus       145 ~~~~~~~~~~~~~~~~I~~~c---------~G~~lplal~  175 (377)
                      ........-.++..+.|++.+         +|  .|..+.
T Consensus       207 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G--~~r~~~  244 (389)
T 1fnn_A          207 KAGLAEGSYSEDILQMIADITGAQTPLDTNRG--DARLAI  244 (389)
T ss_dssp             HHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSC--CHHHHH
T ss_pred             HhhcCCCCCCHHHHHHHHHHHhhcccCCCCCC--cHHHHH
Confidence            321001111246778888998         68  765443

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.68  E-value=1.1e-07  Score=82.20  Aligned_cols=154  Identities=12%  Similarity=0.108  Sum_probs=86.8

Q ss_pred             CCCCcHHHHHHHHHchhccc-cccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHE-FDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      .+|+|||+||+.+++++... +.......+.+...    ....+. ..+.......               .....++.+
T Consensus        46 ~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~~-~~~~~~~~~~---------------~~~~~~~~v  105 (226)
T 2chg_A           46 PPGTGKTATAIALARDLFGENWRDNFIEMNASDER----GIDVVR-HKIKEFARTA---------------PIGGAPFKI  105 (226)
T ss_dssp             STTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTT----CHHHHH-HHHHHHHTSC---------------CSTTCSCEE
T ss_pred             CCCCCHHHHHHHHHHHHhccccccceEEecccccc----ChHHHH-HHHHHHhccc---------------CCCccCceE
Confidence            37999999999999865433 22222222122211    222221 1111111100               001356889


Q ss_pred             EEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecchhH-Hhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHH
Q 040234           80 VVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNEHL-LKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYV  155 (377)
Q Consensus        80 LVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~~v-~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~  155 (377)
                      |||||++..  +..+.+...+.....+.++|+||+.... ... ......+++.+++.++..+++.+.+.......  ..
T Consensus       106 liiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~--~~  183 (226)
T 2chg_A          106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKI--TE  183 (226)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB--CH
T ss_pred             EEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHHHHHHHHHHHcCCCC--CH
Confidence            999999763  3333333332222456788888876531 111 12234789999999999999988764222111  13


Q ss_pred             HHHHHHHHHhCCCCchhhHHHHH
Q 040234          156 ELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       156 ~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      +..+.|++.++|  .|..+....
T Consensus       184 ~~~~~l~~~~~g--~~r~l~~~l  204 (226)
T 2chg_A          184 DGLEALIYISGG--DFRKAINAL  204 (226)
T ss_dssp             HHHHHHHHHHTT--CHHHHHHHH
T ss_pred             HHHHHHHHHcCC--CHHHHHHHH
Confidence            567789999999  998765433

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.37  E-value=1e-06  Score=81.02  Aligned_cols=151  Identities=11%  Similarity=0.184  Sum_probs=85.2

Q ss_pred             CCCCcHHHHHHHHHchhccc-cccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-cCceE
Q 040234            1 MGGLGKTTLARVVYDLISHE-FDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-RRKKV   78 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-~~k~~   78 (377)
                      ++|+|||++|+.+++.+... +...+...+.+...    .. ..++.++..+.....               .+ .+++.
T Consensus        50 ~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~----~~-~~i~~~~~~~~~~~~---------------~~~~~~~~  109 (323)
T 1sxj_B           50 MPGIGKTTSVHCLAHELLGRSYADGVLELNASDDR----GI-DVVRNQIKHFAQKKL---------------HLPPGKHK  109 (323)
T ss_dssp             STTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCC----SH-HHHHTHHHHHHHBCC---------------CCCTTCCE
T ss_pred             cCCCCHHHHHHHHHHHhcCCcccCCEEEecCcccc----Ch-HHHHHHHHHHHhccc---------------cCCCCCce
Confidence            47999999999999975332 22222222122211    21 222222222211000               01 34588


Q ss_pred             EEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh-HHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCCchhH
Q 040234           79 LVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH-LLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEY  154 (377)
Q Consensus        79 LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~  154 (377)
                      ++||||++.  .+..+.|...+.....++.+|+||+... +... ......+++.+++.++..+++...+.......  .
T Consensus       110 viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~~--~  187 (323)
T 1sxj_B          110 IVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKY--T  187 (323)
T ss_dssp             EEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB--C
T ss_pred             EEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHHHHHHHHHHHcCCCC--C
Confidence            999999976  2334434333222245678888876542 1111 12345899999999999999988763221111  1


Q ss_pred             HHHHHHHHHHhCCCCchhhHH
Q 040234          155 VELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       155 ~~~~~~I~~~c~G~~lplal~  175 (377)
                      ++.+..|++.++|  .|..+.
T Consensus       188 ~~~~~~l~~~~~G--~~r~a~  206 (323)
T 1sxj_B          188 NDGLEAIIFTAEG--DMRQAI  206 (323)
T ss_dssp             HHHHHHHHHHHTT--CHHHHH
T ss_pred             HHHHHHHHHHcCC--CHHHHH
Confidence            3567889999999  996543

>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=98.21  E-value=3.7e-06  Score=81.10  Aligned_cols=156  Identities=18%  Similarity=0.158  Sum_probs=89.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+||||||+.+++.+...++..-++. +        +...+...+...+...          ....+.+.+..+.-+|
T Consensus       138 p~G~GKTtLa~aia~~l~~~~~~~~v~~-v--------~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~vL  198 (440)
T 2z4s_A          138 GVGLGKTHLLQSIGNYVVQNEPDLRVMY-I--------TSEKFLNDLVDSMKEG----------KLNEFREKYRKKVDIL  198 (440)
T ss_dssp             SSSSSHHHHHHHHHHHHHHHCCSSCEEE-E--------EHHHHHHHHHHHHHTT----------CHHHHHHHHTTTCSEE
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCCCeEEE-e--------eHHHHHHHHHHHHHcc----------cHHHHHHHhcCCCCEE
Confidence            3799999999999997766654332222 1        2223344444443221          1223444444466799


Q ss_pred             EEeCCCCh----hhhhHhhCCCCC-CCCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcC
Q 040234           81 VIDDAAHP----DHLRRLVGEPDW-FGPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        81 VLDdv~~~----~~~~~l~~~l~~-~~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      +|||++..    ...+.+...+.. ...|..||+||...         .+..++.....+.+++++.++-.+++.+.+..
T Consensus       199 ~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~  278 (440)
T 2z4s_A          199 LIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEI  278 (440)
T ss_dssp             EEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHH
T ss_pred             EEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHH
Confidence            99999642    122222221110 03466788888752         22333333457889999999999999887632


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ..-..+  .+....|++.++|  .+-.+..+..
T Consensus       279 ~~~~i~--~e~l~~la~~~~g--n~R~l~~~L~  307 (440)
T 2z4s_A          279 EHGELP--EEVLNFVAENVDD--NLRRLRGAII  307 (440)
T ss_dssp             HTCCCC--TTHHHHHHHHCCS--CHHHHHHHHH
T ss_pred             cCCCCC--HHHHHHHHHhcCC--CHHHHHHHHH
Confidence            111111  2456778889999  7766654433

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=98.11  E-value=6.7e-06  Score=75.62  Aligned_cols=99  Identities=13%  Similarity=0.131  Sum_probs=63.6

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecchhH-HhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNEHL-LKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~~v-~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++.++|+|+++..  +..+.+...+.....+.++|+||....- ...+ .....+.+.+++.++..+++...+......
T Consensus       109 ~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~~~  188 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE  188 (327)
T ss_dssp             CSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE
T ss_pred             CCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHHHHHHHHHHhcCCC
Confidence            56789999999763  3444444333222456788888865421 1111 123478999999999999998876433221


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                        -..+..+.|++.++|  .|..+...
T Consensus       189 --~~~~~~~~l~~~~~g--~~r~~~~~  211 (327)
T 1iqp_A          189 --LTEEGLQAILYIAEG--DMRRAINI  211 (327)
T ss_dssp             --ECHHHHHHHHHHHTT--CHHHHHHH
T ss_pred             --CCHHHHHHHHHHCCC--CHHHHHHH
Confidence              124567889999999  88865443

>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=98.10  E-value=2.1e-05  Score=71.96  Aligned_cols=98  Identities=11%  Similarity=0.115  Sum_probs=64.3

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh-HHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH-LLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++.  .+..+.+...+.....+.++|+||.... +... ......+++.+++.++..+++...+......
T Consensus       101 ~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~  180 (319)
T 2chq_A          101 APFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK  180 (319)
T ss_dssp             CCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHHHHHHHHHHHTTCCC
T ss_pred             CCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            5678999999976  3444555555544345677887776543 2111 1224579999999999999998877433222


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALM  176 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~  176 (377)
                        -.++..+.|++.++|  .+..+..
T Consensus       181 --i~~~~l~~l~~~~~G--~~r~~~~  202 (319)
T 2chq_A          181 --ITEDGLEALIYISGG--DFRKAIN  202 (319)
T ss_dssp             --BCHHHHHHHHHTTTT--CHHHHHH
T ss_pred             --CCHHHHHHHHHHcCC--CHHHHHH
Confidence              124567788889999  8776543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.07  E-value=2e-05  Score=72.33  Aligned_cols=139  Identities=12%  Similarity=-0.004  Sum_probs=74.8

Q ss_pred             CCCCcHHHHHHHHHchhccccc-------cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHH-
Q 040234            1 MGGLGKTTLARVVYDLISHEFD-------GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVR-   72 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~-------~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~-   72 (377)
                      .+|+|||++|+.+++++.....       ..+.+. .....    +...++..|++++.+.........+.+...+... 
T Consensus        53 pPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~IN-c~~~~----t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~  127 (318)
T 3te6_A           53 ADDSTKFQLVNDVMDELITSSARKELPIFDYIHID-ALELA----GMDALYEKIWFAISKENLCGDISLEALNFYITNVP  127 (318)
T ss_dssp             CCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEE-TTCCC------HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEe-ccccC----CHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhh
Confidence            4799999999999997653221       123343 22222    6678888899888654221111222222222221 


Q ss_pred             -hcCceEEEEEeCCCCh---hhhhHhhCCCCCCCCCCeEEEEecchh-----H----HhhCCCCCeeecCCCChhhhHHH
Q 040234           73 -LRRKKVLVVIDDAAHP---DHLRRLVGEPDWFGPGSRIIITTRNEH-----L----LKLHPVKKVYKLEALTYDEAFRL  139 (377)
Q Consensus        73 -l~~k~~LLVLDdv~~~---~~~~~l~~~l~~~~~gs~IIvTTR~~~-----v----~~~~~~~~~~~l~~L~~~ea~~L  139 (377)
                       -.+++.+++||+++..   +.+..+............||.++....     +    ..++. ...+.+.+++.++-.++
T Consensus       128 ~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~L~~~v~SR~~-~~~i~F~pYt~~el~~I  206 (318)
T 3te6_A          128 KAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAH-FTEIKLNKVDKNELQQM  206 (318)
T ss_dssp             GGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHHHHTCHHHHTT-EEEEECCCCCHHHHHHH
T ss_pred             hccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccchhhcchhhhccCC-ceEEEeCCCCHHHHHHH
Confidence             1456899999999863   222222210000011223444443321     1    12221 24689999999999999


Q ss_pred             HHHHhc
Q 040234          140 LCLKAF  145 (377)
Q Consensus       140 ~~~~~~  145 (377)
                      +.+++.
T Consensus       207 l~~Rl~  212 (318)
T 3te6_A          207 IITRLK  212 (318)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988764

>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=98.00  E-value=3.2e-06  Score=74.04  Aligned_cols=144  Identities=12%  Similarity=0.038  Sum_probs=79.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++..........++. ......   ..                      .+..    +.+ .++-+|
T Consensus        60 ~~G~GKT~la~~l~~~~~~~~~~~~~~~-~~~~~~---~~----------------------~~~~----~~~-~~~~vl  108 (242)
T 3bos_A           60 PVKSGRTHLIHAACARANELERRSFYIP-LGIHAS---IS----------------------TALL----EGL-EQFDLI  108 (242)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTCCEEEEE-GGGGGG---SC----------------------GGGG----TTG-GGSSEE
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCeEEEEE-HHHHHH---HH----------------------HHHH----Hhc-cCCCEE
Confidence            3799999999999996654433334443 322210   00                      0000    011 345689


Q ss_pred             EEeCCCChh--h--hhHhhCCCCCC-CCCC-eEEEEecchh---------HHhhCCCCCeeecCCCChhhhHHHHHHHhc
Q 040234           81 VIDDAAHPD--H--LRRLVGEPDWF-GPGS-RIIITTRNEH---------LLKLHPVKKVYKLEALTYDEAFRLLCLKAF  145 (377)
Q Consensus        81 VLDdv~~~~--~--~~~l~~~l~~~-~~gs-~IIvTTR~~~---------v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~  145 (377)
                      ||||++...  .  .+.+...+... ..+. ++|+||+...         +.........+++++++.++..+++...+.
T Consensus       109 iiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~  188 (242)
T 3bos_A          109 CIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAA  188 (242)
T ss_dssp             EEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHH
T ss_pred             EEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHH
Confidence            999986531  1  22222211100 1122 4788776421         122111236789999999999999988764


Q ss_pred             CCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          146 DTHKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       146 ~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      .....  -.++..+.|++.++|  .+-.+..+..
T Consensus       189 ~~~~~--~~~~~~~~l~~~~~g--~~r~l~~~l~  218 (242)
T 3bos_A          189 MRGLQ--LPEDVGRFLLNRMAR--DLRTLFDVLD  218 (242)
T ss_dssp             HTTCC--CCHHHHHHHHHHTTT--CHHHHHHHHH
T ss_pred             HcCCC--CCHHHHHHHHHHccC--CHHHHHHHHH
Confidence            22211  124567789999999  7766654433

>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=97.96  E-value=4.7e-05  Score=71.34  Aligned_cols=101  Identities=14%  Similarity=0.072  Sum_probs=63.4

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh-HHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH-LLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++.++|+||++.  .+..+.+...+.....+..+|++|.... +... ......+++.+++.++..+++...+......
T Consensus       118 ~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~  197 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA  197 (373)
T ss_dssp             SSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC
T ss_pred             CCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            4578999999975  3334444433322244566777775432 2111 1234678999999999999998766321111


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      .  ..+.+..|++.++|  .|..+.....
T Consensus       198 ~--~~~a~~~l~~~~~G--~~r~~~~~l~  222 (373)
T 1jr3_A          198 H--EPRALQLLARAAEG--SLRDALSLTD  222 (373)
T ss_dssp             B--CHHHHHHHHHHSSS--CHHHHHHHHH
T ss_pred             C--CHHHHHHHHHHCCC--CHHHHHHHHH
Confidence            1  14567889999999  9988765443

>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=97.87  E-value=8.1e-05  Score=68.97  Aligned_cols=95  Identities=17%  Similarity=0.057  Sum_probs=62.3

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++..  +..+.|+..+..-.++..+|++|.... +...+ +....+++.++++++..+.+....    ..
T Consensus       107 ~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~----~~  182 (334)
T 1a5t_A          107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV----TM  182 (334)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHC----CC
T ss_pred             CCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhc----CC
Confidence            45779999999863  334444443333245667777766542 32222 345689999999999999998775    11


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                      .   ++.+..+++.++|  .|..+....
T Consensus       183 ~---~~~~~~l~~~s~G--~~r~a~~~l  205 (334)
T 1a5t_A          183 S---QDALLAALRLSAG--SPGAALALF  205 (334)
T ss_dssp             C---HHHHHHHHHHTTT--CHHHHHHTT
T ss_pred             C---HHHHHHHHHHcCC--CHHHHHHHh
Confidence            1   3456789999999  887665443

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=97.85  E-value=6.5e-05  Score=68.99  Aligned_cols=72  Identities=17%  Similarity=-0.078  Sum_probs=46.8

Q ss_pred             CCeEEEEecchh-HHhhC--CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          104 GSRIIITTRNEH-LLKLH--PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       104 gs~IIvTTR~~~-v~~~~--~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ...+|.||.... +...+  .....+.+.+++.++..+++...+.......  .++..+.|++.++|  .|..+..+..
T Consensus       138 ~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~--~~~~~~~l~~~~~G--~~r~l~~~l~  212 (324)
T 1hqc_A          138 RFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRI--TEEAALEIGRRSRG--TMRVAKRLFR  212 (324)
T ss_dssp             CCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCCC--CHHHHHHHHHHSCS--CHHHHHHHHH
T ss_pred             CEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHccC--CHHHHHHHHH
Confidence            345666665432 11111  1135789999999999999988774332221  24667889999999  9987765544

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.84  E-value=0.00024  Score=65.40  Aligned_cols=146  Identities=14%  Similarity=0.118  Sum_probs=78.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++.....-...+++.           ...+...+...+...          ....+...+. +.-+|
T Consensus        45 ~~GtGKT~la~~i~~~~~~~~~~~~~i~-----------~~~~~~~~~~~~~~~----------~~~~~~~~~~-~~~vL  102 (324)
T 1l8q_A           45 SVGTGKTHLLQAAGNEAKKRGYRVIYSS-----------ADDFAQAMVEHLKKG----------TINEFRNMYK-SVDLL  102 (324)
T ss_dssp             SSSSSHHHHHHHHHHHHHHTTCCEEEEE-----------HHHHHHHHHHHHHHT----------CHHHHHHHHH-TCSEE
T ss_pred             CCCCcHHHHHHHHHHHHHHCCCEEEEEE-----------HHHHHHHHHHHHHcC----------cHHHHHHHhc-CCCEE
Confidence            3799999999999996643311122322           223333333333211          1122233332 36699


Q ss_pred             EEeCCCChh----hhhHhhCCCCC-CCCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcC
Q 040234           81 VIDDAAHPD----HLRRLVGEPDW-FGPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        81 VLDdv~~~~----~~~~l~~~l~~-~~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      +||++....    ..+.+...+.. ...+..||+||...         .+..++.....+++++ +.++-.+++...+..
T Consensus       103 ~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~  181 (324)
T 1l8q_A          103 LLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKE  181 (324)
T ss_dssp             EEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHH
T ss_pred             EEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHHHHh
Confidence            999986532    11222211110 02355788887642         2222223335689999 999999999887742


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhhH
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                      .....+  ++....|++.+ |  ..-.+
T Consensus       182 ~~~~l~--~~~l~~l~~~~-g--~~r~l  204 (324)
T 1l8q_A          182 FNLELR--KEVIDYLLENT-K--NVREI  204 (324)
T ss_dssp             TTCCCC--HHHHHHHHHHC-S--SHHHH
T ss_pred             cCCCCC--HHHHHHHHHhC-C--CHHHH
Confidence            222111  45677788888 7  55443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.67  E-value=0.00033  Score=65.51  Aligned_cols=92  Identities=13%  Similarity=0.092  Sum_probs=54.2

Q ss_pred             eEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecc-----------------hhHHhhCCCCCeeecCCCChhhhH
Q 040234           77 KVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRN-----------------EHLLKLHPVKKVYKLEALTYDEAF  137 (377)
Q Consensus        77 ~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~-----------------~~v~~~~~~~~~~~l~~L~~~ea~  137 (377)
                      +-+|+||+++..  +....+...+.. .....++++|..                 +.+..   ....+.+.+++.++..
T Consensus       190 ~~vl~IDEi~~l~~~~~~~L~~~le~-~~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s---R~~~i~~~~~~~~e~~  265 (368)
T 3uk6_A          190 PGVLFIDEVHMLDIESFSFLNRALES-DMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLD---RLLIVSTTPYSEKDTK  265 (368)
T ss_dssp             BCEEEEESGGGSBHHHHHHHHHHTTC-TTCCEEEEEESCSEEECBTSSCEEETTCCHHHHT---TEEEEEECCCCHHHHH
T ss_pred             CceEEEhhccccChHHHHHHHHHhhC-cCCCeeeeecccceeeeeccCCCCcccCCHHHHh---hccEEEecCCCHHHHH
Confidence            359999999763  334444433332 222234444431                 12222   2345799999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhC-CCCchhhHHH
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICH-CQKSTLNALM  176 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~-G~~lplal~~  176 (377)
                      +++..++......  -..+....|++.+. |  .|-.+..
T Consensus       266 ~il~~~~~~~~~~--~~~~~l~~l~~~~~~G--~~r~~~~  301 (368)
T 3uk6_A          266 QILRIRCEEEDVE--MSEDAYTVLTRIGLET--SLRYAIQ  301 (368)
T ss_dssp             HHHHHHHHHTTCC--BCHHHHHHHHHHHHHS--CHHHHHH
T ss_pred             HHHHHHHHHcCCC--CCHHHHHHHHHHhcCC--CHHHHHH
Confidence            9998876432222  12456778888887 7  6665543

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.60  E-value=0.00028  Score=63.19  Aligned_cols=88  Identities=16%  Similarity=0.106  Sum_probs=49.8

Q ss_pred             hcCceEEEEEeCCCCh------------hhhh---HhhCCCCCCCCCCeEEEEecchhHHhh--C-C-CCCeeecCCCCh
Q 040234           73 LRRKKVLVVIDDAAHP------------DHLR---RLVGEPDWFGPGSRIIITTRNEHLLKL--H-P-VKKVYKLEALTY  133 (377)
Q Consensus        73 l~~k~~LLVLDdv~~~------------~~~~---~l~~~l~~~~~gs~IIvTTR~~~v~~~--~-~-~~~~~~l~~L~~  133 (377)
                      ...+.-+|+||+++..            ..++   .+............||.||........  . . -...+++++++.
T Consensus       121 ~~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~  200 (272)
T 1d2n_A          121 YKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIAT  200 (272)
T ss_dssp             HTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEE
T ss_pred             HhcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccH
Confidence            3456889999998542            1222   332222212233456777877654333  1 1 145688899988


Q ss_pred             -hhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          134 -DEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       134 -~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                       ++..+++.+..    ...   .+....|++.+.|
T Consensus       201 r~~i~~i~~~~~----~~~---~~~~~~l~~~~~g  228 (272)
T 1d2n_A          201 GEQLLEALELLG----NFK---DKERTTIAQQVKG  228 (272)
T ss_dssp             HHHHHHHHHHHT----CSC---HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcC----CCC---HHHHHHHHHHhcC
Confidence             66666655432    111   3456788888877

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.58  E-value=0.00024  Score=65.91  Aligned_cols=99  Identities=11%  Similarity=0.103  Sum_probs=59.7

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      .++-+|++|+++..  .....+...+.......++|++|.... +...+ .....+.+.+++.++..+.+...+......
T Consensus       132 ~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~~~~~  211 (353)
T 1sxj_D          132 PPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVK  211 (353)
T ss_dssp             CSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCC
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEEeCCCCHHHHHHHHHHHHHHhCCC
Confidence            35569999998652  223333332222234566777765432 11111 113478899999999999998876432211


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      .  .++..+.|++.++|  .|..+...
T Consensus       212 i--~~~~l~~l~~~~~G--~~r~~~~~  234 (353)
T 1sxj_D          212 C--DDGVLERILDISAG--DLRRGITL  234 (353)
T ss_dssp             C--CHHHHHHHHHHTSS--CHHHHHHH
T ss_pred             C--CHHHHHHHHHHcCC--CHHHHHHH
Confidence            1  24577899999999  88765433

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=97.55  E-value=0.00074  Score=59.75  Aligned_cols=145  Identities=16%  Similarity=0.096  Sum_probs=74.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++....|   +.+. .+........                    .........+.......+.+|
T Consensus        47 ~~GtGKT~la~~la~~~~~~~---~~~~-~~~~~~~~~~--------------------~~~~~~~~~~~~a~~~~~~vl  102 (262)
T 2qz4_A           47 PPGCGKTLLAKAVATEAQVPF---LAMA-GAEFVEVIGG--------------------LGAARVRSLFKEARARAPCIV  102 (262)
T ss_dssp             CTTSSHHHHHHHHHHHHTCCE---EEEE-TTTTSSSSTT--------------------HHHHHHHHHHHHHHHTCSEEE
T ss_pred             CCCCCHHHHHHHHHHHhCCCE---EEec-hHHHHhhccC--------------------hhHHHHHHHHHHHHhcCCeEE
Confidence            479999999999998664332   1121 2221100000                    001111222333334457899


Q ss_pred             EEeCCCCh-----------------hhhhHhhCCCCC--CCCCCeEEEEecchhHHh-hC----CCCCeeecCCCChhhh
Q 040234           81 VIDDAAHP-----------------DHLRRLVGEPDW--FGPGSRIIITTRNEHLLK-LH----PVKKVYKLEALTYDEA  136 (377)
Q Consensus        81 VLDdv~~~-----------------~~~~~l~~~l~~--~~~gs~IIvTTR~~~v~~-~~----~~~~~~~l~~L~~~ea  136 (377)
                      +||+++..                 ..+..++..+..  ...+..||.||....... ..    .-...+.++..+.++-
T Consensus       103 ~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r  182 (262)
T 2qz4_A          103 YIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQER  182 (262)
T ss_dssp             EEECC-------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHH
T ss_pred             EEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHH
Confidence            99999753                 112223221111  123446666775543211 11    2235678899999999


Q ss_pred             HHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchh
Q 040234          137 FRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       137 ~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpl  172 (377)
                      .+++...+....... ........+++.+.|  .+-
T Consensus       183 ~~il~~~~~~~~~~~-~~~~~~~~l~~~~~g--~~~  215 (262)
T 2qz4_A          183 REIFEQHLKSLKLTQ-SSTFYSQRLAELTPG--FSG  215 (262)
T ss_dssp             HHHHHHHHHHTTCCB-THHHHHHHHHHTCTT--CCH
T ss_pred             HHHHHHHHHhCCCCc-chhhHHHHHHHHCCC--CCH
Confidence            999987764322221 112235778888888  654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.54  E-value=0.00027  Score=68.08  Aligned_cols=144  Identities=18%  Similarity=0.215  Sum_probs=77.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+||||||+.+++.....|..   +. ....     ....+ +.++....                 .....+++.+|
T Consensus        58 ppGtGKTtlAr~ia~~~~~~f~~---l~-a~~~-----~~~~i-r~~~~~a~-----------------~~~~~~~~~iL  110 (447)
T 3pvs_A           58 PPGTGKTTLAEVIARYANADVER---IS-AVTS-----GVKEI-REAIERAR-----------------QNRNAGRRTIL  110 (447)
T ss_dssp             STTSSHHHHHHHHHHHTTCEEEE---EE-TTTC-----CHHHH-HHHHHHHH-----------------HHHHTTCCEEE
T ss_pred             CCCCcHHHHHHHHHHHhCCCeEE---EE-eccC-----CHHHH-HHHHHHHH-----------------HhhhcCCCcEE
Confidence            37999999999999976544321   11 1111     22222 12211110                 01114567899


Q ss_pred             EEeCCCCh--hhhhHhhCCCCCCCCCCeEEE-Eecchh--HH-hhCCCCCeeecCCCChhhhHHHHHHHhcCCC-----C
Q 040234           81 VIDDAAHP--DHLRRLVGEPDWFGPGSRIII-TTRNEH--LL-KLHPVKKVYKLEALTYDEAFRLLCLKAFDTH-----K  149 (377)
Q Consensus        81 VLDdv~~~--~~~~~l~~~l~~~~~gs~IIv-TTR~~~--v~-~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~-----~  149 (377)
                      +||++...  .+.+.|+..+..  ....+|. ||.+..  +. .......++.+.+++.++..+++.+.+....     .
T Consensus       111 fIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~  188 (447)
T 3pvs_A          111 FVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQ  188 (447)
T ss_dssp             EEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTS
T ss_pred             EEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccc
Confidence            99999763  333444433322  2233443 555442  11 1113345788999999999999988764311     1


Q ss_pred             CchhHHHHHHHHHHHhCCCCchhhHH
Q 040234          150 PLEEYVELAESVVRICHCQKSTLNAL  175 (377)
Q Consensus       150 ~~~~~~~~~~~I~~~c~G~~lplal~  175 (377)
                      ...-..+..+.|++.++|  .+-.+.
T Consensus       189 ~~~i~~~al~~L~~~~~G--d~R~ll  212 (447)
T 3pvs_A          189 DIVLPDETRRAIAELVNG--DARRAL  212 (447)
T ss_dssp             SEECCHHHHHHHHHHHCS--CHHHHH
T ss_pred             cCcCCHHHHHHHHHHCCC--CHHHHH
Confidence            112234567778888888  666543

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.50  E-value=0.0012  Score=60.60  Aligned_cols=90  Identities=11%  Similarity=-0.013  Sum_probs=52.2

Q ss_pred             cCceEEEEEeCCCChh-------------hhhHhhC---CCCCCCCCCeEEEEecch-----hHHhhCCCCCeeecCCCC
Q 040234           74 RRKKVLVVIDDAAHPD-------------HLRRLVG---EPDWFGPGSRIIITTRNE-----HLLKLHPVKKVYKLEALT  132 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~~-------------~~~~l~~---~l~~~~~gs~IIvTTR~~-----~v~~~~~~~~~~~l~~L~  132 (377)
                      ..++.+|+||+++...             ....++.   .+.....+..||.||...     .+.+  .-...+.++..+
T Consensus       103 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~  180 (322)
T 1xwi_A          103 ENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPE  180 (322)
T ss_dssp             HTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHH--TCCEEEECCCCC
T ss_pred             hcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHh--hcCeEEEeCCcC
Confidence            3567899999997531             1122221   111112344555566543     2222  234567889999


Q ss_pred             hhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          133 YDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       133 ~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .++-.+++...........  .......|++.+.|
T Consensus       181 ~~~r~~il~~~l~~~~~~l--~~~~l~~la~~t~G  213 (322)
T 1xwi_A          181 PHARAAMFKLHLGTTQNSL--TEADFRELGRKTDG  213 (322)
T ss_dssp             HHHHHHHHHHHHTTCCBCC--CHHHHHHHHHTCTT
T ss_pred             HHHHHHHHHHHHhcCCCCC--CHHHHHHHHHHcCC
Confidence            9999999988774332211  13456788888888

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.49  E-value=0.00012  Score=66.03  Aligned_cols=140  Identities=16%  Similarity=0.154  Sum_probs=73.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++.....|-   .+. ........  ...                  ........+......++.+|
T Consensus        59 ~~GtGKT~la~~la~~~~~~~~---~v~-~~~~~~~~--~~~------------------~~~~~~~~~~~~~~~~~~vl  114 (285)
T 3h4m_A           59 PPGTGKTLLAKAVATETNATFI---RVV-GSELVKKF--IGE------------------GASLVKDIFKLAKEKAPSII  114 (285)
T ss_dssp             SSSSSHHHHHHHHHHHTTCEEE---EEE-GGGGCCCS--TTH------------------HHHHHHHHHHHHHHTCSEEE
T ss_pred             CCCCcHHHHHHHHHHHhCCCEE---EEe-hHHHHHhc--cch------------------HHHHHHHHHHHHHHcCCeEE
Confidence            4799999999999987644321   111 22211110  000                  00111122222234456899


Q ss_pred             EEeCCCCh----------------hhhhHhhCCCC--CCCCCCeEEEEecchhH-----HhhCCCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHP----------------DHLRRLVGEPD--WFGPGSRIIITTRNEHL-----LKLHPVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~----------------~~~~~l~~~l~--~~~~gs~IIvTTR~~~v-----~~~~~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++..                ..+..+...+.  ....+..||.||.....     .....-...+.++..+.++..
T Consensus       115 ~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~  194 (285)
T 3h4m_A          115 FIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRL  194 (285)
T ss_dssp             EEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHH
T ss_pred             EEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHH
Confidence            99999642                11222222111  11235567778775422     111122347889999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      +++............   .....|++...|
T Consensus       195 ~il~~~~~~~~~~~~---~~~~~l~~~~~g  221 (285)
T 3h4m_A          195 EILKIHTRKMNLAED---VNLEEIAKMTEG  221 (285)
T ss_dssp             HHHHHHHTTSCBCTT---CCHHHHHHHCTT
T ss_pred             HHHHHHHhcCCCCCc---CCHHHHHHHcCC
Confidence            999887743221111   124567777777

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.46  E-value=0.00066  Score=63.02  Aligned_cols=100  Identities=11%  Similarity=0.090  Sum_probs=59.9

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      .++-++|||++...  +..+.+...+.....+..+|++|... .+...+ .....+++.+++.++..+.+...+....-.
T Consensus       133 ~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~  212 (354)
T 1sxj_E          133 HRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQ  212 (354)
T ss_dssp             -CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCE
T ss_pred             CCCeEEEEeCccccCHHHHHHHHHHHHhhcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCC
Confidence            46679999999763  22233332222113466777777653 221111 234678999999999999998776322111


Q ss_pred             chhH-HHHHHHHHHHhCCCCchhhHHHHH
Q 040234          151 LEEY-VELAESVVRICHCQKSTLNALMSV  178 (377)
Q Consensus       151 ~~~~-~~~~~~I~~~c~G~~lplal~~~~  178 (377)
                        -. ++.+..|++.++|  .+-.+....
T Consensus       213 --~~~~~~l~~i~~~~~G--~~r~a~~~l  237 (354)
T 1sxj_E          213 --LETKDILKRIAQASNG--NLRVSLLML  237 (354)
T ss_dssp             --ECCSHHHHHHHHHHTT--CHHHHHHHH
T ss_pred             --CCcHHHHHHHHHHcCC--CHHHHHHHH
Confidence              11 2467788899999  776654433

>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=97.45  E-value=0.00038  Score=68.45  Aligned_cols=93  Identities=9%  Similarity=0.080  Sum_probs=53.9

Q ss_pred             CceEEEEEeCCCChh-----hhhHhhCCCCCCCCCCeEEEEecchh---HHhhCCCCCeeecCCCChhhhHHHHHHHhcC
Q 040234           75 RKKVLVVIDDAAHPD-----HLRRLVGEPDWFGPGSRIIITTRNEH---LLKLHPVKKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        75 ~k~~LLVLDdv~~~~-----~~~~l~~~l~~~~~gs~IIvTTR~~~---v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      .++.+|+||+++...     .+..+...+.  ..+..||+++....   +.........+.+++++.++..+++...+..
T Consensus       147 ~~~~vliIDEid~l~~~~~~~l~~L~~~l~--~~~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~  224 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCR--KTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIR  224 (516)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHH--HCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCccchhhHHHHHHHHHHHH--hcCCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHH
Confidence            567899999996521     1222222111  12334665554322   2222234567899999999999998876643


Q ss_pred             CC-CCchhHHHHHHHHHHHhCCCCchhhH
Q 040234          147 TH-KPLEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       147 ~~-~~~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                      .. ...   ++....|++.++|  .+-.+
T Consensus       225 ~~~~i~---~~~l~~la~~s~G--diR~~  248 (516)
T 1sxj_A          225 EKFKLD---PNVIDRLIQTTRG--DIRQV  248 (516)
T ss_dssp             HTCCCC---TTHHHHHHHHTTT--CHHHH
T ss_pred             cCCCCC---HHHHHHHHHHcCC--cHHHH
Confidence            21 112   2356788888888  55443

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=97.45  E-value=0.00066  Score=62.43  Aligned_cols=90  Identities=11%  Similarity=0.031  Sum_probs=52.7

Q ss_pred             cCceEEEEEeCCCChh-------------hhhHhh---CCCCCCCCCCeEEEEecchh-----HHhhCCCCCeeecCCCC
Q 040234           74 RRKKVLVVIDDAAHPD-------------HLRRLV---GEPDWFGPGSRIIITTRNEH-----LLKLHPVKKVYKLEALT  132 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~~-------------~~~~l~---~~l~~~~~gs~IIvTTR~~~-----v~~~~~~~~~~~l~~L~  132 (377)
                      ..++.+|+||+++...             ....++   ..+.....+..||.||....     +.++  -...+.++..+
T Consensus       108 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~R--f~~~i~~~~p~  185 (322)
T 3eie_A          108 ENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRR--FERRIYIPLPD  185 (322)
T ss_dssp             HTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHHH--CCEEEECCCCC
T ss_pred             hcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHcc--cCeEEEeCCCC
Confidence            3466899999997421             112222   21111134555666776532     2222  23567888899


Q ss_pred             hhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          133 YDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       133 ~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .++-.+++...+........  ......|++.+.|
T Consensus       186 ~~~r~~il~~~~~~~~~~~~--~~~l~~la~~t~g  218 (322)
T 3eie_A          186 LAARTTMFEINVGDTPCVLT--KEDYRTLGAMTEG  218 (322)
T ss_dssp             HHHHHHHHHHHHTTCCCCCC--HHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHhccCCCCCC--HHHHHHHHHHcCC
Confidence            99999999888754322211  3456788888877

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=97.40  E-value=0.0011  Score=61.89  Aligned_cols=90  Identities=11%  Similarity=0.042  Sum_probs=52.1

Q ss_pred             cCceEEEEEeCCCChh-------------hhhHhhCC---CCCCCCCCeEEEEecch-----hHHhhCCCCCeeecCCCC
Q 040234           74 RRKKVLVVIDDAAHPD-------------HLRRLVGE---PDWFGPGSRIIITTRNE-----HLLKLHPVKKVYKLEALT  132 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~~-------------~~~~l~~~---l~~~~~gs~IIvTTR~~-----~v~~~~~~~~~~~l~~L~  132 (377)
                      ..++.+|+||+++...             ....++..   +.....+..||.||...     .+.+  .-...+.++..+
T Consensus       141 ~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~  218 (355)
T 2qp9_X          141 ENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPD  218 (355)
T ss_dssp             HTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHH--TCCEEEECCCCC
T ss_pred             HcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHc--ccCEEEEeCCcC
Confidence            4567899999987521             12222211   11112344566666543     2223  334567889999


Q ss_pred             hhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          133 YDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       133 ~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .++-.+++............  ......|++.+.|
T Consensus       219 ~~~r~~il~~~l~~~~~~~~--~~~l~~la~~t~G  251 (355)
T 2qp9_X          219 LAARTTMFEINVGDTPSVLT--KEDYRTLGAMTEG  251 (355)
T ss_dssp             HHHHHHHHHHHHTTSCBCCC--HHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhhCCCCCC--HHHHHHHHHHcCC
Confidence            99999999887743321111  3456788888888

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.36  E-value=7.3e-05  Score=62.52  Aligned_cols=18  Identities=28%  Similarity=0.339  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+|||+||+.+++.+.
T Consensus        51 ~~G~GKT~l~~~~~~~~~   68 (195)
T 1jbk_A           51 EPGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999998653

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.35  E-value=0.0014  Score=59.59  Aligned_cols=67  Identities=10%  Similarity=0.081  Sum_probs=43.2

Q ss_pred             eEEEEEeCCC-----------ChhhhhHhhCCCCCCCCCCeEEEEecchh----------HHhhCCCCCeeecCCCChhh
Q 040234           77 KVLVVIDDAA-----------HPDHLRRLVGEPDWFGPGSRIIITTRNEH----------LLKLHPVKKVYKLEALTYDE  135 (377)
Q Consensus        77 ~~LLVLDdv~-----------~~~~~~~l~~~l~~~~~gs~IIvTTR~~~----------v~~~~~~~~~~~l~~L~~~e  135 (377)
                      .-+|+||+++           +.+....|...+.....+..||+||....          +..+  ....+.+++++.++
T Consensus       131 ~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~R--~~~~i~~~~~~~~~  208 (309)
T 3syl_A          131 GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSR--IAHHIEFPDYSDEE  208 (309)
T ss_dssp             TSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEECHHHHHHHHHHSTTHHHH--EEEEEEECCCCHHH
T ss_pred             CCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeCChHHHHHHHhhCHHHHHh--CCeEEEcCCcCHHH
Confidence            4599999997           33334444433333345667888875432          2222  13678999999999


Q ss_pred             hHHHHHHHhc
Q 040234          136 AFRLLCLKAF  145 (377)
Q Consensus       136 a~~L~~~~~~  145 (377)
                      -.+++...+.
T Consensus       209 ~~~il~~~l~  218 (309)
T 3syl_A          209 LFEIAGHMLD  218 (309)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999988764

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=97.34  E-value=0.002  Score=62.01  Aligned_cols=90  Identities=11%  Similarity=0.015  Sum_probs=54.5

Q ss_pred             cCceEEEEEeCCCCh-------------hhhhHhhCCCCC---CCCCCeEEEEecchh-----HHhhCCCCCeeecCCCC
Q 040234           74 RRKKVLVVIDDAAHP-------------DHLRRLVGEPDW---FGPGSRIIITTRNEH-----LLKLHPVKKVYKLEALT  132 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~-------------~~~~~l~~~l~~---~~~gs~IIvTTR~~~-----v~~~~~~~~~~~l~~L~  132 (377)
                      ..++.+|+||+++..             .....++..+..   ...+..||.||....     +.+  .-...+.++..+
T Consensus       225 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~  302 (444)
T 2zan_A          225 ENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPE  302 (444)
T ss_dssp             HSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHT--TCCEEEECCCCC
T ss_pred             HcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHh--hcceEEEeCCcC
Confidence            456789999999753             123344444432   133456666776542     222  233567888888


Q ss_pred             hhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          133 YDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       133 ~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .++-.++|...........  .......|++.+.|
T Consensus       303 ~~~r~~il~~~l~~~~~~l--~~~~l~~la~~t~G  335 (444)
T 2zan_A          303 AHARAAMFRLHLGSTQNSL--TEADFQELGRKTDG  335 (444)
T ss_dssp             HHHHHHHHHHHHTTSCEEC--CHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhcCCCCC--CHHHHHHHHHHcCC
Confidence            8888898888764322111  13456788888888

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.28  E-value=0.00027  Score=59.03  Aligned_cols=90  Identities=19%  Similarity=0.129  Sum_probs=46.5

Q ss_pred             CCCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ..|+||||||+.+++.+..... ..+++           +..++...+.......      ......    +.+. +.-+
T Consensus        46 ~~G~GKTtL~~~i~~~~~~~~g~~~~~~-----------~~~~~~~~~~~~~~~~------~~~~~~----~~~~-~~~l  103 (180)
T 3ec2_A           46 SPGVGKTHLAVATLKAIYEKKGIRGYFF-----------DTKDLIFRLKHLMDEG------KDTKFL----KTVL-NSPV  103 (180)
T ss_dssp             SSSSSHHHHHHHHHHHHHHHSCCCCCEE-----------EHHHHHHHHHHHHHHT------CCSHHH----HHHH-TCSE
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCeEEEE-----------EHHHHHHHHHHHhcCc------hHHHHH----HHhc-CCCE
Confidence            3699999999999996642212 22232           3334444444333221      111112    2222 4568


Q ss_pred             EEEeCCCC--hhh-----hhHhhCCCCCCCCCCeEEEEecch
Q 040234           80 VVIDDAAH--PDH-----LRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        80 LVLDdv~~--~~~-----~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      ||||++..  .+.     +..+.....  ..+..+|+||...
T Consensus       104 lilDE~~~~~~~~~~~~~l~~ll~~~~--~~~~~ii~tsn~~  143 (180)
T 3ec2_A          104 LVLDDLGSERLSDWQRELISYIITYRY--NNLKSTIITTNYS  143 (180)
T ss_dssp             EEEETCSSSCCCHHHHHHHHHHHHHHH--HTTCEEEEECCCC
T ss_pred             EEEeCCCCCcCCHHHHHHHHHHHHHHH--HcCCCEEEEcCCC
Confidence            99999973  222     222222111  2467888888744

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.28  E-value=0.00053  Score=63.31  Aligned_cols=71  Identities=15%  Similarity=0.059  Sum_probs=44.3

Q ss_pred             CeEEEEecchhH-Hhh--CCCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHh
Q 040234          105 SRIIITTRNEHL-LKL--HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVS  179 (377)
Q Consensus       105 s~IIvTTR~~~v-~~~--~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~  179 (377)
                      ..+|.+|..... ...  ......+.+++++.++..+++...+.....  ....+..+.|++.++|  .|-.+..+..
T Consensus       155 ~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~--~~~~~~~~~l~~~~~G--~~r~l~~~l~  228 (338)
T 3pfi_A          155 FTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNK--TCEEKAALEIAKRSRS--TPRIALRLLK  228 (338)
T ss_dssp             CEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC--EECHHHHHHHHHTTTT--CHHHHHHHHH
T ss_pred             eEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCC--CCCHHHHHHHHHHHCc--CHHHHHHHHH
Confidence            456666654321 111  122367999999999999999877643221  1124567788889999  8865554433

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.23  E-value=0.0012  Score=60.43  Aligned_cols=140  Identities=16%  Similarity=0.233  Sum_probs=73.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      +|+|||++|+.+++.+...   .+.+. .+..     .. ..++..+........                ..+++-+|+
T Consensus        57 ~G~GKT~la~~la~~l~~~---~~~i~-~~~~-----~~-~~i~~~~~~~~~~~~----------------~~~~~~vli  110 (324)
T 3u61_B           57 PGTGKTTVAKALCHDVNAD---MMFVN-GSDC-----KI-DFVRGPLTNFASAAS----------------FDGRQKVIV  110 (324)
T ss_dssp             TTSSHHHHHHHHHHHTTEE---EEEEE-TTTC-----CH-HHHHTHHHHHHHBCC----------------CSSCEEEEE
T ss_pred             CCCCHHHHHHHHHHHhCCC---EEEEc-cccc-----CH-HHHHHHHHHHHhhcc----------------cCCCCeEEE
Confidence            6999999999999876322   12222 2221     22 222222222111100                123678999


Q ss_pred             EeCCCChh---hhhHhhCCCCCCCCCCeEEEEecchh-----HHhhCCCCCeeecCCCChhhhHHHHH-------HHhcC
Q 040234           82 IDDAAHPD---HLRRLVGEPDWFGPGSRIIITTRNEH-----LLKLHPVKKVYKLEALTYDEAFRLLC-------LKAFD  146 (377)
Q Consensus        82 LDdv~~~~---~~~~l~~~l~~~~~gs~IIvTTR~~~-----v~~~~~~~~~~~l~~L~~~ea~~L~~-------~~~~~  146 (377)
                      ||+++...   ..+.|...+.....+.++|+||....     +..+   ...+++++++.++-.+++.       ..+..
T Consensus       111 iDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR---~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~  187 (324)
T 3u61_B          111 IDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSR---CRVITFGQPTDEDKIEMMKQMIRRLTEICKH  187 (324)
T ss_dssp             EESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHH---SEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhh---CcEEEeCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99998743   33333332221134567888876543     2222   3578999999888543332       22211


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      .....+. .+....|++.++|  ..-.
T Consensus       188 ~~~~~~~-~~~~~~l~~~~~g--d~R~  211 (324)
T 3u61_B          188 EGIAIAD-MKVVAALVKKNFP--DFRK  211 (324)
T ss_dssp             HTCCBSC-HHHHHHHHHHTCS--CTTH
T ss_pred             cCCCCCc-HHHHHHHHHhCCC--CHHH
Confidence            1111110 2567788888888  5544

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=97.14  E-value=0.0057  Score=55.51  Aligned_cols=143  Identities=11%  Similarity=0.070  Sum_probs=75.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++.....|     +. +        +...+..    ...+.      ........+.......+.+|
T Consensus        57 p~GtGKT~la~ala~~~~~~~-----i~-v--------~~~~l~~----~~~g~------~~~~~~~~f~~a~~~~p~il  112 (301)
T 3cf0_A           57 PPGCGKTLLAKAIANECQANF-----IS-I--------KGPELLT----MWFGE------SEANVREIFDKARQAAPCVL  112 (301)
T ss_dssp             SSSSSHHHHHHHHHHHTTCEE-----EE-E--------CHHHHHH----HHHTT------CTTHHHHHHHHHHHTCSEEE
T ss_pred             CCCcCHHHHHHHHHHHhCCCE-----EE-E--------EhHHHHh----hhcCc------hHHHHHHHHHHHHhcCCeEE
Confidence            379999999999998764322     11 1        2222222    11121      11222333444444567899


Q ss_pred             EEeCCCChh----------------hhhHhhCCCCC--CCCCCeEEEEecchhHH-hh-C---CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHPD----------------HLRRLVGEPDW--FGPGSRIIITTRNEHLL-KL-H---PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~~----------------~~~~l~~~l~~--~~~gs~IIvTTR~~~v~-~~-~---~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++...                ....++..+..  ...+..||.||...... .. .   .-...+.++..+.++-.
T Consensus       113 ~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~  192 (301)
T 3cf0_A          113 FFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRV  192 (301)
T ss_dssp             EECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHH
T ss_pred             EEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHH
Confidence            999997421                01222211110  12345677777654321 11 1   22457889999999988


Q ss_pred             HHHHHHhcCCCCC-chhHHHHHHHHHHHhCCCCchhh
Q 040234          138 RLLCLKAFDTHKP-LEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       138 ~L~~~~~~~~~~~-~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      +++.......... ...    ...+++.+.|  .|-+
T Consensus       193 ~il~~~l~~~~~~~~~~----~~~la~~~~g--~sg~  223 (301)
T 3cf0_A          193 AILKANLRKSPVAKDVD----LEFLAKMTNG--FSGA  223 (301)
T ss_dssp             HHHHHHHTTSCBCSSCC----HHHHHHTCSS--CCHH
T ss_pred             HHHHHHHccCCCCccch----HHHHHHHcCC--CCHH
Confidence            9887776332211 112    2356666777  6554

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.09  E-value=0.0049  Score=57.44  Aligned_cols=99  Identities=9%  Similarity=-0.024  Sum_probs=54.2

Q ss_pred             cCceEEEEEeCCCCh-------------hhhhHhhCCCC----CCCCCCeEEEEecchh-----HHhhCCCCCeeecCCC
Q 040234           74 RRKKVLVVIDDAAHP-------------DHLRRLVGEPD----WFGPGSRIIITTRNEH-----LLKLHPVKKVYKLEAL  131 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~-------------~~~~~l~~~l~----~~~~gs~IIvTTR~~~-----v~~~~~~~~~~~l~~L  131 (377)
                      ..++.+|+||+++..             .....++..+.    ....+..||.||....     +..  .-...+.+...
T Consensus       174 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--Rf~~~i~i~~p  251 (357)
T 3d8b_A          174 CQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLP  251 (357)
T ss_dssp             HTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHT--TCCEEEECCCC
T ss_pred             hcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHh--hCceEEEeCCc
Confidence            346789999998432             11222221111    1123345565665432     222  22356788889


Q ss_pred             ChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchh-hHHHHH
Q 040234          132 TYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTL-NALMSV  178 (377)
Q Consensus       132 ~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpl-al~~~~  178 (377)
                      +.++..+++...+.......  ..+....|++.+.|  ..- .+..+.
T Consensus       252 ~~~~r~~il~~~~~~~~~~l--~~~~l~~la~~t~G--~s~~dl~~l~  295 (357)
T 3d8b_A          252 EASARKQIVINLMSKEQCCL--SEEEIEQIVQQSDA--FSGADMTQLC  295 (357)
T ss_dssp             CHHHHHHHHHHHHHTSCBCC--CHHHHHHHHHHTTT--CCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhhcCCCc--cHHHHHHHHHHcCC--CCHHHHHHHH
Confidence            99999998887764322111  13567788888887  543 344433

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.05  E-value=0.0035  Score=57.88  Aligned_cols=95  Identities=11%  Similarity=0.135  Sum_probs=55.1

Q ss_pred             ceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           76 KKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        76 k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      .+-++|+|+++.  .+..+.|+..+..-....++|++|.... +...+ .....+.+.+++.++..+.+...+....-..
T Consensus       110 ~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~~i  189 (340)
T 1sxj_C          110 GFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKL  189 (340)
T ss_dssp             SCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCB
T ss_pred             CceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHHHHHHHHHHHcCCCC
Confidence            467899999865  2233333322211134556776665432 21111 2245788999999999988877663222111


Q ss_pred             hhHHHHHHHHHHHhCCCCchhhH
Q 040234          152 EEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lplal  174 (377)
                        .++..+.|++.++|  .+-.+
T Consensus       190 --~~~~~~~i~~~s~G--~~r~~  208 (340)
T 1sxj_C          190 --SPNAEKALIELSNG--DMRRV  208 (340)
T ss_dssp             --CHHHHHHHHHHHTT--CHHHH
T ss_pred             --CHHHHHHHHHHcCC--CHHHH
Confidence              13567788888998  66543

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.98  E-value=0.0048  Score=58.17  Aligned_cols=50  Identities=12%  Similarity=0.002  Sum_probs=33.9

Q ss_pred             CeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchh-hHHHH
Q 040234          124 KVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTL-NALMS  177 (377)
Q Consensus       124 ~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpl-al~~~  177 (377)
                      ..+.++..+.++-.+++...+........  .+....|++.+.|  ..- ++..+
T Consensus       275 ~~i~i~~p~~~~r~~il~~~~~~~~~~l~--~~~~~~la~~~~g--~~~~~l~~L  325 (389)
T 3vfd_A          275 KRVYVSLPNEETRLLLLKNLLCKQGSPLT--QKELAQLARMTDG--YSGSDLTAL  325 (389)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHTTSCCCSC--HHHHHHHHHHTTT--CCHHHHHHH
T ss_pred             eEEEcCCcCHHHHHHHHHHHHHhcCCCCC--HHHHHHHHHHcCC--CCHHHHHHH
Confidence            46888999999999999887744322211  3466788999888  655 44433

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.98  E-value=0.014  Score=52.54  Aligned_cols=68  Identities=13%  Similarity=0.003  Sum_probs=40.7

Q ss_pred             CCeEEEEecch-----hHHhhCCCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchh-hHHHH
Q 040234          104 GSRIIITTRNE-----HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTL-NALMS  177 (377)
Q Consensus       104 gs~IIvTTR~~-----~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpl-al~~~  177 (377)
                      +..||.||...     .+..++  ...+.++..+.++-.+++...+.......  ..+....|++.+.|  .+- ++..+
T Consensus       159 ~v~vi~~tn~~~~l~~~l~~R~--~~~i~~~~p~~~~r~~il~~~~~~~~~~~--~~~~~~~la~~~~g--~~~~~l~~l  232 (297)
T 3b9p_A          159 RIVVLAATNRPQELDEAALRRF--TKRVYVSLPDEQTRELLLNRLLQKQGSPL--DTEALRRLAKITDG--YSGSDLTAL  232 (297)
T ss_dssp             CEEEEEEESCGGGBCHHHHHHC--CEEEECCCCCHHHHHHHHHHHHGGGSCCS--CHHHHHHHHHHTTT--CCHHHHHHH
T ss_pred             cEEEEeecCChhhCCHHHHhhC--CeEEEeCCcCHHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHcCC--CCHHHHHHH
Confidence            34566677653     223322  35677888888888888877663322111  13456788899988  775 44333

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.74  E-value=0.029  Score=52.77  Aligned_cols=142  Identities=14%  Similarity=0.132  Sum_probs=76.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhccccc-CHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEG-SVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ++|+|||.||+.++++....|    +..+.+...+.+. .....++                     +.+...-...+.+
T Consensus       190 PPGTGKTllAkAiA~e~~~~f----~~v~~s~l~sk~vGese~~vr---------------------~lF~~Ar~~aP~I  244 (405)
T 4b4t_J          190 PPGTGKTLLARAVAHHTDCKF----IRVSGAELVQKYIGEGSRMVR---------------------ELFVMAREHAPSI  244 (405)
T ss_dssp             CSSSSHHHHHHHHHHHHTCEE----EEEEGGGGSCSSTTHHHHHHH---------------------HHHHHHHHTCSEE
T ss_pred             CCCCCHHHHHHHHHHhhCCCc----eEEEhHHhhccccchHHHHHH---------------------HHHHHHHHhCCce
Confidence            589999999999999766554    1121222211110 1111112                     2222222456889


Q ss_pred             EEEeCCCChh----------------hhhHhhCCCCC--CCCCCeEEEEecchhH-----HhhCCCCCeeecCCCChhhh
Q 040234           80 VVIDDAAHPD----------------HLRRLVGEPDW--FGPGSRIIITTRNEHL-----LKLHPVKKVYKLEALTYDEA  136 (377)
Q Consensus        80 LVLDdv~~~~----------------~~~~l~~~l~~--~~~gs~IIvTTR~~~v-----~~~~~~~~~~~l~~L~~~ea  136 (377)
                      |.+|+++...                .+..++..+..  ...+-.||.||.....     .+.-.-...+.++..+.++-
T Consensus       245 IFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R  324 (405)
T 4b4t_J          245 IFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAAR  324 (405)
T ss_dssp             EEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHH
T ss_pred             EeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHH
Confidence            9999987420                12223222211  1233356667764432     22123467889999999988


Q ss_pred             HHHHHHHhcCCCC-CchhHHHHHHHHHHHhCCCCchhh
Q 040234          137 FRLLCLKAFDTHK-PLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       137 ~~L~~~~~~~~~~-~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      .++|..+...-.. ...+    ...|++.+.|  ..-|
T Consensus       325 ~~Il~~~~~~~~l~~dvd----l~~lA~~t~G--~SGA  356 (405)
T 4b4t_J          325 AEILRIHSRKMNLTRGIN----LRKVAEKMNG--CSGA  356 (405)
T ss_dssp             HHHHHHHHTTSBCCSSCC----HHHHHHHCCS--CCHH
T ss_pred             HHHHHHHhcCCCCCccCC----HHHHHHHCCC--CCHH
Confidence            9998877633221 1112    4578888888  5443

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=96.70  E-value=0.0026  Score=57.91  Aligned_cols=121  Identities=11%  Similarity=-0.004  Sum_probs=69.1

Q ss_pred             CCCCcHHHHHHHHHchh---ccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCce
Q 040234            1 MGGLGKTTLARVVYDLI---SHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKK   77 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~---~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~   77 (377)
                      ..|+|||++|+.+++..   +...++...+...+...    .+.. .+++.+.+....                 ..+++
T Consensus        26 p~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~----~id~-ir~li~~~~~~p-----------------~~~~~   83 (305)
T 2gno_A           26 EDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENI----GIDD-IRTIKDFLNYSP-----------------ELYTR   83 (305)
T ss_dssp             SSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCB----CHHH-HHHHHHHHTSCC-----------------SSSSS
T ss_pred             CCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCC----CHHH-HHHHHHHHhhcc-----------------ccCCc
Confidence            37999999999998742   22233444443111111    2222 233433321110                 02356


Q ss_pred             EEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234           78 VLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        78 ~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      -++|+|+++.  .+..+.|+..+..-.+.+.+|++|.++ .+...+... .+++.++++++..+.+.+..
T Consensus        84 kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           84 KYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             EEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEEEECCCCHHHHHHHHHHH
T ss_pred             eEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEeCCCCCHHHHHHHHHHHh
Confidence            7899999976  334455544433224566777766543 333333233 89999999999999998776

>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=96.49  E-value=0.0058  Score=54.19  Aligned_cols=72  Identities=13%  Similarity=0.247  Sum_probs=41.0

Q ss_pred             cCceEEEEEeCCCChh-----------------hhhHhhCCCCCC---CCCCeEEEEecchhH-----HhhCCCCCeeec
Q 040234           74 RRKKVLVVIDDAAHPD-----------------HLRRLVGEPDWF---GPGSRIIITTRNEHL-----LKLHPVKKVYKL  128 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~~-----------------~~~~l~~~l~~~---~~gs~IIvTTR~~~v-----~~~~~~~~~~~l  128 (377)
                      ..++.+|+||+++...                 .+..++..+...   .....||.||.....     .....-...+.+
T Consensus       101 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i  180 (268)
T 2r62_A          101 KQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLV  180 (268)
T ss_dssp             HSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBC
T ss_pred             hcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEe
Confidence            3466899999996421                 133344333221   112356666665432     111122356788


Q ss_pred             CCCChhhhHHHHHHHhc
Q 040234          129 EALTYDEAFRLLCLKAF  145 (377)
Q Consensus       129 ~~L~~~ea~~L~~~~~~  145 (377)
                      +..+.++-.+++.....
T Consensus       181 ~~p~~~~r~~il~~~~~  197 (268)
T 2r62_A          181 DKPDFNGRVEILKVHIK  197 (268)
T ss_dssp             CCCCTTTHHHHHHHHTS
T ss_pred             cCcCHHHHHHHHHHHHh
Confidence            89999999998877663

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.30  E-value=0.071  Score=50.93  Aligned_cols=138  Identities=14%  Similarity=0.170  Sum_probs=73.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhccccc-CHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEG-SVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ++|+|||.||+.++++....|    +..+.+...+.+. .....+                     .+.+...-...+.+
T Consensus       251 PPGTGKTlLAkAiA~e~~~~f----i~vs~s~L~sk~vGesek~i---------------------r~lF~~Ar~~aP~I  305 (467)
T 4b4t_H          251 PPGTGKTLCARAVANRTDATF----IRVIGSELVQKYVGEGARMV---------------------RELFEMARTKKACI  305 (467)
T ss_dssp             CTTSSHHHHHHHHHHHHTCEE----EEEEGGGGCCCSSSHHHHHH---------------------HHHHHHHHHTCSEE
T ss_pred             CCCCcHHHHHHHHHhccCCCe----EEEEhHHhhcccCCHHHHHH---------------------HHHHHHHHhcCCce
Confidence            479999999999999776553    1111222211110 111111                     12222223456899


Q ss_pred             EEEeCCCChh----------------hhhHhhCCCCCC--CCCCeEEEEecchhH-----HhhCCCCCeeecCCCChhhh
Q 040234           80 VVIDDAAHPD----------------HLRRLVGEPDWF--GPGSRIIITTRNEHL-----LKLHPVKKVYKLEALTYDEA  136 (377)
Q Consensus        80 LVLDdv~~~~----------------~~~~l~~~l~~~--~~gs~IIvTTR~~~v-----~~~~~~~~~~~l~~L~~~ea  136 (377)
                      |++|+++...                .+..++..+...  ..+-.||.||.....     .+.-.-...+.++..+.++-
T Consensus       306 IfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R  385 (467)
T 4b4t_H          306 IFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGR  385 (467)
T ss_dssp             EEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHH
T ss_pred             EeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHH
Confidence            9999987420                111222221111  223345666654322     22113467788888898888


Q ss_pred             HHHHHHHhcCCCC-CchhHHHHHHHHHHHhCC
Q 040234          137 FRLLCLKAFDTHK-PLEEYVELAESVVRICHC  167 (377)
Q Consensus       137 ~~L~~~~~~~~~~-~~~~~~~~~~~I~~~c~G  167 (377)
                      .++|..+...-.. ...+    ...|++.+.|
T Consensus       386 ~~Ilk~~l~~~~l~~dvd----l~~LA~~T~G  413 (467)
T 4b4t_H          386 ANIFRIHSKSMSVERGIR----WELISRLCPN  413 (467)
T ss_dssp             HHHHHHHHTTSCBCSSCC----HHHHHHHCCS
T ss_pred             HHHHHHHhcCCCCCCCCC----HHHHHHHCCC
Confidence            8998877633221 1112    3567888888

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=96.26  E-value=0.031  Score=50.28  Aligned_cols=19  Identities=26%  Similarity=0.177  Sum_probs=16.4

Q ss_pred             CeeecCCCChhhhHHHHHH
Q 040234          124 KVYKLEALTYDEAFRLLCL  142 (377)
Q Consensus       124 ~~~~l~~L~~~ea~~L~~~  142 (377)
                      ..+.+++++.++..+++.+
T Consensus       195 ~~i~~~~~~~~~~~~il~~  213 (310)
T 1ofh_A          195 IRVELTALSAADFERILTE  213 (310)
T ss_dssp             EEEECCCCCHHHHHHHHHS
T ss_pred             ceEEcCCcCHHHHHHHHHh
Confidence            5689999999999998874

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.22  E-value=0.0027  Score=51.28  Aligned_cols=18  Identities=22%  Similarity=0.222  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      .|+|||||++.++.....
T Consensus        45 ~G~GKTtL~~~i~~~~~~   62 (149)
T 2kjq_A           45 EGAGKSHLLQAWVAQALE   62 (149)
T ss_dssp             STTTTCHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            699999999999996543

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.17  E-value=0.033  Score=53.12  Aligned_cols=142  Identities=17%  Similarity=0.178  Sum_probs=75.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccC-HHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGS-VISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ++|+|||.||+.++++....|    +..+.+...+.+.+ ....+                     ...+...-...+.+
T Consensus       223 PPGtGKTllAkAiA~e~~~~~----~~v~~s~l~sk~~Gese~~i---------------------r~~F~~A~~~~P~I  277 (437)
T 4b4t_L          223 PPGTGKTLLAKAVAATIGANF----IFSPASGIVDKYIGESARII---------------------REMFAYAKEHEPCI  277 (437)
T ss_dssp             CTTSSHHHHHHHHHHHHTCEE----EEEEGGGTCCSSSSHHHHHH---------------------HHHHHHHHHSCSEE
T ss_pred             CCCCcHHHHHHHHHHHhCCCE----EEEehhhhccccchHHHHHH---------------------HHHHHHHHhcCCce
Confidence            589999999999999766543    22213222211101 11111                     11222222456899


Q ss_pred             EEEeCCCChh----------------hhhHhhCCCCC--CCCCCeEEEEecchhHHhh-C--C--CCCeeecCCCChhhh
Q 040234           80 VVIDDAAHPD----------------HLRRLVGEPDW--FGPGSRIIITTRNEHLLKL-H--P--VKKVYKLEALTYDEA  136 (377)
Q Consensus        80 LVLDdv~~~~----------------~~~~l~~~l~~--~~~gs~IIvTTR~~~v~~~-~--~--~~~~~~l~~L~~~ea  136 (377)
                      |.+|+++...                .+..|+..+..  ...+..||.||........ +  +  -...+.++..+.++-
T Consensus       278 ifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R  357 (437)
T 4b4t_L          278 IFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGR  357 (437)
T ss_dssp             EEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHH
T ss_pred             eeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHH
Confidence            9999987410                12223322211  1234467777765533221 1  1  245678888888888


Q ss_pred             HHHHHHHhcCCCC-CchhHHHHHHHHHHHhCCCCchhh
Q 040234          137 FRLLCLKAFDTHK-PLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       137 ~~L~~~~~~~~~~-~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      .++|..+...-.. ...+    ...|++.+.|  ..-|
T Consensus       358 ~~Il~~~~~~~~~~~d~d----l~~lA~~t~G--~sGA  389 (437)
T 4b4t_L          358 LEIFKIHTAKVKKTGEFD----FEAAVKMSDG--FNGA  389 (437)
T ss_dssp             HHHHHHHHHTSCBCSCCC----HHHHHHTCCS--CCHH
T ss_pred             HHHHHHHhcCCCCCcccC----HHHHHHhCCC--CCHH
Confidence            8888776643221 1112    3567888888  5433

>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=96.15  E-value=0.0082  Score=58.34  Aligned_cols=139  Identities=13%  Similarity=0.088  Sum_probs=70.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++....|   +.+. ...          +...+    .      ..........+.....+++.+|
T Consensus       246 ppGtGKT~lAraia~~~~~~f---v~vn-~~~----------l~~~~----~------g~~~~~~~~~f~~A~~~~p~iL  301 (489)
T 3hu3_A          246 PPGTGKTLIARAVANETGAFF---FLIN-GPE----------IMSKL----A------GESESNLRKAFEEAEKNAPAII  301 (489)
T ss_dssp             STTSSHHHHHHHHHHHCSSEE---EEEE-HHH----------HHTSC----T------THHHHHHHHHHHHHHHTCSEEE
T ss_pred             cCCCCHHHHHHHHHHHhCCCE---EEEE-chH----------hhhhh----c------chhHHHHHHHHHHHHhcCCcEE
Confidence            379999999999998663322   1121 211          11000    0      0011112233344445667899


Q ss_pred             EEeCCCCh-------------hhhhHh---hCCCCCCCCCCeEEEEecchh-HHhh----CCCCCeeecCCCChhhhHHH
Q 040234           81 VIDDAAHP-------------DHLRRL---VGEPDWFGPGSRIIITTRNEH-LLKL----HPVKKVYKLEALTYDEAFRL  139 (377)
Q Consensus        81 VLDdv~~~-------------~~~~~l---~~~l~~~~~gs~IIvTTR~~~-v~~~----~~~~~~~~l~~L~~~ea~~L  139 (377)
                      +||+++..             .....|   +..+.. ..+..||.||.... +...    ..-...+.++..+.++-.++
T Consensus       302 fLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~-~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~I  380 (489)
T 3hu3_A          302 FIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQ-RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEI  380 (489)
T ss_dssp             EEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCT-TSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHH
T ss_pred             EecchhhhccccccccchHHHHHHHHHHHHhhcccc-CCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHH
Confidence            99998321             111222   222111 23445666666542 1111    12244688999999999999


Q ss_pred             HHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          140 LCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      |..++........   ....++++.+.|
T Consensus       381 L~~~~~~~~l~~~---~~l~~la~~t~g  405 (489)
T 3hu3_A          381 LQIHTKNMKLADD---VDLEQVANETHG  405 (489)
T ss_dssp             HHHHTTTSCBCTT---CCHHHHHHTCTT
T ss_pred             HHHHHhcCCCcch---hhHHHHHHHccC
Confidence            9887643221111   113456666666

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.12  E-value=0.012  Score=53.21  Aligned_cols=19  Identities=32%  Similarity=0.433  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+|||+||+.+++....
T Consensus        55 ~~GtGKt~la~~la~~~~~   73 (311)
T 4fcw_A           55 PTGVGKTELAKTLAATLFD   73 (311)
T ss_dssp             CSSSSHHHHHHHHHHHHHS
T ss_pred             CCCcCHHHHHHHHHHHHcC
Confidence            3799999999999996543

>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=96.06  E-value=0.028  Score=54.32  Aligned_cols=142  Identities=17%  Similarity=0.108  Sum_probs=73.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++.+....|    +..+.+.........                    ........+.+.....+.+|
T Consensus        57 ppGtGKT~Laraia~~~~~~f----~~is~~~~~~~~~g~--------------------~~~~~r~lf~~A~~~~p~IL  112 (476)
T 2ce7_A           57 PPGTGKTLLARAVAGEANVPF----FHISGSDFVELFVGV--------------------GAARVRDLFAQAKAHAPCIV  112 (476)
T ss_dssp             CTTSSHHHHHHHHHHHHTCCE----EEEEGGGTTTCCTTH--------------------HHHHHHHHHHHHHHTCSEEE
T ss_pred             CCCCCHHHHHHHHHHHcCCCe----eeCCHHHHHHHHhcc--------------------cHHHHHHHHHHHHhcCCCEE
Confidence            479999999999998654332    111122211110000                    11112233444445678899


Q ss_pred             EEeCCCCh----------------hhhhHhhCCCCC--CCCCCeEEEEecchhHHh-h-C---CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHP----------------DHLRRLVGEPDW--FGPGSRIIITTRNEHLLK-L-H---PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~----------------~~~~~l~~~l~~--~~~gs~IIvTTR~~~v~~-~-~---~~~~~~~l~~L~~~ea~  137 (377)
                      +||+++..                ..+..++..+..  ...+..||.||....... . .   .-...+.++..+.++-.
T Consensus       113 fIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~  192 (476)
T 2ce7_A          113 FIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRK  192 (476)
T ss_dssp             EEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHH
T ss_pred             EEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHH
Confidence            99998541                122333322110  123446677776654321 1 1   12347788888888888


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCch
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHCQKST  171 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lp  171 (377)
                      +++..++....-....   ....|++.+.|  ..
T Consensus       193 ~Il~~~~~~~~l~~~v---~l~~la~~t~G--~s  221 (476)
T 2ce7_A          193 KILEIHTRNKPLAEDV---NLEIIAKRTPG--FV  221 (476)
T ss_dssp             HHHHHHHTTSCBCTTC---CHHHHHHTCTT--CC
T ss_pred             HHHHHHHHhCCCcchh---hHHHHHHhcCC--Cc
Confidence            8887666332111111   13447777888  66

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.06  E-value=0.013  Score=48.31  Aligned_cols=19  Identities=26%  Similarity=0.258  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+|||+||+.+++....
T Consensus        51 ~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           51 DPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             CGGGCHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            3699999999999986533

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.06  E-value=0.0031  Score=53.19  Aligned_cols=47  Identities=17%  Similarity=0.115  Sum_probs=28.3

Q ss_pred             hHHHHHHHhcCceE-EEEEeCCCC--------hhhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           65 GINMLRVRLRRKKV-LVVIDDAAH--------PDHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        65 ~~~~l~~~l~~k~~-LLVLDdv~~--------~~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      ..+..++.+.+.+| |||||++-.        .+++-.++..   ...+..||+|+|..
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~---Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNA---RPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHT---SCTTCEEEEECSSC
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHh---CcCCCEEEEECCCC
Confidence            34445566655544 999999732        2333333222   24567899999985

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.99  E-value=0.018  Score=51.98  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+|||+||+.+++....
T Consensus        44 ppGtGKT~la~aiA~~l~~   62 (293)
T 3t15_A           44 GKGQGKSFQCELVFRKMGI   62 (293)
T ss_dssp             CTTSCHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHhCC
Confidence            4799999999999997743

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.98  E-value=0.0082  Score=50.72  Aligned_cols=27  Identities=22%  Similarity=0.212  Sum_probs=19.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      .+|+|||+||+.+++.........+++
T Consensus        62 ~~GtGKT~la~~i~~~~~~~~~~~~~~   88 (202)
T 2w58_A           62 SFGVGKTYLLAAIANELAKRNVSSLIV   88 (202)
T ss_dssp             STTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            379999999999999765543334444

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.97  E-value=0.0088  Score=61.54  Aligned_cols=117  Identities=16%  Similarity=0.166  Sum_probs=59.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++.....-...+.+. ++.........                     .....+.+++   ...-+|
T Consensus       529 p~GtGKT~lA~ala~~l~~~~~~~i~i~-~s~~~~~~~~~---------------------~~~l~~~~~~---~~~~vl  583 (758)
T 3pxi_A          529 PTGVGKTELARALAESIFGDEESMIRID-MSEYMEKHSTS---------------------GGQLTEKVRR---KPYSVV  583 (758)
T ss_dssp             CTTSSHHHHHHHHHHHHHSCTTCEEEEE-GGGGCSSCCCC------------------------CHHHHHH---CSSSEE
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcceEEEe-chhcccccccc---------------------cchhhHHHHh---CCCeEE
Confidence            3799999999999996533222223333 44433211000                     0111112221   223489


Q ss_pred             EEeCCCCh--hhhhHhhCCCCC-----------CCCCCeEEEEecc-----------------hhHHhhCCCCCeeecCC
Q 040234           81 VIDDAAHP--DHLRRLVGEPDW-----------FGPGSRIIITTRN-----------------EHLLKLHPVKKVYKLEA  130 (377)
Q Consensus        81 VLDdv~~~--~~~~~l~~~l~~-----------~~~gs~IIvTTR~-----------------~~v~~~~~~~~~~~l~~  130 (377)
                      +||+++..  +....|+..+..           .....+||+||..                 +.+..++  ...+.+.+
T Consensus       584 ~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~Rl--~~~i~~~~  661 (758)
T 3pxi_A          584 LLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFINRI--DEIIVFHS  661 (758)
T ss_dssp             EEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHTTS--SEEEECC-
T ss_pred             EEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHhhC--CeEEecCC
Confidence            99999752  333333221111           1235588888872                 1112222  35788999


Q ss_pred             CChhhhHHHHHHHh
Q 040234          131 LTYDEAFRLLCLKA  144 (377)
Q Consensus       131 L~~~ea~~L~~~~~  144 (377)
                      |+.++-.+++....
T Consensus       662 l~~~~~~~i~~~~l  675 (758)
T 3pxi_A          662 LEKKHLTEIVSLMS  675 (758)
T ss_dssp             -CHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99998888876654

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.93  E-value=0.026  Score=53.65  Aligned_cols=21  Identities=33%  Similarity=0.428  Sum_probs=17.5

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      ++|+|||.||+.++++..-.|
T Consensus       214 PPGtGKT~lakAiA~~~~~~~  234 (428)
T 4b4t_K          214 PPGTGKTMLVKAVANSTKAAF  234 (428)
T ss_dssp             CTTTTHHHHHHHHHHHHTCEE
T ss_pred             CCCCCHHHHHHHHHHHhCCCe
Confidence            589999999999999765443

>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=95.87  E-value=0.014  Score=51.72  Aligned_cols=17  Identities=35%  Similarity=0.333  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+|||+||+.+++...
T Consensus        38 ~GtGKt~la~~i~~~~~   54 (265)
T 2bjv_A           38 RGTGKELIASRLHYLSS   54 (265)
T ss_dssp             TTSCHHHHHHHHHHTST
T ss_pred             CCCcHHHHHHHHHHhcC
Confidence            79999999999998543

>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=95.87  E-value=0.05  Score=55.87  Aligned_cols=68  Identities=9%  Similarity=0.059  Sum_probs=40.2

Q ss_pred             CceEEEEEeCCCCh----------hh-hhHhhCCCCCCCCCCeEEEEecchhHHhhC-------CCCCeeecCCCChhhh
Q 040234           75 RKKVLVVIDDAAHP----------DH-LRRLVGEPDWFGPGSRIIITTRNEHLLKLH-------PVKKVYKLEALTYDEA  136 (377)
Q Consensus        75 ~k~~LLVLDdv~~~----------~~-~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~-------~~~~~~~l~~L~~~ea  136 (377)
                      .++.+|+||++...          .+ .+.+.+.+.  ..+..+|.+|.........       .....+.++..+.++.
T Consensus       277 ~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~--~~~~~~I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~  354 (758)
T 1r6b_X          277 DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEET  354 (758)
T ss_dssp             SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHH
T ss_pred             cCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHh--CCCeEEEEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHH
Confidence            35789999999743          12 233444433  2345666666544322111       1123588999999999


Q ss_pred             HHHHHHHh
Q 040234          137 FRLLCLKA  144 (377)
Q Consensus       137 ~~L~~~~~  144 (377)
                      .+++....
T Consensus       355 ~~il~~l~  362 (758)
T 1r6b_X          355 VQIINGLK  362 (758)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88887654

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.78  E-value=0.027  Score=53.63  Aligned_cols=138  Identities=14%  Similarity=0.149  Sum_probs=71.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhccccc-CHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEG-SVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ++|+|||.||+.++++....|    +..+.+.....+. .....++.++                     ...-...+.+
T Consensus       223 PPGTGKTllAkAiA~e~~~~f----~~v~~s~l~~~~vGese~~ir~lF---------------------~~A~~~aP~I  277 (434)
T 4b4t_M          223 PPGTGKTLLARACAAQTNATF----LKLAAPQLVQMYIGEGAKLVRDAF---------------------ALAKEKAPTI  277 (434)
T ss_dssp             CTTSSHHHHHHHHHHHHTCEE----EEEEGGGGCSSCSSHHHHHHHHHH---------------------HHHHHHCSEE
T ss_pred             cCCCCHHHHHHHHHHHhCCCE----EEEehhhhhhcccchHHHHHHHHH---------------------HHHHhcCCeE
Confidence            589999999999999765543    1221222211110 1112222222                     1112335789


Q ss_pred             EEEeCCCCh-------h---------hhhHhhCCCCCC--CCCCeEEEEecchhHHh-hC----CCCCeeecCCCChhhh
Q 040234           80 VVIDDAAHP-------D---------HLRRLVGEPDWF--GPGSRIIITTRNEHLLK-LH----PVKKVYKLEALTYDEA  136 (377)
Q Consensus        80 LVLDdv~~~-------~---------~~~~l~~~l~~~--~~gs~IIvTTR~~~v~~-~~----~~~~~~~l~~L~~~ea  136 (377)
                      |.+|+++..       .         .+..++..+...  ..+-.||.||....... .+    .-...+.++..+.++-
T Consensus       278 ifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R  357 (434)
T 4b4t_M          278 IFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSR  357 (434)
T ss_dssp             EEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHH
T ss_pred             EeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHH
Confidence            999998531       0         122233222211  22335566776543322 11    2245788888888888


Q ss_pred             HHHHHHHhcCCCC-CchhHHHHHHHHHHHhCC
Q 040234          137 FRLLCLKAFDTHK-PLEEYVELAESVVRICHC  167 (377)
Q Consensus       137 ~~L~~~~~~~~~~-~~~~~~~~~~~I~~~c~G  167 (377)
                      .++|..+...-.. ...+    ...|++.+.|
T Consensus       358 ~~Il~~~~~~~~~~~dvd----l~~lA~~t~G  385 (434)
T 4b4t_M          358 AQILQIHSRKMTTDDDIN----WQELARSTDE  385 (434)
T ss_dssp             HHHHHHHHHHSCBCSCCC----HHHHHHHCSS
T ss_pred             HHHHHHHhcCCCCCCcCC----HHHHHHhCCC
Confidence            8888766532211 1112    3568888888

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=95.68  E-value=0.14  Score=49.06  Aligned_cols=93  Identities=11%  Similarity=0.011  Sum_probs=53.6

Q ss_pred             EEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEE-EE---------ec----chhHH-hhCCCCCeeecCCCChhhhHHHH
Q 040234           78 VLVVIDDAAH--PDHLRRLVGEPDWFGPGSRII-IT---------TR----NEHLL-KLHPVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        78 ~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~II-vT---------TR----~~~v~-~~~~~~~~~~l~~L~~~ea~~L~  140 (377)
                      -++++|++..  .+..+.|+..+...... .+| .|         |.    ...+. ........+.+++++.++..+++
T Consensus       297 ~VliIDEa~~l~~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL  375 (456)
T 2c9o_A          297 GVLFVDEVHMLDIECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQII  375 (456)
T ss_dssp             CEEEEESGGGCBHHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHH
T ss_pred             eEEEEechhhcCHHHHHHHHHHhhccCCC-EEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHH
Confidence            3899999975  45566666555432333 344 44         22    11111 11122445799999999999999


Q ss_pred             HHHhcCCCCCchhHHHHHHHHHHHh-CCCCchhhHH
Q 040234          141 CLKAFDTHKPLEEYVELAESVVRIC-HCQKSTLNAL  175 (377)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~I~~~c-~G~~lplal~  175 (377)
                      ..++......  -.++.+..|++.+ +|  .|....
T Consensus       376 ~~~~~~~~~~--~~~~~~~~i~~~a~~g--~~r~a~  407 (456)
T 2c9o_A          376 KIRAQTEGIN--ISEEALNHLGEIGTKT--TLRYSV  407 (456)
T ss_dssp             HHHHHHHTCC--BCHHHHHHHHHHHHHS--CHHHHH
T ss_pred             HHHHHHhCCC--CCHHHHHHHHHHccCC--CHHHHH
Confidence            8776311111  1135667788887 67  666544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.68  E-value=0.011  Score=47.22  Aligned_cols=16  Identities=31%  Similarity=0.304  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||+||+.+++..
T Consensus        33 ~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A           33 PGTGRMTGARYLHQFG   48 (145)
T ss_dssp             TTSSHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHHHhC
Confidence            7999999999999843

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=95.55  E-value=0.028  Score=54.35  Aligned_cols=67  Identities=15%  Similarity=0.100  Sum_probs=36.6

Q ss_pred             cCceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhH---HhhC----CCCCeeecCCCChhhhHHHHHHHh
Q 040234           74 RRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHL---LKLH----PVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v---~~~~----~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      ..++.+|++|  ...+..+.|.+.+.  ....++|.+|.....   ....    .....+.+++.+.++..+++....
T Consensus       265 ~~~~~iLfiD--~~~~a~~~L~~~L~--~g~v~vI~at~~~e~~~~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~  338 (468)
T 3pxg_A          265 QAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLR  338 (468)
T ss_dssp             TCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTT
T ss_pred             hcCCeEEEEe--CchhHHHHHHHhhc--CCCEEEEecCCHHHHHHHhhcCHHHHHhCccceeCCCCHHHHHHHHHHHH
Confidence            3567899999  33333444555543  223456665554331   1111    123468999999999999998765

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.53  E-value=0.075  Score=50.28  Aligned_cols=138  Identities=19%  Similarity=0.131  Sum_probs=71.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhccccc-CHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEG-SVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ++|+|||.||+.++++....|-    ..+.+...+.+. .....++.++                     ...-...+.+
T Consensus       224 PPGTGKTlLAkAiA~e~~~~fi----~v~~s~l~sk~vGesek~ir~lF---------------------~~Ar~~aP~I  278 (437)
T 4b4t_I          224 APGTGKTLLAKAVANQTSATFL----RIVGSELIQKYLGDGPRLCRQIF---------------------KVAGENAPSI  278 (437)
T ss_dssp             STTTTHHHHHHHHHHHHTCEEE----EEESGGGCCSSSSHHHHHHHHHH---------------------HHHHHTCSEE
T ss_pred             CCCchHHHHHHHHHHHhCCCEE----EEEHHHhhhccCchHHHHHHHHH---------------------HHHHhcCCcE
Confidence            4899999999999997665431    111222211110 1112222222                     2222345789


Q ss_pred             EEEeCCCCh----------------hhhhHhhCCCCC--CCCCCeEEEEecchhHHhh-C----CCCCeeecCCCChhhh
Q 040234           80 VVIDDAAHP----------------DHLRRLVGEPDW--FGPGSRIIITTRNEHLLKL-H----PVKKVYKLEALTYDEA  136 (377)
Q Consensus        80 LVLDdv~~~----------------~~~~~l~~~l~~--~~~gs~IIvTTR~~~v~~~-~----~~~~~~~l~~L~~~ea  136 (377)
                      |.+|+++..                ..+..++..+..  ...+-.||.||........ +    .-...+.++.-+.++-
T Consensus       279 IfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R  358 (437)
T 4b4t_I          279 VFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTK  358 (437)
T ss_dssp             EEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHH
T ss_pred             EEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHH
Confidence            999997631                012222222111  1233456667765443221 1    1245677888888888


Q ss_pred             HHHHHHHhcCCCC-CchhHHHHHHHHHHHhCC
Q 040234          137 FRLLCLKAFDTHK-PLEEYVELAESVVRICHC  167 (377)
Q Consensus       137 ~~L~~~~~~~~~~-~~~~~~~~~~~I~~~c~G  167 (377)
                      .++|..+...-.- ...+    ...|++.+.|
T Consensus       359 ~~Il~~~l~~~~l~~dvd----l~~LA~~T~G  386 (437)
T 4b4t_I          359 KKILGIHTSKMNLSEDVN----LETLVTTKDD  386 (437)
T ss_dssp             HHHHHHHHTTSCBCSCCC----HHHHHHHCCS
T ss_pred             HHHHHHHhcCCCCCCcCC----HHHHHHhCCC
Confidence            8888777633221 1112    4567888888

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=95.47  E-value=0.057  Score=56.29  Aligned_cols=67  Identities=15%  Similarity=0.013  Sum_probs=34.6

Q ss_pred             CceEEEEEeCCCChh----------hhhHhhCCCCCCCCCCeEEEEecchhH-----HhhC-CCCCeeecCCCChhhhHH
Q 040234           75 RKKVLVVIDDAAHPD----------HLRRLVGEPDWFGPGSRIIITTRNEHL-----LKLH-PVKKVYKLEALTYDEAFR  138 (377)
Q Consensus        75 ~k~~LLVLDdv~~~~----------~~~~l~~~l~~~~~gs~IIvTTR~~~v-----~~~~-~~~~~~~l~~L~~~ea~~  138 (377)
                      +++.+|+||++....          ..+.+.+.+.  ..+..+|.+|.....     ...+ .....+.+++++.++..+
T Consensus       262 ~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~--~~~i~~I~at~~~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~  339 (854)
T 1qvr_A          262 QGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETIS  339 (854)
T ss_dssp             CSSEEEEECCC-------------------HHHHH--TTCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHH
T ss_pred             CCCeEEEEecHHHHhccCCccchHHHHHHHHHHHh--CCCeEEEEecCchHHhhhccCHHHHhCCceEEeCCCCHHHHHH
Confidence            367899999997532          1111222221  123345555543322     1111 223458899999999999


Q ss_pred             HHHHH
Q 040234          139 LLCLK  143 (377)
Q Consensus       139 L~~~~  143 (377)
                      ++...
T Consensus       340 iL~~~  344 (854)
T 1qvr_A          340 ILRGL  344 (854)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            98644

>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=95.27  E-value=0.038  Score=47.01  Aligned_cols=15  Identities=40%  Similarity=0.036  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHHc
Q 040234            1 MGGLGKTTLARVVYD   15 (377)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (377)
                      .+|+||||||..++.
T Consensus        28 ~~GsGKTtl~~~l~~   42 (220)
T 2cvh_A           28 PYASGKTTLALQTGL   42 (220)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            379999999999987

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=95.17  E-value=0.084  Score=46.24  Aligned_cols=19  Identities=32%  Similarity=0.300  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||||+.+++....
T Consensus        53 ~~GtGKT~la~~la~~~~~   71 (257)
T 1lv7_A           53 PPGTGKTLLAKAIAGEAKV   71 (257)
T ss_dssp             CTTSCHHHHHHHHHHHHTC
T ss_pred             cCCCCHHHHHHHHHHHcCC
Confidence            3799999999999986543

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=95.14  E-value=0.052  Score=49.18  Aligned_cols=16  Identities=31%  Similarity=0.399  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||++|+.+++..
T Consensus        34 ~GtGKt~lAr~i~~~~   49 (304)
T 1ojl_A           34 SGTGKELVARALHACS   49 (304)
T ss_dssp             TTSCHHHHHHHHHHHS
T ss_pred             CCchHHHHHHHHHHhC
Confidence            7999999999999844

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.13  E-value=0.23  Score=50.92  Aligned_cols=71  Identities=14%  Similarity=0.063  Sum_probs=38.6

Q ss_pred             HHHhcCceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhH---HhhC----CCCCeeecCCCChhhhHHHHHH
Q 040234           70 RVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHL---LKLH----PVKKVYKLEALTYDEAFRLLCL  142 (377)
Q Consensus        70 ~~~l~~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v---~~~~----~~~~~~~l~~L~~~ea~~L~~~  142 (377)
                      ......++.+|++|  ...+....+.+.+.  ....++|.||.....   ....    .....+.++..+.++..+++..
T Consensus       261 ~~~~~~~~~iLfiD--~~~~~~~~L~~~l~--~~~v~~I~at~~~~~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~  336 (758)
T 3pxi_A          261 DEIRQAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQG  336 (758)
T ss_dssp             HHHHTCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHH
T ss_pred             HHHHhcCCEEEEEc--CchhHHHHHHHHHh--cCCEEEEeCCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHH
Confidence            33334677899999  33333344555543  234566666654331   0100    1125689999999999999986


Q ss_pred             Hh
Q 040234          143 KA  144 (377)
Q Consensus       143 ~~  144 (377)
                      ..
T Consensus       337 ~~  338 (758)
T 3pxi_A          337 LR  338 (758)
T ss_dssp             TT
T ss_pred             HH
Confidence            54

>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=95.08  E-value=0.019  Score=59.01  Aligned_cols=144  Identities=15%  Similarity=0.070  Sum_probs=74.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++...+|    +..+.....+.                    ..........+.+.......+.+|
T Consensus       246 PPGTGKT~LAraiA~elg~~~----~~v~~~~l~sk--------------------~~gese~~lr~lF~~A~~~~PsII  301 (806)
T 3cf2_A          246 PPGTGKTLIARAVANETGAFF----FLINGPEIMSK--------------------LAGESESNLRKAFEEAEKNAPAII  301 (806)
T ss_dssp             CTTSCHHHHHHHHHTTTTCEE----EEEEHHHHHSS--------------------CTTHHHHHHHHHHHHHTTSCSEEE
T ss_pred             CCCCCHHHHHHHHHHHhCCeE----EEEEhHHhhcc--------------------cchHHHHHHHHHHHHHHHcCCeEE
Confidence            479999999999999765443    22212111100                    001122223333444445678999


Q ss_pred             EEeCCCChh-------------hhhHhhCCCCCC--CCCCeEEEEecchhH-HhhC----CCCCeeecCCCChhhhHHHH
Q 040234           81 VIDDAAHPD-------------HLRRLVGEPDWF--GPGSRIIITTRNEHL-LKLH----PVKKVYKLEALTYDEAFRLL  140 (377)
Q Consensus        81 VLDdv~~~~-------------~~~~l~~~l~~~--~~gs~IIvTTR~~~v-~~~~----~~~~~~~l~~L~~~ea~~L~  140 (377)
                      +||+++...             ....|+..+...  ..+-.||.||..... -..+    .-...++++..+.++-.++|
T Consensus       302 fIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL  381 (806)
T 3cf2_A          302 FIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEIL  381 (806)
T ss_dssp             EEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHH
T ss_pred             EEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHH
Confidence            999986420             122222221111  123345556654422 1111    22457888888888888888


Q ss_pred             HHHhcCCCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          141 CLKAFDTHKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      ..+.........   .....|++.+.|  ..-|
T Consensus       382 ~~~l~~~~~~~d---vdl~~lA~~T~G--fsga  409 (806)
T 3cf2_A          382 QIHTKNMKLADD---VDLEQVANETHG--HVGA  409 (806)
T ss_dssp             HHTCSSSEECTT---CCHHHHHHHCCS--CCHH
T ss_pred             HHHhcCCCCCcc---cCHHHHHHhcCC--CCHH
Confidence            766532211111   124567888877  5443

>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=95.07  E-value=0.02  Score=52.10  Aligned_cols=63  Identities=16%  Similarity=0.150  Sum_probs=36.8

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||+||.+++..   .-...+|+. +....    .+           ..    ...+.+...+.+.+.+...+ ||
T Consensus       131 pPGsGKTtLAlqlA~~---~G~~VlyIs-~~~eE----~v-----------~~----~~~~le~~l~~i~~~l~~~~-LL  186 (331)
T 2vhj_A          131 KGNSGKTPLVHALGEA---LGGKDKYAT-VRFGE----PL-----------SG----YNTDFNVFVDDIARAMLQHR-VI  186 (331)
T ss_dssp             SCSSSHHHHHHHHHHH---HHTTSCCEE-EEBSC----SS-----------TT----CBCCHHHHHHHHHHHHHHCS-EE
T ss_pred             CCCCCHHHHHHHHHHh---CCCCEEEEE-ecchh----hh-----------hh----hhcCHHHHHHHHHHHHhhCC-EE
Confidence            4799999999999986   111234554 31000    10           00    00234455555666666656 99


Q ss_pred             EEeCCCC
Q 040234           81 VIDDAAH   87 (377)
Q Consensus        81 VLDdv~~   87 (377)
                      |+|++..
T Consensus       187 VIDsI~a  193 (331)
T 2vhj_A          187 VIDSLKN  193 (331)
T ss_dssp             EEECCTT
T ss_pred             EEecccc
Confidence            9999965

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.05  E-value=0.15  Score=45.26  Aligned_cols=39  Identities=10%  Similarity=0.077  Sum_probs=25.9

Q ss_pred             eEEEEecchhHHhh-----CCCCCeeecCCCChhhhHHHHHHHh
Q 040234          106 RIIITTRNEHLLKL-----HPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus       106 ~IIvTTR~~~v~~~-----~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      -++.+|..+.+...     -.-...+.++..+.++-.++|....
T Consensus       148 i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~  191 (274)
T 2x8a_A          148 FIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTIT  191 (274)
T ss_dssp             EEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHT
T ss_pred             EEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHH
Confidence            45566766544221     1235677888899998889988766

>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=94.73  E-value=0.048  Score=50.07  Aligned_cols=50  Identities=14%  Similarity=-0.019  Sum_probs=35.9

Q ss_pred             CeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHH
Q 040234          124 KVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMS  177 (377)
Q Consensus       124 ~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~  177 (377)
                      ....+++.+.++-.+++.+.+......  -..+.+..|++.++|  .|-.+..+
T Consensus       173 l~~~Ld~~~~~~l~~iL~~~~~~~~~~--~~~~~~~~ia~~~~G--~~R~a~~l  222 (334)
T 1in4_A          173 IILELDFYTVKELKEIIKRAASLMDVE--IEDAAAEMIAKRSRG--TPRIAIRL  222 (334)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHHHTTCC--BCHHHHHHHHHTSTT--CHHHHHHH
T ss_pred             ceeeCCCCCHHHHHHHHHHHHHHcCCC--cCHHHHHHHHHhcCC--ChHHHHHH
Confidence            457899999999999998876322212  124668899999999  88655433

>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=94.67  E-value=0.15  Score=44.54  Aligned_cols=59  Identities=8%  Similarity=0.030  Sum_probs=32.7

Q ss_pred             eEEEEecchhHHhh-----CCCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          106 RIIITTRNEHLLKL-----HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       106 ~IIvTTR~~~v~~~-----~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .++.||..+.....     ..-...+.++..+.++-.+++........-...   .....|++.+.|
T Consensus       156 i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~---~~~~~la~~~~G  219 (254)
T 1ixz_A          156 VVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED---VDLALLAKRTPG  219 (254)
T ss_dssp             EEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTT---CCHHHHHHTCTT
T ss_pred             EEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcc---cCHHHHHHHcCC
Confidence            34456665544221     123456788888888888888766522111111   113457777777

>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=94.66  E-value=0.066  Score=52.73  Aligned_cols=38  Identities=16%  Similarity=0.077  Sum_probs=24.8

Q ss_pred             CCeEEEEecch-----hHHhhCCCCCeeecCCCChhhhHHHHHHHh
Q 040234          104 GSRIIITTRNE-----HLLKLHPVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus       104 gs~IIvTTR~~-----~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      ...+|.||...     .+..++   ..+.+.+++.++-.+++..+.
T Consensus       224 ~v~iI~ttN~~~~l~~aL~~R~---~vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          224 KVLFIATANNLATIPGPLRDRM---EIINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             SCEEEEECSSTTTSCHHHHHHE---EEEECCCCCHHHHHHHHHHTH
T ss_pred             ceEEEeccCccccCCHHHHhhc---ceeeeCCCCHHHHHHHHHHHH
Confidence            34566666543     223333   468899999999888887654

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=94.30  E-value=0.16  Score=45.15  Aligned_cols=43  Identities=7%  Similarity=-0.031  Sum_probs=26.4

Q ss_pred             CCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          122 VKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       122 ~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      -...+.++..+.++-.+++...+....-...   .....+++.+.|
T Consensus       201 f~~~i~i~~p~~~~r~~il~~~~~~~~~~~~---~~~~~la~~~~G  243 (278)
T 1iy2_A          201 FDRQIAIDAPDVKGREQILRIHARGKPLAED---VDLALLAKRTPG  243 (278)
T ss_dssp             SCCEEECCCCCHHHHHHHHHHHHTTSCBCTT---CCHHHHHHTCTT
T ss_pred             CCeEEEeCCcCHHHHHHHHHHHHccCCCCcc---cCHHHHHHHcCC
Confidence            3567888888988888888766532111111   113457777777

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.28  E-value=0.017  Score=45.96  Aligned_cols=17  Identities=24%  Similarity=0.055  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+|||++|+.+++...
T Consensus        36 ~GtGKt~lA~~i~~~~~   52 (143)
T 3co5_A           36 AGSPFETVARYFHKNGT   52 (143)
T ss_dssp             TTCCHHHHHGGGCCTTS
T ss_pred             CCccHHHHHHHHHHhCC
Confidence            69999999999998544

>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=94.18  E-value=0.13  Score=49.25  Aligned_cols=32  Identities=38%  Similarity=0.550  Sum_probs=21.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREK   33 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~   33 (377)
                      +|+|||||++.+......++....-+..+++.
T Consensus       160 sGvGKTtL~~~l~~~~~~~~~~i~V~~~iGer  191 (473)
T 1sky_E          160 AGVGKTVLIQELIHNIAQEHGGISVFAGVGER  191 (473)
T ss_dssp             SSSCHHHHHHHHHHHHHHHTCCCEEEEEESSC
T ss_pred             CCCCccHHHHHHHhhhhhccCcEEEEeeeccC
Confidence            69999999999998665544433333335443

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=93.94  E-value=0.27  Score=47.74  Aligned_cols=60  Identities=8%  Similarity=0.016  Sum_probs=33.5

Q ss_pred             CeEEEEecchhHHhh-C----CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          105 SRIIITTRNEHLLKL-H----PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       105 s~IIvTTR~~~v~~~-~----~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      ..|+.||..+..... .    .-...+.++..+.++-.+++..++....-...   .....|++.+.|
T Consensus       170 viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~d---v~l~~lA~~t~G  234 (499)
T 2dhr_A          170 IVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED---VDLALLAKRTPG  234 (499)
T ss_dssp             CEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCS---STTHHHHTTSCS
T ss_pred             EEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChH---HHHHHHHHhcCC
Confidence            345556666554221 1    22457888888888888888766532111111   113456777777

>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=93.48  E-value=0.095  Score=48.55  Aligned_cols=77  Identities=17%  Similarity=0.110  Sum_probs=41.5

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc----cCccchhhhHHHHHHHhc-C
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD----NNIRNVYDGINMLRVRLR-R   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~   75 (377)
                      .+|+||||||.+++......-..++|+. .....    +..     .+++++....    ....+.++..+.++..++ .
T Consensus        69 ppGsGKSTLal~la~~~~~~gg~VlyId-~E~s~----~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~~  138 (356)
T 3hr8_A           69 QESSGKTTLALHAIAEAQKMGGVAAFID-AEHAL----DPV-----YAKNLGVDLKSLLISQPDHGEQALEIVDELVRSG  138 (356)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTCCEEEEE-SSCCC----CHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTS
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCeEEEEe-ccccc----chH-----HHHHcCCchhhhhhhhccCHHHHHHHHHHHhhhc
Confidence            3799999999999986543322345654 32221    221     3344332211    122344455555555544 4


Q ss_pred             ceEEEEEeCCCC
Q 040234           76 KKVLVVIDDAAH   87 (377)
Q Consensus        76 k~~LLVLDdv~~   87 (377)
                      +.-++|+|.+..
T Consensus       139 ~~dlvVIDSi~~  150 (356)
T 3hr8_A          139 VVDLIVVDSVAA  150 (356)
T ss_dssp             CCSEEEEECTTT
T ss_pred             CCCeEEehHhhh
Confidence            455888888754

>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=93.43  E-value=0.065  Score=49.91  Aligned_cols=75  Identities=20%  Similarity=0.208  Sum_probs=39.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc----cCccchhhhHHHHHHHhcC-c
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD----NNIRNVYDGINMLRVRLRR-K   76 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~----~~~~~~~~~~~~l~~~l~~-k   76 (377)
                      +|+||||||.+++......-..++|+. .....    +  .+   .+++++....    ..+.+.++..+.+++..+. .
T Consensus        83 pGsGKTtlal~la~~~~~~g~~vlyi~-~E~s~----~--~~---~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~~~~  152 (366)
T 1xp8_A           83 ESGGKTTLALAIVAQAQKAGGTCAFID-AEHAL----D--PV---YARALGVNTDELLVSQPDNGEQALEIMELLVRSGA  152 (366)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEEE-SSCCC----C--HH---HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTC
T ss_pred             CCCChHHHHHHHHHHHHHCCCeEEEEE-CCCCh----h--HH---HHHHcCCCHHHceeecCCcHHHHHHHHHHHHhcCC
Confidence            799999999999885543323456665 33222    2  11   1233322111    1123444555555555443 3


Q ss_pred             eEEEEEeCCC
Q 040234           77 KVLVVIDDAA   86 (377)
Q Consensus        77 ~~LLVLDdv~   86 (377)
                      .-+||+|.+.
T Consensus       153 ~~lVVIDsl~  162 (366)
T 1xp8_A          153 IDVVVVDSVA  162 (366)
T ss_dssp             CSEEEEECTT
T ss_pred             CCEEEEeChH
Confidence            4588888874

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=93.39  E-value=0.074  Score=45.44  Aligned_cols=17  Identities=24%  Similarity=0.094  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+|||||++.++....
T Consensus        32 ~GsGKTtl~~~l~~~~~   48 (235)
T 2w0m_A           32 PGTGKTIFSLHFIAKGL   48 (235)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999997443

>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=93.21  E-value=0.056  Score=50.47  Aligned_cols=32  Identities=19%  Similarity=0.189  Sum_probs=21.4

Q ss_pred             CCCcHHHHHHHHHchhccccccc-eEEecchhh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGS-SFLADVREK   33 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~-~w~~~~~~~   33 (377)
                      +|+|||||++.+++.+.+..+.. +.+..+++.
T Consensus       183 sG~GKTtLl~~Iar~i~~~~~~v~~I~~lIGER  215 (422)
T 3ice_A          183 PKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDER  215 (422)
T ss_dssp             SSSSHHHHHHHHHHHHHHHCTTSEEEEEEESSC
T ss_pred             CCCChhHHHHHHHHHHhhcCCCeeEEEEEecCC
Confidence            79999999999998665544432 334435543

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=93.17  E-value=0.067  Score=48.58  Aligned_cols=28  Identities=7%  Similarity=0.007  Sum_probs=19.6

Q ss_pred             CCCCcHHHHHHHHHchhcccc--ccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEF--DGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f--~~~~w~~   28 (377)
                      .+|+||||||.+++......+  ...+|+.
T Consensus        36 ~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId   65 (333)
T 3io5_A           36 PSKSFKSNFGLTMVSSYMRQYPDAVCLFYD   65 (333)
T ss_dssp             SSSSSHHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            379999999999988655443  2345554

>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=93.17  E-value=0.18  Score=52.46  Aligned_cols=18  Identities=33%  Similarity=0.449  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ..|+|||+||+.+++...
T Consensus       596 p~GtGKT~lA~~la~~~~  613 (854)
T 1qvr_A          596 PTGVGKTELAKTLAATLF  613 (854)
T ss_dssp             CSSSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhc
Confidence            369999999999998653

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=93.14  E-value=0.087  Score=54.06  Aligned_cols=17  Identities=24%  Similarity=0.354  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+|||+||+.+++..
T Consensus       496 ~~GtGKT~la~~la~~l  512 (758)
T 1r6b_X          496 PTGVGKTEVTVQLSKAL  512 (758)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHh
Confidence            37999999999999866

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=92.84  E-value=0.059  Score=48.93  Aligned_cols=17  Identities=29%  Similarity=0.386  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+|||+||..+++...
T Consensus       161 ~GtGKT~La~aia~~~~  177 (308)
T 2qgz_A          161 MGIGKSYLLAAMAHELS  177 (308)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            79999999999999665

>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=92.83  E-value=1.1  Score=40.92  Aligned_cols=98  Identities=6%  Similarity=-0.051  Sum_probs=61.7

Q ss_pred             CceEEEEEeCCCC---hhhhhHhhCCCCCCCCCCeEEEEecc-------hhHHhh-CCCCCeeecCCCChhhhHHHHHHH
Q 040234           75 RKKVLVVIDDAAH---PDHLRRLVGEPDWFGPGSRIIITTRN-------EHLLKL-HPVKKVYKLEALTYDEAFRLLCLK  143 (377)
Q Consensus        75 ~k~~LLVLDdv~~---~~~~~~l~~~l~~~~~gs~IIvTTR~-------~~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~  143 (377)
                      +++-++|+|++..   .+.++.|...+..-.+++.+|+++..       ..+... ......++..++++++..+.+.+.
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            4566888999865   34445554433322456677666532       234443 344678899999999999888777


Q ss_pred             hcCCCCCchhHHHHHHHHHHHhCCCCchhhHHH
Q 040234          144 AFDTHKPLEEYVELAESVVRICHCQKSTLNALM  176 (377)
Q Consensus       144 ~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~  176 (377)
                      +....-  .-.++.+..|++.++|  ....+..
T Consensus       155 ~~~~g~--~i~~~a~~~l~~~~~g--dl~~~~~  183 (343)
T 1jr3_D          155 AKQLNL--ELDDAANQVLCYCYEG--NLLALAQ  183 (343)
T ss_dssp             HHHTTC--EECHHHHHHHHHSSTT--CHHHHHH
T ss_pred             HHHcCC--CCCHHHHHHHHHHhch--HHHHHHH
Confidence            632221  1124677888899998  7766654

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=92.80  E-value=0.32  Score=44.15  Aligned_cols=43  Identities=19%  Similarity=0.117  Sum_probs=27.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDL   51 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l   51 (377)
                      +|+||||||.+++.....+-..++|+. .- .     +..++...++...
T Consensus        77 pG~GKTtl~l~ia~~~a~~g~~vl~~s-lE-~-----s~~~l~~R~~~~~  119 (315)
T 3bh0_A           77 PSMGKTAFALKQAKNMSDNDDVVNLHS-LE-M-----GKKENIKRLIVTA  119 (315)
T ss_dssp             TTSSHHHHHHHHHHHHHTTTCEEEEEE-SS-S-----CHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcCCeEEEEE-CC-C-----CHHHHHHHHHHHH
Confidence            799999999999874432223445554 21 1     5667777766553

>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=92.79  E-value=0.23  Score=45.75  Aligned_cols=16  Identities=25%  Similarity=0.144  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||+||.+++...
T Consensus       131 ~GsGKTtla~~la~~~  146 (343)
T 1v5w_A          131 FRTGKTQLSHTLCVTA  146 (343)
T ss_dssp             TTCTHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            6999999999998753

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=92.47  E-value=0.4  Score=45.93  Aligned_cols=45  Identities=24%  Similarity=0.374  Sum_probs=26.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+|+.++++.+....+..+-+..+++..+   .+.++.+++..
T Consensus       162 ~G~GKT~L~~~i~~~~~~~~~~v~V~~~iGER~r---Ev~e~~~~~~~  206 (482)
T 2ck3_D          162 AGVGKTVLIMELINNVAKAHGGYSVFAGVGERTR---EGNDLYHEMIE  206 (482)
T ss_dssp             TTSSHHHHHHHHHHHTTTTCSSEEEEEEESCCHH---HHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHhhHhhCCCEEEEEECCCcch---HHHHHHHHhhh
Confidence            6999999999999865433233333333555431   44555555554

>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=92.42  E-value=0.11  Score=44.42  Aligned_cols=16  Identities=38%  Similarity=0.337  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      ..|+|||||++.++..
T Consensus        33 ~nGsGKSTll~~l~g~   48 (231)
T 4a74_A           33 EFGSGKTQLAHTLAVM   48 (231)
T ss_dssp             STTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            3799999999999873

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=92.33  E-value=0.28  Score=42.19  Aligned_cols=16  Identities=19%  Similarity=0.046  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      .+|+|||||+..++..
T Consensus        32 ~~GsGKTtl~~~l~~~   47 (243)
T 1n0w_A           32 EFRTGKTQICHTLAVT   47 (243)
T ss_dssp             CTTSSHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHH
Confidence            3799999999999874

>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=92.31  E-value=0.022  Score=49.16  Aligned_cols=102  Identities=10%  Similarity=-0.071  Sum_probs=49.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc-cCccchhhhHHHHHHHhcCc-eEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD-NNIRNVYDGINMLRVRLRRK-KVL   79 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~~~~~~~~l~~~l~~k-~~L   79 (377)
                      .|+||||++..++++...+-..++.+. .....      . -...++++++.... .......+..+.+++.+.+. .-+
T Consensus        21 mGsGKTT~ll~~~~r~~~~g~kVli~~-~~~d~------r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dv   92 (223)
T 2b8t_A           21 MFAGKTAELIRRLHRLEYADVKYLVFK-PKIDT------R-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKV   92 (223)
T ss_dssp             TTSCHHHHHHHHHHHHHHTTCCEEEEE-ECCCG------G-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCE
T ss_pred             CCCcHHHHHHHHHHHHHhcCCEEEEEE-eccCc------h-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCE
Confidence            599999999999987655432233322 11100      0 00112222211100 01122233444444444334 449


Q ss_pred             EEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           80 VVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        80 LVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      ||+|.+..  .++++.+.. +.  ..+-.||+|.+..
T Consensus        93 ViIDEaQ~l~~~~ve~l~~-L~--~~gi~Vil~Gl~~  126 (223)
T 2b8t_A           93 IGIDEVQFFDDRICEVANI-LA--ENGFVVIISGLDK  126 (223)
T ss_dssp             EEECSGGGSCTHHHHHHHH-HH--HTTCEEEEECCSB
T ss_pred             EEEecCccCcHHHHHHHHH-HH--hCCCeEEEEeccc
Confidence            99999864  334333322 11  1267899998854

>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=92.15  E-value=0.21  Score=45.49  Aligned_cols=16  Identities=31%  Similarity=0.258  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      +|+|||+||.+++...
T Consensus       116 ~GsGKT~la~~la~~~  131 (324)
T 2z43_A          116 FGSGKTQLCHQLSVNV  131 (324)
T ss_dssp             TTSSHHHHHHHHHHHT
T ss_pred             CCCCHhHHHHHHHHHH
Confidence            7999999999998754

>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=92.12  E-value=0.42  Score=38.41  Aligned_cols=13  Identities=38%  Similarity=0.746  Sum_probs=12.1

Q ss_pred             CCCCcHHHHHHHH
Q 040234            1 MGGLGKTTLARVV   13 (377)
Q Consensus         1 mgGiGKTtLA~~v   13 (377)
                      ++|+||||+|+.+
T Consensus         9 ~~GsGKsT~a~~L   21 (179)
T 3lw7_A            9 MPGSGKSEFAKLL   21 (179)
T ss_dssp             CTTSCHHHHHHHH
T ss_pred             CCCCCHHHHHHHH
Confidence            5899999999999

>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=91.87  E-value=0.15  Score=47.23  Aligned_cols=27  Identities=30%  Similarity=0.284  Sum_probs=19.5

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+||||||.+++......-..++|+.
T Consensus        72 pGsGKTtLal~la~~~~~~g~~vlyid   98 (356)
T 1u94_A           72 ESSGKTTLTLQVIAAAQREGKTCAFID   98 (356)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            799999999999985543323455665

>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=91.80  E-value=0.071  Score=43.70  Aligned_cols=18  Identities=17%  Similarity=0.362  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+++++.
T Consensus        11 ~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A           11 GSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CTTSSHHHHHHHHHHHSS
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            589999999999998664

>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=91.65  E-value=0.57  Score=45.02  Aligned_cols=44  Identities=25%  Similarity=0.219  Sum_probs=27.2

Q ss_pred             CCCcHHHHHHHHHchhcc-ccccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISH-EFDGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+|+.++++.+.. +-+..+++ .+++..+   ...++.+++..
T Consensus       174 ~GvGKT~L~~~l~~~~a~~~~~v~V~~-~iGER~r---Ev~e~~~~~~~  218 (498)
T 1fx0_B          174 AGVGKTVLIMELINNIAKAHGGVSVFG-GVGERTR---EGNDLYMEMKE  218 (498)
T ss_dssp             SSSSHHHHHHHHHHHTTTTCSSCEEEE-EESCCSH---HHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHhhCCCEEEEE-EcccCcH---HHHHHHHhhhc
Confidence            699999999999986543 33344444 3665431   44555555543

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=91.65  E-value=0.2  Score=40.92  Aligned_cols=19  Identities=16%  Similarity=0.023  Sum_probs=13.9

Q ss_pred             HHHHHhcCceEEEEEeCCC
Q 040234           68 MLRVRLRRKKVLVVIDDAA   86 (377)
Q Consensus        68 ~l~~~l~~k~~LLVLDdv~   86 (377)
                      .+-+.+..++-+|+||.-.
T Consensus        93 ~iAral~~~p~~lllDEPt  111 (171)
T 4gp7_A           93 EMAKDYHCFPVAVVFNLPE  111 (171)
T ss_dssp             HHHHHTTCEEEEEEECCCH
T ss_pred             HHHHHcCCcEEEEEEeCCH
Confidence            3445567788899999864

>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=91.43  E-value=0.18  Score=46.55  Aligned_cols=27  Identities=22%  Similarity=0.110  Sum_probs=19.0

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+||||||.+++......-...+|+.
T Consensus        70 pGsGKTtLal~la~~~~~~g~~vlyi~   96 (349)
T 2zr9_A           70 ESSGKTTVALHAVANAQAAGGIAAFID   96 (349)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            799999999999975543323445555

>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=90.95  E-value=0.5  Score=45.86  Aligned_cols=43  Identities=16%  Similarity=0.113  Sum_probs=27.7

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDL   51 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l   51 (377)
                      +|+|||+||.+++........ .++|+. .-.      +..++...++...
T Consensus       251 pG~GKT~lal~~a~~~a~~~g~~vl~~s-~E~------s~~~l~~r~~~~~  294 (503)
T 1q57_A          251 SGMVMSTFVRQQALQWGTAMGKKVGLAM-LEE------SVEETAEDLIGLH  294 (503)
T ss_dssp             SCHHHHHHHHHHHHHHTTTSCCCEEEEE-SSS------CHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHHhcCCcEEEEe-ccC------CHHHHHHHHHHHH
Confidence            799999999999986554322 345544 211      5567777666554

>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=90.74  E-value=0.37  Score=43.76  Aligned_cols=15  Identities=27%  Similarity=0.122  Sum_probs=13.4

Q ss_pred             CCCcHHHHHHHHHch
Q 040234            2 GGLGKTTLARVVYDL   16 (377)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (377)
                      +|+|||+||.+++..
T Consensus       107 ~gsGKT~la~~la~~  121 (322)
T 2i1q_A          107 FGSGKTQIMHQSCVN  121 (322)
T ss_dssp             TTSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH
Confidence            799999999999864

>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=90.64  E-value=0.33  Score=44.91  Aligned_cols=51  Identities=14%  Similarity=0.179  Sum_probs=36.9

Q ss_pred             hhHHHHHHHhcCceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHH
Q 040234           64 DGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLL  117 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~  117 (377)
                      ...+.+.+.|...+=+|++|.+.+.+.++.+....   ..|..||+|+.....+
T Consensus       184 ~~~~~La~aL~~~PdvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~~  234 (356)
T 3jvv_A          184 GFSEALRSALREDPDIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSAA  234 (356)
T ss_dssp             CHHHHHHHHTTSCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSHH
T ss_pred             CHHHHHHHHhhhCcCEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChHH
Confidence            45568888999999999999999877666544331   2356688888876544

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=90.58  E-value=0.088  Score=49.12  Aligned_cols=32  Identities=19%  Similarity=0.245  Sum_probs=21.2

Q ss_pred             CCCcHHHHHHHHHchhcccccc-ceEEecchhh
Q 040234            2 GGLGKTTLARVVYDLISHEFDG-SSFLADVREK   33 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~-~~w~~~~~~~   33 (377)
                      +|+|||+|+.++++.+....+. .+.+..+++.
T Consensus       184 ~g~GKT~Ll~~Ia~~i~~~~~dv~~V~~lIGER  216 (427)
T 3l0o_A          184 PKAGKTTILKEIANGIAENHPDTIRIILLIDER  216 (427)
T ss_dssp             TTCCHHHHHHHHHHHHHHHCTTSEEEEEECSCC
T ss_pred             CCCChhHHHHHHHHHHhhcCCCeEEEEEEeccC
Confidence            6999999999999866544333 2334435554

>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=90.35  E-value=0.38  Score=49.41  Aligned_cols=20  Identities=30%  Similarity=0.348  Sum_probs=16.9

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|.|||.||+.++++....
T Consensus       519 PPGtGKT~lAkaiA~e~~~~  538 (806)
T 3cf2_A          519 PPGCGKTLLAKAIANECQAN  538 (806)
T ss_dssp             STTSSHHHHHHHHHHTTTCE
T ss_pred             CCCCCchHHHHHHHHHhCCc
Confidence            47999999999999976543

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=90.04  E-value=0.78  Score=43.72  Aligned_cols=44  Identities=14%  Similarity=0.197  Sum_probs=27.7

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHHHHh
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLSDLL   52 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~   52 (377)
                      +|+|||+||.+++........ .++|+. .- .     +..++...++....
T Consensus       209 pg~GKT~lal~ia~~~a~~~g~~vl~~s-lE-~-----~~~~l~~R~~~~~~  253 (444)
T 2q6t_A          209 PAMGKTAFALTIAQNAALKEGVGVGIYS-LE-M-----PAAQLTLRMMCSEA  253 (444)
T ss_dssp             TTSCHHHHHHHHHHHHHHTTCCCEEEEE-SS-S-----CHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCeEEEEE-CC-C-----CHHHHHHHHHHHHc
Confidence            799999999999985543222 344443 21 1     55677777665543

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=89.89  E-value=0.72  Score=42.24  Aligned_cols=43  Identities=28%  Similarity=0.281  Sum_probs=27.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDL   51 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l   51 (377)
                      +|+||||||..++.....+=..++|+. . +.     +..++...++...
T Consensus        55 pG~GKTt~al~ia~~~a~~g~~Vl~fS-l-Em-----s~~ql~~Rlls~~   97 (338)
T 4a1f_A           55 PSMGKTSLMMNMVLSALNDDRGVAVFS-L-EM-----SAEQLALRALSDL   97 (338)
T ss_dssp             TTSCHHHHHHHHHHHHHHTTCEEEEEE-S-SS-----CHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcCCeEEEEe-C-CC-----CHHHHHHHHHHHh
Confidence            799999999999985443212334443 2 11     6667777776654

>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=89.85  E-value=1.6  Score=37.60  Aligned_cols=16  Identities=31%  Similarity=0.410  Sum_probs=13.6

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|.|||.+|..++.+.
T Consensus       117 tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A          117 TGSGKTHVAMAAINEL  132 (237)
T ss_dssp             SSTTHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHc
Confidence            5999999999888754

>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=89.85  E-value=0.14  Score=41.47  Aligned_cols=18  Identities=17%  Similarity=-0.023  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.++++..
T Consensus         9 ~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            9 PDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             SSSSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998654

>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=89.74  E-value=0.76  Score=41.48  Aligned_cols=27  Identities=33%  Similarity=0.389  Sum_probs=18.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+||||++..++...+.. ...+.+.
T Consensus       112 ~~GsGKTTl~~~LA~~l~~~-g~kV~lv  138 (306)
T 1vma_A          112 VNGTGKTTSCGKLAKMFVDE-GKSVVLA  138 (306)
T ss_dssp             CTTSSHHHHHHHHHHHHHHT-TCCEEEE
T ss_pred             CCCChHHHHHHHHHHHHHhc-CCEEEEE
Confidence            37999999999999866543 2334443

>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=89.71  E-value=0.62  Score=44.36  Aligned_cols=45  Identities=13%  Similarity=0.060  Sum_probs=26.2

Q ss_pred             CCCcHHHHHHHHHchhcccc---ccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEF---DGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f---~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+|+.++++....+-   +..+.+..+++..+   .+.++.+.+..
T Consensus       160 ~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~---Ev~e~~~~~~~  207 (465)
T 3vr4_D          160 SGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFE---EAEFFMEDFRQ  207 (465)
T ss_dssp             TTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHH---HHHHHHHHHHH
T ss_pred             CCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcH---HHHHHHHHHhh
Confidence            69999999999998654322   22333343555431   44555555443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=89.68  E-value=0.4  Score=42.23  Aligned_cols=102  Identities=13%  Similarity=0.113  Sum_probs=52.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||||++.+...+...+.+.+.+....-..... ....        +..+..... +.......+.+.|..++=+|+
T Consensus        34 ~GsGKSTll~~l~g~~~~~~~G~I~~~g~~i~~~~~-~~~~--------~v~q~~~gl-~~~~l~~~la~aL~~~p~ill  103 (261)
T 2eyu_A           34 TGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFK-HKKS--------IVNQREVGE-DTKSFADALRAALREDPDVIF  103 (261)
T ss_dssp             TTCSHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCC-CSSS--------EEEEEEBTT-TBSCHHHHHHHHHHHCCSEEE
T ss_pred             CCccHHHHHHHHHHhCCCCCCCEEEEcCCcceeecC-Ccce--------eeeHHHhCC-CHHHHHHHHHHHHhhCCCEEE
Confidence            699999999999985543334444443110000000 0000        000000000 112335566677776777899


Q ss_pred             EeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhH
Q 040234           82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHL  116 (377)
Q Consensus        82 LDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v  116 (377)
                      +|...|.+....+....   ..|..|++||.....
T Consensus       104 lDEp~D~~~~~~~l~~~---~~g~~vl~t~H~~~~  135 (261)
T 2eyu_A          104 VGEMRDLETVETALRAA---ETGHLVFGTLHTNTA  135 (261)
T ss_dssp             ESCCCSHHHHHHHHHHH---HTTCEEEEEECCSSH
T ss_pred             eCCCCCHHHHHHHHHHH---ccCCEEEEEeCcchH
Confidence            99998765544333221   235668888876543

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=89.28  E-value=0.99  Score=43.14  Aligned_cols=41  Identities=17%  Similarity=0.264  Sum_probs=24.9

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+||||||..++..+..... .++|+. .-.      +..++...++.
T Consensus       212 pG~GKTtl~l~ia~~~~~~~g~~Vl~~s-~E~------s~~~l~~r~~~  253 (454)
T 2r6a_A          212 PSVGKTAFALNIAQNVATKTNENVAIFS-LEM------SAQQLVMRMLC  253 (454)
T ss_dssp             TTSCHHHHHHHHHHHHHHHSSCCEEEEE-SSS------CHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCcEEEEE-CCC------CHHHHHHHHHH
Confidence            799999999999986543222 344443 211      44566655544

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=89.22  E-value=0.16  Score=41.76  Aligned_cols=18  Identities=28%  Similarity=0.422  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.++++..
T Consensus        13 ~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A           13 LMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999998653

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=89.21  E-value=0.96  Score=37.66  Aligned_cols=17  Identities=18%  Similarity=0.460  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||||+.++..+
T Consensus        26 ~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           26 VSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             STTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999865

>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=88.82  E-value=0.82  Score=38.65  Aligned_cols=17  Identities=29%  Similarity=0.184  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||+|+|+.++++.
T Consensus         8 pPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            8 PPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            48999999999999754

>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=88.82  E-value=0.62  Score=42.56  Aligned_cols=97  Identities=13%  Similarity=0.087  Sum_probs=51.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+|||||++.+...+.. -...+.+.+.......  ...           ................+.+.|..++=+|+
T Consensus       180 ~GsGKTTll~~l~g~~~~-~~g~i~i~~~~e~~~~--~~~-----------~~i~~~~ggg~~~r~~la~aL~~~p~ili  245 (330)
T 2pt7_A          180 TGSGKTTYIKSIMEFIPK-EERIISIEDTEEIVFK--HHK-----------NYTQLFFGGNITSADCLKSCLRMRPDRII  245 (330)
T ss_dssp             TTSCHHHHHHHGGGGSCT-TSCEEEEESSCCCCCS--SCS-----------SEEEEECBTTBCHHHHHHHHTTSCCSEEE
T ss_pred             CCCCHHHHHHHHhCCCcC-CCcEEEECCeeccccc--cch-----------hEEEEEeCCChhHHHHHHHHhhhCCCEEE
Confidence            699999999999985543 2345555432211000  000           00000000123345567777888888999


Q ss_pred             EeCCCChhhhhHhhCCCCCCCCCCeEEEEecchh
Q 040234           82 IDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEH  115 (377)
Q Consensus        82 LDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~  115 (377)
                      ||.+.+.+.++.+... .  ..+..+|+||....
T Consensus       246 ldE~~~~e~~~~l~~~-~--~g~~tvi~t~H~~~  276 (330)
T 2pt7_A          246 LGELRSSEAYDFYNVL-C--SGHKGTLTTLHAGS  276 (330)
T ss_dssp             ECCCCSTHHHHHHHHH-H--TTCCCEEEEEECSS
T ss_pred             EcCCChHHHHHHHHHH-h--cCCCEEEEEEcccH
Confidence            9999886555544322 1  11223677776543

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=88.71  E-value=0.19  Score=42.14  Aligned_cols=17  Identities=35%  Similarity=0.434  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++...
T Consensus        33 ~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           33 YMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            57999999999999866

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.54  E-value=1.8  Score=35.90  Aligned_cols=17  Identities=47%  Similarity=0.517  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+|||||++.++...
T Consensus        37 ~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           37 VSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            47999999999999865

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=88.51  E-value=0.3  Score=40.78  Aligned_cols=19  Identities=37%  Similarity=0.452  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus        11 gG~GKTt~a~~la~~la~~   29 (206)
T 4dzz_A           11 GGSGKTTAVINIATALSRS   29 (206)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCccHHHHHHHHHHHHHHC
Confidence            8999999999999865543

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=88.22  E-value=0.78  Score=43.77  Aligned_cols=42  Identities=19%  Similarity=0.124  Sum_probs=25.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSD   50 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~   50 (377)
                      +|+|||+||.+++......=..++|+. .-.      +..++...++..
T Consensus       206 pG~GKTtlal~ia~~~a~~g~~vl~fS-lEm------s~~ql~~R~~~~  247 (444)
T 3bgw_A          206 PSMGKTAFALKQAKNMSDNDDVVNLHS-LEM------GKKENIKRLIVT  247 (444)
T ss_dssp             SSSSHHHHHHHHHHHHHHTTCEEEEEC-SSS------CTTHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHcCCEEEEEE-CCC------CHHHHHHHHHHH
Confidence            799999999999985543312334443 211      444666665554

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=87.96  E-value=0.21  Score=40.75  Aligned_cols=15  Identities=40%  Similarity=0.432  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHHc
Q 040234            1 MGGLGKTTLARVVYD   15 (377)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (377)
                      ++|+||||+|+.+++
T Consensus        10 ~~GsGKST~a~~L~~   24 (181)
T 1ly1_A           10 CPGSGKSTWAREFIA   24 (181)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHh
Confidence            589999999999987

>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=87.89  E-value=1.1  Score=43.26  Aligned_cols=30  Identities=17%  Similarity=0.194  Sum_probs=18.3

Q ss_pred             CCCcHHHHHH-HHHchhccccccceEEecchhh
Q 040234            2 GGLGKTTLAR-VVYDLISHEFDGSSFLADVREK   33 (377)
Q Consensus         2 gGiGKTtLA~-~v~~~~~~~f~~~~w~~~~~~~   33 (377)
                      +|+|||+||. .+++...  -+..+.+..+++.
T Consensus       172 ~g~GKT~Lal~~I~~~~~--~dv~~V~~~iGeR  202 (507)
T 1fx0_A          172 RQTGKTAVATDTILNQQG--QNVICVYVAIGQK  202 (507)
T ss_dssp             SSSSHHHHHHHHHHTCCT--TTCEEEEEEESCC
T ss_pred             CCCCccHHHHHHHHHhhc--CCcEEEEEEcCCC
Confidence            6999999964 7777543  2333344446654

>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=87.88  E-value=0.92  Score=43.34  Aligned_cols=45  Identities=11%  Similarity=0.003  Sum_probs=26.3

Q ss_pred             CCCcHHHHHHHHHchhcccc---ccceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEF---DGSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f---~~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+|+.++++......   +..+.+..+++..+   .+.++.+.+..
T Consensus       161 ~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~---Ev~e~~~~~~~  208 (469)
T 2c61_A          161 SGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNE---EAQYFMSDFEK  208 (469)
T ss_dssp             TTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHH---HHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcH---HHHHHHHHHHh
Confidence            69999999999998543211   12333443555431   44555555543

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=87.86  E-value=0.56  Score=39.33  Aligned_cols=20  Identities=20%  Similarity=0.312  Sum_probs=16.7

Q ss_pred             CCCcHHHHHHHHHchhcccc
Q 040234            2 GGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f   21 (377)
                      -|+||||.++.+++.++.+-
T Consensus         9 DGsGKsTq~~~L~~~L~~~g   28 (197)
T 3hjn_A            9 DGSGKSTQIQLLAQYLEKRG   28 (197)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHCC
Confidence            59999999999999776553

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=87.78  E-value=0.23  Score=40.57  Aligned_cols=18  Identities=39%  Similarity=0.501  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.++.+..
T Consensus        12 ~~GsGKsTla~~La~~l~   29 (175)
T 1via_A           12 FMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999998653

>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=87.50  E-value=1.3  Score=42.67  Aligned_cols=78  Identities=18%  Similarity=0.227  Sum_probs=39.2

Q ss_pred             CCCcHHHHH-HHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc------ccCccch----------hh
Q 040234            2 GGLGKTTLA-RVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA------DNNIRNV----------YD   64 (377)
Q Consensus         2 gGiGKTtLA-~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~------~~~~~~~----------~~   64 (377)
                      .|+|||+|| ..+.++-  +-+..+.+..+++..+   .+.++.+.+... +...      .......          -.
T Consensus       171 ~g~GKT~l~l~~I~n~~--~~dv~~V~~~IGeR~~---ev~e~~~~l~~~-g~m~~tvvV~atad~p~~~r~~a~~~a~t  244 (513)
T 3oaa_A          171 RQTGKTALAIDAIINQR--DSGIKCIYVAIGQKAS---TISNVVRKLEEH-GALANTIVVVATASESAALQYLAPYAGCA  244 (513)
T ss_dssp             SSSSHHHHHHHHHHTTS--SSSCEEEEEEESCCHH---HHHHHHHHHHHH-SCSTTEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHhhc--cCCceEEEEEecCChH---HHHHHHHHHhhc-CcccceEEEEECCCCChHHHHHHHHHHHH
Confidence            489999997 4666642  2233333444665432   444555544332 1000      0000110          12


Q ss_pred             hHHHHHHHhcCceEEEEEeCCCC
Q 040234           65 GINMLRVRLRRKKVLVVIDDAAH   87 (377)
Q Consensus        65 ~~~~l~~~l~~k~~LLVLDdv~~   87 (377)
                      ..+.++.  +++..||++||+-.
T Consensus       245 iAEyfrd--~G~dVLli~Dsltr  265 (513)
T 3oaa_A          245 MGEYFRD--RGEDALIIYDDLSK  265 (513)
T ss_dssp             HHHHHHH--TTCEEEEEEETHHH
T ss_pred             HHHHHHh--cCCCEEEEecChHH
Confidence            2334443  58999999999743

>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=87.36  E-value=1.1  Score=42.54  Aligned_cols=17  Identities=18%  Similarity=0.241  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      +|+|||+|+.++++...
T Consensus       156 ~G~GKt~L~~~Ia~~~~  172 (464)
T 3gqb_B          156 SGLPANEIAAQIARQAT  172 (464)
T ss_dssp             TTSCHHHHHHHHHHHCB
T ss_pred             CCCCchHHHHHHHHHHH
Confidence            69999999999998543

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=87.30  E-value=0.24  Score=40.77  Aligned_cols=19  Identities=26%  Similarity=0.574  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||+|+.+++++..
T Consensus         9 ~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            9 IPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             CTTSCHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            4799999999999987653

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=87.21  E-value=0.25  Score=41.14  Aligned_cols=18  Identities=22%  Similarity=0.362  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.+++.+.
T Consensus         8 ~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            8 TVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             CTTSCHHHHHHHHHHHHC
T ss_pred             CCccCHHHHHHHHHHhcC
Confidence            479999999999998654

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=87.16  E-value=0.8  Score=45.23  Aligned_cols=32  Identities=19%  Similarity=0.470  Sum_probs=21.7

Q ss_pred             EEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEec
Q 040234           78 VLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTR  112 (377)
Q Consensus        78 ~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR  112 (377)
                      =+||+|.+..  ...+..+...++   .+.++|+.--
T Consensus       281 dvlIIDEasml~~~~~~~Ll~~~~---~~~~lilvGD  314 (574)
T 3e1s_A          281 DLLIVDEVSMMGDALMLSLLAAVP---PGARVLLVGD  314 (574)
T ss_dssp             SEEEECCGGGCCHHHHHHHHTTSC---TTCEEEEEEC
T ss_pred             CEEEEcCccCCCHHHHHHHHHhCc---CCCEEEEEec
Confidence            4899999864  456777777654   4567776543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=87.08  E-value=0.32  Score=41.81  Aligned_cols=20  Identities=20%  Similarity=0.107  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .||+||||+|..++.....+
T Consensus        14 kgGvGKTt~a~~la~~l~~~   33 (228)
T 2r8r_A           14 APGVGKTYAMLQAAHAQLRQ   33 (228)
T ss_dssp             STTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHHHHHHHHC
Confidence            38999999999999865443

>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=87.07  E-value=1.1  Score=43.23  Aligned_cols=44  Identities=20%  Similarity=0.218  Sum_probs=24.4

Q ss_pred             CCCcHHHHH-HHHHchhcc------ccccceEEecchhhcccccCHHHHHHHHH
Q 040234            2 GGLGKTTLA-RVVYDLISH------EFDGSSFLADVREKCDKEGSVISLQKQLL   48 (377)
Q Consensus         2 gGiGKTtLA-~~v~~~~~~------~f~~~~w~~~~~~~~~~~~~~~~~~~~i~   48 (377)
                      +|+|||+|| ..++++...      +-+..+.+..+++..+   .+.++.+.+.
T Consensus       171 ~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~---Ev~~~~~~~~  221 (510)
T 2ck3_A          171 RQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRS---TVAQLVKRLT  221 (510)
T ss_dssp             TTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHH---HHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcH---HHHHHHHHHH
Confidence            699999996 466665542      2333344444665431   4444444444

>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=86.97  E-value=0.26  Score=40.34  Aligned_cols=17  Identities=35%  Similarity=0.442  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        19 ~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           19 TPGVGKTTLGKELASKS   35 (180)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            57999999999999765

>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=86.72  E-value=0.28  Score=40.41  Aligned_cols=18  Identities=28%  Similarity=0.493  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.++++..
T Consensus        11 ~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A           11 VPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999998665

>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=86.68  E-value=0.29  Score=40.40  Aligned_cols=17  Identities=29%  Similarity=0.311  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++.+.
T Consensus        13 ~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A           13 HPATGKTTLSQALATGL   29 (193)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            57999999999998865

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=86.50  E-value=0.39  Score=40.62  Aligned_cols=28  Identities=32%  Similarity=0.394  Sum_probs=20.6

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecch
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVR   31 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~   31 (377)
                      ||+||||+|..++..+...-  .+.+.|..
T Consensus        10 GGvGKTT~a~~LA~~la~~g--~VlliD~D   37 (209)
T 3cwq_A           10 GGVGKTTTAVHLSAYLALQG--ETLLIDGD   37 (209)
T ss_dssp             TTSSHHHHHHHHHHHHHTTS--CEEEEEEC
T ss_pred             CCCcHHHHHHHHHHHHHhcC--CEEEEECC
Confidence            89999999999998665553  45444443

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=86.44  E-value=0.3  Score=39.57  Aligned_cols=18  Identities=28%  Similarity=0.416  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+|||||++.++....
T Consensus        12 ~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A           12 PMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CTTSCHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998653

>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=86.37  E-value=0.3  Score=40.34  Aligned_cols=16  Identities=38%  Similarity=0.561  Sum_probs=14.3

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      +.|+|||||++.++..
T Consensus        17 ~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A           17 HPGSGKSTIAEALANL   32 (191)
T ss_dssp             CTTSCHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHhc
Confidence            4799999999999875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=86.19  E-value=0.33  Score=39.21  Aligned_cols=18  Identities=28%  Similarity=0.314  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.+++++.
T Consensus        15 ~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A           15 FMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998654

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=86.15  E-value=0.45  Score=40.95  Aligned_cols=19  Identities=32%  Similarity=0.354  Sum_probs=16.5

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+...
T Consensus        14 GGvGKTt~a~~LA~~la~~   32 (245)
T 3ea0_A           14 GGDGGSCIAANFAFALSQE   32 (245)
T ss_dssp             TTSSHHHHHHHHHHHHTTS
T ss_pred             CCcchHHHHHHHHHHHHhC
Confidence            8999999999999866654

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=86.04  E-value=0.77  Score=44.16  Aligned_cols=42  Identities=21%  Similarity=0.211  Sum_probs=23.3

Q ss_pred             CCCcHHHHHH-HHHchhccccccceEEecchhhcccccCHHHHHHHHH
Q 040234            2 GGLGKTTLAR-VVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLL   48 (377)
Q Consensus         2 gGiGKTtLA~-~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~   48 (377)
                      +|+|||+||. .+++...  -+..+.+..+++..+   .+.++.+.+.
T Consensus       171 ~g~GKT~Lal~~I~~~~~--~dv~~V~~~iGeR~~---Ev~~~~~~~~  213 (502)
T 2qe7_A          171 RQTGKTTIAIDTIINQKG--QDVICIYVAIGQKQS---TVAGVVETLR  213 (502)
T ss_dssp             SSSCHHHHHHHHHHGGGS--CSEEEEEEEESCCHH---HHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHhhc--CCcEEEEEECCCcch---HHHHHHHHHh
Confidence            6999999964 7776542  233333443655431   3444444443

>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=85.50  E-value=0.89  Score=41.82  Aligned_cols=16  Identities=38%  Similarity=0.443  Sum_probs=14.3

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      .|+|||||+..++...
T Consensus       140 ~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          140 FGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             TTSSHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            7999999999999855

>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=85.44  E-value=0.75  Score=44.03  Aligned_cols=20  Identities=25%  Similarity=0.444  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+|||+++..++..+...
T Consensus        53 ~aGTGKT~ll~~~~~~l~~~   72 (459)
T 3upu_A           53 PAGTGATTLTKFIIEALIST   72 (459)
T ss_dssp             CTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHhc
Confidence            37999999999999865444

>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=85.31  E-value=0.99  Score=41.92  Aligned_cols=49  Identities=12%  Similarity=0.194  Sum_probs=32.2

Q ss_pred             hhHHHHHHHhcCceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchh
Q 040234           64 DGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEH  115 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~  115 (377)
                      .....++..+...+=+|++|.+.+.+.+.......   ..|..||.|+....
T Consensus       197 ~~~~~l~~~L~~~pd~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~~  245 (372)
T 2ewv_A          197 SFADALRAALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNT  245 (372)
T ss_dssp             CSHHHHHHHTTSCCSEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCCS
T ss_pred             HHHHHHHHHhhhCcCEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcch
Confidence            34567788888788899999998866554433221   33556777776543

>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=85.29  E-value=1.5  Score=42.16  Aligned_cols=42  Identities=14%  Similarity=0.157  Sum_probs=23.5

Q ss_pred             CCCcHHHHHH-HHHchhccccccceEEecchhhcccccCHHHHHHHHH
Q 040234            2 GGLGKTTLAR-VVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLL   48 (377)
Q Consensus         2 gGiGKTtLA~-~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~   48 (377)
                      +|+|||+||. .+++...  -+..+.+..+++..+   .+.++.+.+.
T Consensus       184 ~g~GKT~Lal~~I~~~~~--~dv~~V~~~IGeR~~---Ev~e~~~~~~  226 (515)
T 2r9v_A          184 RQTGKTAIAIDTIINQKG--QGVYCIYVAIGQKKS---AIARIIDKLR  226 (515)
T ss_dssp             TTSSHHHHHHHHHHTTTT--TTEEEEEEEESCCHH---HHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHhhc--CCcEEEEEEcCCCcH---HHHHHHHHHH
Confidence            6999999964 7777542  233333443655431   4445555544

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=85.29  E-value=0.37  Score=42.16  Aligned_cols=18  Identities=22%  Similarity=0.091  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||||+.++.+..
T Consensus         9 ~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            9 PTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCcCHHHHHHHHHhcCC
Confidence            479999999999998553

>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=85.14  E-value=0.38  Score=38.91  Aligned_cols=18  Identities=28%  Similarity=0.372  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.++++..
T Consensus        10 ~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A           10 ARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998653

>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=85.10  E-value=1.6  Score=39.01  Aligned_cols=18  Identities=28%  Similarity=0.220  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      .+|+||||++..++....
T Consensus       113 ~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          113 STGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            379999999999998654

>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=85.05  E-value=0.36  Score=40.36  Aligned_cols=18  Identities=33%  Similarity=0.571  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||||+.++..+.
T Consensus        33 ~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           33 LSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999998765

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=85.04  E-value=0.25  Score=40.45  Aligned_cols=18  Identities=28%  Similarity=0.331  Sum_probs=11.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.++++..
T Consensus        13 ~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A           13 PFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CC----CHHHHHHHHHST
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            479999999999987654

>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=84.96  E-value=0.4  Score=39.34  Aligned_cols=18  Identities=28%  Similarity=0.512  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.++++..
T Consensus        10 ~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A           10 LPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999998653

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=84.78  E-value=0.42  Score=38.42  Aligned_cols=18  Identities=17%  Similarity=0.241  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.+.++..
T Consensus         8 ~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            8 FMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998653

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=84.73  E-value=0.53  Score=38.74  Aligned_cols=19  Identities=42%  Similarity=0.621  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||+++.++..+..
T Consensus        21 ~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           21 LPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            4799999999999986643

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=84.64  E-value=2.3  Score=36.31  Aligned_cols=23  Identities=17%  Similarity=0.222  Sum_probs=13.3

Q ss_pred             hhHHHHHHHhcCceEEEEEeCCCC
Q 040234           64 DGINMLRVRLRRKKVLVVIDDAAH   87 (377)
Q Consensus        64 ~~~~~l~~~l~~k~~LLVLDdv~~   87 (377)
                      .+.+.+++.+.+ --+||+|.++.
T Consensus       165 ~l~~~l~~~l~~-~~~lVlDEah~  187 (235)
T 3llm_A          165 VLLRKLEAGIRG-ISHVIVDEIHE  187 (235)
T ss_dssp             HHHHHHHHCCTT-CCEEEECCTTS
T ss_pred             HHHHHHHhhhcC-CcEEEEECCcc
Confidence            333444443333 34789999976

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=84.63  E-value=0.41  Score=39.27  Aligned_cols=17  Identities=29%  Similarity=0.231  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus        12 ~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A           12 PPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999754

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=84.40  E-value=0.43  Score=39.20  Aligned_cols=18  Identities=11%  Similarity=0.279  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+|||||++.+.....
T Consensus        13 psGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A           13 AHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CTTSSHHHHHHHHHHHCT
T ss_pred             CCCCCHHHHHHHHHhhCC
Confidence            479999999999988544

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=84.26  E-value=0.42  Score=39.98  Aligned_cols=20  Identities=30%  Similarity=0.493  Sum_probs=16.5

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      +.|+||||+|+.++++....
T Consensus        12 ~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A           12 IDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHTTT
T ss_pred             CCCCCHHHHHHHHHHHHhhc
Confidence            47999999999999866543

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=84.22  E-value=0.57  Score=41.03  Aligned_cols=19  Identities=26%  Similarity=0.426  Sum_probs=16.0

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus        10 GGvGKTT~a~nLA~~la~~   28 (269)
T 1cp2_A           10 GGIGKSTTTQNLTSGLHAM   28 (269)
T ss_dssp             TTSSHHHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHHHHHC
Confidence            8999999999999865543

>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=83.97  E-value=0.44  Score=39.66  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=17.0

Q ss_pred             CCCCcHHHHHHHHHchhccccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFD   22 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~   22 (377)
                      ++|+|||||++.+..+....|.
T Consensus         9 PSG~GK~Tl~~~L~~~~~~~~~   30 (186)
T 1ex7_A            9 PSGTGKSTLLKKLFAEYPDSFG   30 (186)
T ss_dssp             CTTSSHHHHHHHHHHHCTTTEE
T ss_pred             CCCCCHHHHHHHHHHhCCCCeE
Confidence            4799999999999876554443

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=83.91  E-value=0.46  Score=39.27  Aligned_cols=17  Identities=24%  Similarity=0.165  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus        17 ~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A           17 GPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999855

>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=83.77  E-value=2.5  Score=39.57  Aligned_cols=14  Identities=21%  Similarity=0.135  Sum_probs=12.2

Q ss_pred             CCCcHHHHHHHHHc
Q 040234            2 GGLGKTTLARVVYD   15 (377)
Q Consensus         2 gGiGKTtLA~~v~~   15 (377)
                      +|+|||||+..++-
T Consensus       187 sGsGKTTLl~~la~  200 (400)
T 3lda_A          187 FRTGKSQLCHTLAV  200 (400)
T ss_dssp             TTSSHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHH
Confidence            79999999998764

>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=83.76  E-value=0.49  Score=40.73  Aligned_cols=19  Identities=37%  Similarity=0.712  Sum_probs=16.2

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+.+.
T Consensus         9 GGvGKTt~a~~LA~~la~~   27 (254)
T 3kjh_A            9 GGVGKTTVAAGLIKIMASD   27 (254)
T ss_dssp             SSHHHHHHHHHHHHHHTTT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            8999999999999866544

>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=83.63  E-value=2.1  Score=40.46  Aligned_cols=20  Identities=30%  Similarity=0.247  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+||||++..++..++..
T Consensus       106 ~~GsGKTT~~~~LA~~l~~~  125 (425)
T 2ffh_A          106 LQGSGKTTTAAKLALYYKGK  125 (425)
T ss_dssp             CTTSSHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHHc
Confidence            47999999999999865543

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=83.48  E-value=0.46  Score=39.85  Aligned_cols=18  Identities=33%  Similarity=0.451  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+|||||++.+.....
T Consensus        20 ~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           20 PSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CTTSCHHHHHHHHHHHCT
T ss_pred             CCCCCHHHHHHHHHHhCc
Confidence            579999999999988653

>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=83.44  E-value=0.46  Score=38.57  Aligned_cols=17  Identities=29%  Similarity=0.458  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||||+.++...
T Consensus        16 ~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A           16 VSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             STTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            47999999999998754

>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=83.21  E-value=0.5  Score=40.10  Aligned_cols=18  Identities=28%  Similarity=0.218  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.++++..
T Consensus        12 ~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A           12 PPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999998653

>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=83.20  E-value=0.53  Score=39.27  Aligned_cols=17  Identities=29%  Similarity=0.251  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus        28 ~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           28 PPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999865

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=83.14  E-value=0.49  Score=40.19  Aligned_cols=18  Identities=17%  Similarity=0.128  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+++++.
T Consensus        13 ~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A           13 APASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999998654

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=83.06  E-value=0.49  Score=38.92  Aligned_cols=17  Identities=24%  Similarity=0.192  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.+++..
T Consensus        11 ~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A           11 GPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998754

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=82.93  E-value=0.52  Score=38.99  Aligned_cols=18  Identities=22%  Similarity=0.172  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.++++..
T Consensus        20 ~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           20 GPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998653

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*

Probab=82.78  E-value=0.65  Score=39.73  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=16.2

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus        12 gGvGKTt~a~~LA~~la~~   30 (237)
T 1g3q_A           12 GGTGKTTVTANLSVALGDR   30 (237)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhc
Confidence            8999999999999866544

>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=82.74  E-value=2.8  Score=35.17  Aligned_cols=19  Identities=5%  Similarity=0.211  Sum_probs=16.3

Q ss_pred             EEEEeCCCChhhhhHhhCC
Q 040234           79 LVVIDDAAHPDHLRRLVGE   97 (377)
Q Consensus        79 LLVLDdv~~~~~~~~l~~~   97 (377)
                      .+|+||+.+..+++.+...
T Consensus       105 ~vII~dvR~~~Ev~~fr~~  123 (202)
T 3ch4_B          105 IWLVSDTRRVSDIQWFREA  123 (202)
T ss_dssp             EEEECCCCSHHHHHHHHHH
T ss_pred             cEEEeCCCCHHHHHHHHHh
Confidence            7999999999988888754

>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=82.69  E-value=2.4  Score=37.91  Aligned_cols=27  Identities=26%  Similarity=0.250  Sum_probs=19.1

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      .+|+||||++..++...+.. ...+.+.
T Consensus       106 ~~G~GKTT~~~~la~~~~~~-~~~v~l~  132 (295)
T 1ls1_A          106 LQGSGKTTTAAKLALYYKGK-GRRPLLV  132 (295)
T ss_dssp             CTTTTHHHHHHHHHHHHHHT-TCCEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHc-CCeEEEe
Confidence            37999999999999865543 3344444

>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=82.68  E-value=0.51  Score=38.88  Aligned_cols=15  Identities=27%  Similarity=0.434  Sum_probs=13.4

Q ss_pred             CCCCcHHHHHHHHHc
Q 040234            1 MGGLGKTTLARVVYD   15 (377)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (377)
                      +.|+|||||++.++.
T Consensus        10 ~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A           10 PAGVGKSTTCKRLAA   24 (189)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHhc
Confidence            479999999999986

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=82.62  E-value=0.88  Score=39.04  Aligned_cols=15  Identities=40%  Similarity=0.352  Sum_probs=13.0

Q ss_pred             CCCcHHHHHHHHHch
Q 040234            2 GGLGKTTLARVVYDL   16 (377)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (377)
                      +|+|||+||.+++..
T Consensus        39 pG~GKT~l~l~~~~~   53 (251)
T 2zts_A           39 TGTGKTTFAAQFIYK   53 (251)
T ss_dssp             TTSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH
Confidence            799999999998764

>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=82.50  E-value=0.52  Score=41.35  Aligned_cols=18  Identities=28%  Similarity=0.647  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.++..+.
T Consensus        12 ~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A           12 LPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CTTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            589999999999998643

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=82.36  E-value=0.55  Score=40.09  Aligned_cols=17  Identities=24%  Similarity=0.284  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus        15 ~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A           15 APGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CTTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999999754

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=82.24  E-value=1  Score=50.81  Aligned_cols=76  Identities=18%  Similarity=0.102  Sum_probs=42.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcc----ccCccchhhhHHHHHHHhc-C
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLA----DNNIRNVYDGINMLRVRLR-R   75 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~----~~~~~~~~~~~~~l~~~l~-~   75 (377)
                      .+|+|||+||.+++.+...+=...+|+. ..+..    +...     ++.++...    -..+.+.++..+.+++..+ .
T Consensus      1435 ppGtGKT~LA~ala~ea~~~G~~v~Fi~-~e~~~----~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~~ 1504 (2050)
T 3cmu_A         1435 PESSGKTTLTLQVIAAAQREGKTCAFID-AEHAL----DPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSG 1504 (2050)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTTCCEEEEC-TTSCC----CHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCcEEEEE-ccccc----CHHH-----HHHcCCCchhceeecCChHHHHHHHHHHHHhcC
Confidence            4799999999999886554433445554 33322    1222     33332110    0122233455555555543 4


Q ss_pred             ceEEEEEeCCC
Q 040234           76 KKVLVVIDDAA   86 (377)
Q Consensus        76 k~~LLVLDdv~   86 (377)
                      +.-+||+|.+.
T Consensus      1505 ~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1505 AVDVIVVDSVA 1515 (2050)
T ss_dssp             CCSEEEESCGG
T ss_pred             CCCEEEEcChh
Confidence            67799999984

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=82.24  E-value=0.78  Score=40.14  Aligned_cols=17  Identities=47%  Similarity=0.753  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      ||+||||+|..++..+.
T Consensus        37 GGvGKTT~a~~LA~~la   53 (267)
T 3k9g_A           37 GGVGKSTSAIILATLLS   53 (267)
T ss_dssp             SSSCHHHHHHHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHH
Confidence            89999999999998666

>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=82.21  E-value=0.55  Score=38.67  Aligned_cols=16  Identities=31%  Similarity=0.457  Sum_probs=14.4

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      +.|+||||+|+.++++
T Consensus        18 ~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           18 TPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             STTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHh
Confidence            5799999999999986

>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=82.14  E-value=2.5  Score=37.81  Aligned_cols=19  Identities=32%  Similarity=0.316  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      .+|+||||++..++.....
T Consensus       106 ~~G~GKTT~~~~la~~~~~  124 (297)
T 1j8m_F          106 VQGTGKTTTAGKLAYFYKK  124 (297)
T ss_dssp             SSCSSTTHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3799999999999985543

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=82.01  E-value=3.8  Score=38.84  Aligned_cols=20  Identities=25%  Similarity=0.365  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+||||++..++..+..+
T Consensus       108 ~~GvGKTT~a~~LA~~l~~~  127 (433)
T 2xxa_A          108 LQGAGKTTSVGKLGKFLREK  127 (433)
T ss_dssp             STTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHh
Confidence            38999999999999865543

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=81.98  E-value=0.58  Score=38.48  Aligned_cols=18  Identities=39%  Similarity=0.720  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.+++++.
T Consensus         8 ~~GsGKsT~~~~L~~~l~   25 (195)
T 2pbr_A            8 IDGSGKTTQAKKLYEYLK   25 (195)
T ss_dssp             STTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999998663

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*

Probab=81.84  E-value=0.71  Score=40.40  Aligned_cols=19  Identities=26%  Similarity=0.525  Sum_probs=15.9

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+...
T Consensus        28 GGvGKTT~a~nLA~~la~~   46 (262)
T 2ph1_A           28 GGVGKSTVTALLAVHYARQ   46 (262)
T ss_dssp             SCTTHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            8999999999999865543

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*

Probab=81.83  E-value=0.73  Score=39.99  Aligned_cols=19  Identities=32%  Similarity=0.546  Sum_probs=15.9

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus        12 gGvGKTt~a~~LA~~la~~   30 (260)
T 3q9l_A           12 GGVGKTTSSAAIATGLAQK   30 (260)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHHHHhC
Confidence            8999999999999865543

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=81.79  E-value=0.59  Score=39.42  Aligned_cols=17  Identities=29%  Similarity=0.389  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus         8 ~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            8 LPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998754

>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=81.74  E-value=0.72  Score=40.96  Aligned_cols=19  Identities=26%  Similarity=0.525  Sum_probs=15.9

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+...
T Consensus        11 GGvGKTT~a~nLA~~La~~   29 (289)
T 2afh_E           11 GGIGKSTTTQNLVAALAEM   29 (289)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CcCcHHHHHHHHHHHHHHC
Confidence            8999999999999865443

>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=81.71  E-value=0.74  Score=38.60  Aligned_cols=19  Identities=21%  Similarity=0.354  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      +.|+||||+|+.+++++..
T Consensus        17 ~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A           17 VDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             STTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            4799999999999986644

>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=81.63  E-value=0.57  Score=40.80  Aligned_cols=17  Identities=35%  Similarity=0.399  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      ||+|||||+..++....
T Consensus        23 gGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           23 AGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            89999999999997554

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=81.55  E-value=1.2  Score=37.75  Aligned_cols=99  Identities=11%  Similarity=0.022  Sum_probs=42.4

Q ss_pred             CCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcccc-CccchhhhHHHHHHHhcCceEEEE
Q 040234            3 GLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN-NIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         3 GiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      |.||||.|...+.+...+-..++.+. ..... ++ +...    +.+.++..... ...+..+    +.+.+.++-=+|+
T Consensus        38 gsGKTT~lL~~a~r~~~~g~kVli~k-~~~d~-R~-ge~~----i~s~~g~~~~a~~~~~~~~----~~~~~~~~~dvVi  106 (214)
T 2j9r_A           38 FSGKSEELIRRVRRTQFAKQHAIVFK-PCIDN-RY-SEED----VVSHNGLKVKAVPVSASKD----IFKHITEEMDVIA  106 (214)
T ss_dssp             TSCHHHHHHHHHHHHHHTTCCEEEEE-CC-----------------------CCEEECSSGGG----GGGGCCSSCCEEE
T ss_pred             CCcHHHHHHHHHHHHHHCCCEEEEEE-eccCC-cc-hHHH----HHhhcCCeeEEeecCCHHH----HHHHHhcCCCEEE
Confidence            89999999888886544432223222 11110 00 1122    33333211110 1111111    1122223334999


Q ss_pred             EeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh
Q 040234           82 IDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH  115 (377)
Q Consensus        82 LDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~  115 (377)
                      +|.+.-  .++++.+....   ..+-.||+|.++-+
T Consensus       107 IDEaQF~~~~~V~~l~~l~---~~~~~Vi~~Gl~~D  139 (214)
T 2j9r_A          107 IDEVQFFDGDIVEVVQVLA---NRGYRVIVAGLDQD  139 (214)
T ss_dssp             ECCGGGSCTTHHHHHHHHH---HTTCEEEEEECSBC
T ss_pred             EECcccCCHHHHHHHHHHh---hCCCEEEEEecccc
Confidence            999853  34443332211   23668999998653

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=81.49  E-value=0.57  Score=39.27  Aligned_cols=19  Identities=16%  Similarity=0.441  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      +.|+||||+|+.+++++..
T Consensus        18 ~~GsGKST~~~~L~~~l~~   36 (212)
T 2wwf_A           18 LDRSGKSTQSKLLVEYLKN   36 (212)
T ss_dssp             STTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            4799999999999986543

>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=81.24  E-value=0.66  Score=39.08  Aligned_cols=19  Identities=26%  Similarity=0.380  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      +.|+|||||++.++.....
T Consensus        16 psGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A           16 PSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CTTSCHHHHHHHHHHSTTC
T ss_pred             cCCCCHHHHHHHHHhhCCC
Confidence            4799999999999986543

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=81.21  E-value=0.57  Score=41.86  Aligned_cols=17  Identities=29%  Similarity=0.520  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||||+.+..+.
T Consensus        41 ~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           41 QPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             CTTSCTHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999998754

>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=81.00  E-value=4.1  Score=38.29  Aligned_cols=17  Identities=24%  Similarity=0.241  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++.+.
T Consensus       266 ~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          266 FPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             CTTSSHHHHHHHHTGGG
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            58999999999998754

>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=81.00  E-value=0.67  Score=37.99  Aligned_cols=17  Identities=24%  Similarity=0.108  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus        14 ~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A           14 GPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998854

>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=80.99  E-value=0.64  Score=39.22  Aligned_cols=17  Identities=24%  Similarity=0.335  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         8 ~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            8 LPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998754

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=80.90  E-value=1.1  Score=40.71  Aligned_cols=19  Identities=32%  Similarity=0.539  Sum_probs=15.9

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++....+.
T Consensus        23 GGvGKTTvA~~LA~~lA~~   41 (324)
T 3zq6_A           23 GGVGKTTISAATALWMARS   41 (324)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHHHC
Confidence            8999999999999865544

>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=80.88  E-value=2.7  Score=39.86  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+||||++..++..++.+
T Consensus       108 ~~G~GKTTt~~kLA~~l~~~  127 (443)
T 3dm5_A          108 IQGSGKTTTVAKLARYFQKR  127 (443)
T ss_dssp             CTTSSHHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHHHHHC
Confidence            37999999999998755443

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=80.54  E-value=0.72  Score=39.09  Aligned_cols=17  Identities=24%  Similarity=0.214  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus        13 ~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A           13 APGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            57999999999999865

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=80.46  E-value=0.69  Score=38.55  Aligned_cols=17  Identities=24%  Similarity=0.112  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus        23 ~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           23 GPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999999754

>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=80.45  E-value=0.67  Score=37.89  Aligned_cols=25  Identities=24%  Similarity=0.154  Sum_probs=18.5

Q ss_pred             CCCcHHHHHHHHHchhccc-cccceE
Q 040234            2 GGLGKTTLARVVYDLISHE-FDGSSF   26 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-f~~~~w   26 (377)
                      .|+|||||+..+...++.+ +...+.
T Consensus        13 sGsGKTTl~~~L~~~l~~~g~~v~~i   38 (169)
T 1xjc_A           13 KHSGKTTLMEKWVAAAVREGWRVGTV   38 (169)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCCHHHHHHHHHHhhHhcCCeeeEE
Confidence            6999999999999876544 444443

>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=80.43  E-value=0.72  Score=39.57  Aligned_cols=18  Identities=28%  Similarity=0.169  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+|+.+++++.
T Consensus        24 ~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           24 PPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998653

>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell division, cell cycle; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.10

Probab=80.27  E-value=0.88  Score=39.64  Aligned_cols=19  Identities=32%  Similarity=0.410  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus        12 gGvGKTt~a~~LA~~la~~   30 (263)
T 1hyq_A           12 GGTGKTTITANLGVALAQL   30 (263)
T ss_dssp             SCSCHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhC
Confidence            8999999999999866543

>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=80.19  E-value=0.72  Score=38.92  Aligned_cols=17  Identities=24%  Similarity=0.190  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      +.|+||||+|+.++++.
T Consensus         8 ~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            8 APVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999865

>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=80.14  E-value=0.72  Score=38.45  Aligned_cols=15  Identities=33%  Similarity=0.457  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHHc
Q 040234            1 MGGLGKTTLARVVYD   15 (377)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (377)
                      +.|+||||+++.++.
T Consensus         9 ~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            9 NIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHH
Confidence            479999999999987

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=80.14  E-value=0.73  Score=40.27  Aligned_cols=18  Identities=33%  Similarity=0.527  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||+++.++..+.
T Consensus        56 ~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           56 MMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             STTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            579999999999998654

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=80.11  E-value=0.88  Score=40.52  Aligned_cols=18  Identities=33%  Similarity=0.602  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      ||+||||+|..++..+..
T Consensus        46 GGvGKTT~a~nLA~~la~   63 (298)
T 2oze_A           46 GGVGKSKLSTMFAYLTDK   63 (298)
T ss_dssp             SSSSHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHh
Confidence            899999999999985543

---

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	377
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-20

>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 = 88.3 bits (218), Expect = 1e-20
 Identities = 27/175 (15%), Positives = 54/175 (30%), Gaps = 18/175 (10%)

Query: 1   MGGLGKTTLARVVYD----LISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD 56
             G GK+ +A         LI   +D   +L        K    +     L+        
Sbjct: 52  RAGSGKSVIASQALSKSDQLIGINYDSIVWL-KDSGTAPKSTFDLFTDILLMLKSEDDLL 110

Query: 57  N-----NIRNVYDGINMLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITT 111
           N     ++ +V     +    + R   L V DD    + +R             R ++TT
Sbjct: 111 NFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRW------AQELRLRCLVTT 164

Query: 112 RNEHLLK-LHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRIC 165
           R+  +        +  ++ +L  DE +  L           E+  ++    + + 
Sbjct: 165 RDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVG-EKEEDVLNKTIELS 218

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	377
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.97
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.42
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.02
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.94
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.89
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.89
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.82
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.79
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.78
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.65
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.65
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.48
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.42
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.28
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.25
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.12
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.08
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.05
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.8
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	96.73
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.73
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.72
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.56
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	95.14
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	94.8
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	94.58
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.28
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.23
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	94.16
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	94.15
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	93.95
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.93
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	93.73
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	93.6
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.24
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	93.15
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	92.98
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	92.68
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	92.63
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	92.57
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	92.49
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	92.19
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.79
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	91.74
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	91.74
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	91.59
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	91.58
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	91.41
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	91.33
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.93
d2qy9a2	211	GTPase domain of the signal recognition particle r	90.71
d1xpua3	289	Transcription termination factor Rho, ATPase domai	90.46
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	90.14
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	90.02
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	90.0
d1okkd2	207	GTPase domain of the signal recognition particle r	89.9
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	89.26
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	89.25
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	89.24
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	89.24
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	88.92
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	88.91
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	88.74
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	88.38
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	88.27
d1ls1a2	207	GTPase domain of the signal sequence recognition p	88.12
d1j8yf2	211	GTPase domain of the signal sequence recognition p	88.07
d1vmaa2	213	GTPase domain of the signal recognition particle r	87.95
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	87.62
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	87.59
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	87.56
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	87.54
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	87.41
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	87.33
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	87.14
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	86.95
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	86.92
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	86.83
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	86.5
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	85.86
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	85.47
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	85.23
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	84.83
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.81
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	84.59
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	84.58
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	84.28
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	84.23
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	84.18
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	84.12
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	84.03
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	83.89
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	83.75
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	83.39
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	81.84
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	81.39
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	81.28
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	81.26
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	81.03

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=99.97  E-value=7.3e-32  Score=244.19  Aligned_cols=205  Identities=13%  Similarity=0.087  Sum_probs=152.3

Q ss_pred             CCCCcHHHHHHHHHch----hccccccceEEecchhhcccccCHHHHHHHH---HHHHhhcccc------CccchhhhHH
Q 040234            1 MGGLGKTTLARVVYDL----ISHEFDGSSFLADVREKCDKEGSVISLQKQL---LSDLLKLADN------NIRNVYDGIN   67 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~----~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i---~~~l~~~~~~------~~~~~~~~~~   67 (377)
                      |||+||||||++++++    ...+|+..+|+. +++.+    +...+...+   +..+......      ..........
T Consensus        52 mgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~-vs~~~----~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (277)
T d2a5yb3          52 RAGSGKSVIASQALSKSDQLIGINYDSIVWLK-DSGTA----PKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRM  126 (277)
T ss_dssp             STTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE-CCCCS----TTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhhhhhhhcCceEEEEE-ecCCC----CHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHH
Confidence            8999999999999984    566688889988 66655    444444443   3332222111      1112223344


Q ss_pred             HHHHHhcCceEEEEEeCCCChhhhhHhhCCCCCCCCCCeEEEEecchhHHhhCCC-CCeeecCCCChhhhHHHHHHHhcC
Q 040234           68 MLRVRLRRKKVLVVIDDAAHPDHLRRLVGEPDWFGPGSRIIITTRNEHLLKLHPV-KKVYKLEALTYDEAFRLLCLKAFD  146 (377)
Q Consensus        68 ~l~~~l~~k~~LLVLDdv~~~~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~~~-~~~~~l~~L~~~ea~~L~~~~~~~  146 (377)
                      .+.+.+.++++|+||||||+.++++.+..      .||+||||||++.++..+.. ...|+|++|+.+||++||.++++.
T Consensus       127 ~~~~~L~~kr~LlVLDDv~~~~~~~~~~~------~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~  200 (277)
T d2a5yb3         127 ICNALIDRPNTLFVFDDVVQEETIRWAQE------LRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMP  200 (277)
T ss_dssp             HHHHHTTSTTEEEEEEEECCHHHHHHHHH------TTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCC
T ss_pred             HHHHHhccCCeeEecchhhHHhhhhhhcc------cCceEEEEeehHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCC
Confidence            57778899999999999999999987753      47899999999999887654 367999999999999999998876


Q ss_pred             CCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhhhchhHHHHHHHHHhhccCchhHHHHHHHHHhhcccCCCCC
Q 040234          147 THKPLEEYVELAESVVRICHCQKSTLNALMSVSYTVSHLLLTLCLKLMQYMLCPFILFVYLLFFSVGLQNMPPSD  221 (377)
Q Consensus       147 ~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l~~~~~~~~~~~L~~~~~~~~~~~~~~~~l~~Sy~~L~~~~  221 (377)
                      ... .+..++++++|+++|||  +|||++++|+.+..+...+|....+++....  ...+.+++.+||+.||+.-
T Consensus       201 ~~~-~~~~~~~~~~iv~~c~G--lPLAl~~ig~~l~~k~~~~~~~~~~~L~~~~--~~~v~~il~~sY~~L~~~l  270 (277)
T d2a5yb3         201 MPV-GEKEEDVLNKTIELSSG--NPATLMMFFKSCEPKTFEKMAQLNNKLESRG--LVGVECITPYSYKSLAMAL  270 (277)
T ss_dssp             CC---CHHHHHHHHHHHHHTT--CHHHHHHHHTTCCSSSHHHHHHHHHHHHHHC--SSTTCCCSSSSSSSHHHHH
T ss_pred             ccC-chhhHHHHHHHHHHhCC--CHHHHHHHHHHhccCCHHHHHHHHHHHhcCc--HHHHHHHHHHHHhcccHHH
Confidence            543 34457889999999999  9999999999999888777766544443211  1247788889999998753

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.42  E-value=8.2e-07  Score=77.37  Aligned_cols=170  Identities=16%  Similarity=0.097  Sum_probs=88.9

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhc-ccccCHHHHHHHHHHHHhhccc-----------------------
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKC-DKEGSVISLQKQLLSDLLKLAD-----------------------   56 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~-~~~~~~~~~~~~i~~~l~~~~~-----------------------   56 (377)
                      ++|+|||+|+++++++....+   .|+. ..... ........+...+.........                       
T Consensus        37 ~~G~GKTsLl~~~~~~~~~~~---~~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  112 (283)
T d2fnaa2          37 LRRTGKSSIIKIGINELNLPY---IYLD-LRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIK  112 (283)
T ss_dssp             STTSSHHHHHHHHHHHHTCCE---EEEE-GGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEE
T ss_pred             CCCCcHHHHHHHHHHHCCCCe---EEEE-eccccccccccHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccc
Confidence            479999999999998765443   3333 22221 1121344444444433221100                       


Q ss_pred             --cCccchhhhHHHHHHH--hcCceEEEEEeCCCChhh------hhHhhCCCCCCCCCCeEEEEecchhHHh-hC-----
Q 040234           57 --NNIRNVYDGINMLRVR--LRRKKVLVVIDDAAHPDH------LRRLVGEPDWFGPGSRIIITTRNEHLLK-LH-----  120 (377)
Q Consensus        57 --~~~~~~~~~~~~l~~~--l~~k~~LLVLDdv~~~~~------~~~l~~~l~~~~~gs~IIvTTR~~~v~~-~~-----  120 (377)
                        ..........+.+...  ...++.++|+|++.....      +..+..... .......+++++...... ..     
T Consensus       113 ~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~  191 (283)
T d2fnaa2         113 FNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYD-NLKRIKFIMSGSEMGLLYDYLRVEDP  191 (283)
T ss_dssp             EC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHHHHHHHH-HCTTEEEEEEESSHHHHHHHTTTTCT
T ss_pred             cccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHHHHHHHH-hhhhhhhhhccccchHHHHHHHhhhh
Confidence              0001111222333322  346889999999754211      111111100 023345555554433211 11     


Q ss_pred             ------CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhHHHHHhhh
Q 040234          121 ------PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNALMSVSYT  181 (377)
Q Consensus       121 ------~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal~~~~~~l  181 (377)
                            .....+.|++++.+++.+++.+......-..+    .+++|.+.+||  .|..+..++..+
T Consensus       192 ~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~----~~~~i~~~~~G--~P~~L~~~~~~~  252 (283)
T d2fnaa2         192 ESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFK----DYEVVYEKIGG--IPGWLTYFGFIY  252 (283)
T ss_dssp             TSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC----CHHHHHHHHCS--CHHHHHHHHHHH
T ss_pred             cchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHH----HHHHHHHHhCC--CHHHHHHHHHHH
Confidence                  12356889999999999999776532111111    25689999999  999988777654

>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=98.02  E-value=2.3e-05  Score=65.43  Aligned_cols=91  Identities=16%  Similarity=0.050  Sum_probs=61.6

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecchh-HHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNEH-LLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      +++-++|+|+++.  .+....++..+..-.+++.+|+||++.. +...+ +....+.+.+++.++....+.+...-    
T Consensus       107 ~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~~~~L~~~~~~----  182 (207)
T d1a5ta2         107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVTM----  182 (207)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCCC----
T ss_pred             CccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEEEecCCCCHHHHHHHHHHcCCC----
Confidence            4566999999986  3344555444443356778787777643 43322 44678999999999999988765411    


Q ss_pred             chhHHHHHHHHHHHhCCCCchhhH
Q 040234          151 LEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                      +   .+.+..|++..+|  .|-.+
T Consensus       183 ~---~~~~~~i~~~s~G--s~r~a  201 (207)
T d1a5ta2         183 S---QDALLAALRLSAG--SPGAA  201 (207)
T ss_dssp             C---HHHHHHHHHHTTT--CHHHH
T ss_pred             C---HHHHHHHHHHcCC--CHHHH
Confidence            1   3567889999999  76544

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.94  E-value=1.9e-05  Score=66.58  Aligned_cols=149  Identities=11%  Similarity=0.101  Sum_probs=82.7

Q ss_pred             CCCCcHHHHHHHHHchhcccc-ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEF-DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f-~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ++|+||||+|+.+++++...+ ...++..+.+...    +...+...+....... ...              ...+.-+
T Consensus        44 p~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~----~~~~i~~~~~~~~~~~-~~~--------------~~~~~kv  104 (224)
T d1sxjb2          44 MPGIGKTTSVHCLAHELLGRSYADGVLELNASDDR----GIDVVRNQIKHFAQKK-LHL--------------PPGKHKI  104 (224)
T ss_dssp             STTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCC----SHHHHHTHHHHHHHBC-CCC--------------CTTCCEE
T ss_pred             CCCCCchhhHHHHHHHHhccccccccccccccccC----CceehhhHHHHHHHhh-ccC--------------CCcceEE
Confidence            479999999999998665432 2233333333332    3333322222221111 000              0234568


Q ss_pred             EEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHH
Q 040234           80 VVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYV  155 (377)
Q Consensus        80 LVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~  155 (377)
                      +|+|+++..  .....++..+......+++++||... .+...+ +....+++.+++.++-...+.+.+....-..  ..
T Consensus       105 iiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~i--~~  182 (224)
T d1sxjb2         105 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKY--TN  182 (224)
T ss_dssp             EEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB--CH
T ss_pred             EEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhhHHHHHHHHHhcccCC--CH
Confidence            899999763  22233322222224455666666543 332222 4467899999999999999987764322111  14


Q ss_pred             HHHHHHHHHhCCCCchh
Q 040234          156 ELAESVVRICHCQKSTL  172 (377)
Q Consensus       156 ~~~~~I~~~c~G~~lpl  172 (377)
                      +....|++.++|  -+-
T Consensus       183 ~~l~~I~~~s~G--d~R  197 (224)
T d1sxjb2         183 DGLEAIIFTAEG--DMR  197 (224)
T ss_dssp             HHHHHHHHHHTT--CHH
T ss_pred             HHHHHHHHHcCC--cHH
Confidence            567899999999  544

>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=97.89  E-value=6.7e-05  Score=64.56  Aligned_cols=140  Identities=20%  Similarity=0.171  Sum_probs=80.0

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhc--CceE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLR--RKKV   78 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~--~k~~   78 (377)
                      ++|+|||++|+.+++.+++.......+.......    ........+.....................+.+.+.  ....
T Consensus        51 ppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (276)
T d1fnna2          51 RPGTGKTVTLRKLWELYKDKTTARFVYINGFIYR----NFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYM  126 (276)
T ss_dssp             CTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCC----SHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCE
T ss_pred             CCCCCHHHHHHHHHHHHhcccCCcEEEecchhhh----hhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhccccc
Confidence            4799999999999998876655443333233332    666777777766544433333344444454544443  3567


Q ss_pred             EEEEeCCCChh-----hhhHhhCCCCCC-CCCCeEEEEecchhHHhhC-------CCCCeeecCCCChhhhHHHHHHHh
Q 040234           79 LVVIDDAAHPD-----HLRRLVGEPDWF-GPGSRIIITTRNEHLLKLH-------PVKKVYKLEALTYDEAFRLLCLKA  144 (377)
Q Consensus        79 LLVLDdv~~~~-----~~~~l~~~l~~~-~~gs~IIvTTR~~~v~~~~-------~~~~~~~l~~L~~~ea~~L~~~~~  144 (377)
                      ++++|++++..     ....+....... .....+|.++.........       .....+.+.+++.++..+++.+++
T Consensus       127 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         127 FLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             EEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             ccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHH
Confidence            77888876632     122222221111 2233455555543332221       123457899999999999998765

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.89  E-value=2.6e-05  Score=65.77  Aligned_cols=145  Identities=10%  Similarity=0.134  Sum_probs=81.6

Q ss_pred             CCCCcHHHHHHHHHchhccc-cccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEE
Q 040234            1 MGGLGKTTLARVVYDLISHE-FDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVL   79 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~L   79 (377)
                      ++|+||||+|+.+++++... +...+.....+...    +..... ..........               ....++.-+
T Consensus        43 p~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~----~~~~~~-~~~~~~~~~~---------------~~~~~~~ki  102 (227)
T d1sxjc2          43 PPGTGKTSTIVALAREIYGKNYSNMVLELNASDDR----GIDVVR-NQIKDFASTR---------------QIFSKGFKL  102 (227)
T ss_dssp             SSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCC----SHHHHH-THHHHHHHBC---------------CSSSCSCEE
T ss_pred             CCCCChhHHHHHHHHHhhcCCCcceeEEecccccC----Ceeeee-cchhhccccc---------------cccCCCeEE
Confidence            47999999999999965432 22222222222221    222221 1111111110               011234458


Q ss_pred             EEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHH
Q 040234           80 VVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYV  155 (377)
Q Consensus        80 LVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~  155 (377)
                      +|+|+++..  .....++..+....+.+.++++|... .+... ......+.+.+++.++-.+++.+.+....-..+  .
T Consensus       103 iiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i~--~  180 (227)
T d1sxjc2         103 IILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLS--P  180 (227)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBC--H
T ss_pred             EEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhccccccccccccccccccccccccCC--H
Confidence            899999763  33334443333335567777777653 22221 244678899999999999999887744322222  4


Q ss_pred             HHHHHHHHHhCC
Q 040234          156 ELAESVVRICHC  167 (377)
Q Consensus       156 ~~~~~I~~~c~G  167 (377)
                      +..+.|++.++|
T Consensus       181 ~~l~~i~~~s~G  192 (227)
T d1sxjc2         181 NAEKALIELSNG  192 (227)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCC
Confidence            567889999998

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.82  E-value=1.4e-05  Score=67.86  Aligned_cols=155  Identities=11%  Similarity=0.100  Sum_probs=80.7

Q ss_pred             CCCCcHHHHHHHHHchhcccc--ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceE
Q 040234            1 MGGLGKTTLARVVYDLISHEF--DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKV   78 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f--~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~   78 (377)
                      .+|+||||||+.+++++....  .......+.+...    ....+...+ ..........     .....+......+.-
T Consensus        41 p~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~----~~~~~~~~~-~~~~~~~~~~-----~~~~~~~~~~~~~~~  110 (237)
T d1sxjd2          41 PPGTGKTSTILALTKELYGPDLMKSRILELNASDER----GISIVREKV-KNFARLTVSK-----PSKHDLENYPCPPYK  110 (237)
T ss_dssp             STTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCC----CHHHHTTHH-HHHHHSCCCC-----CCTTHHHHSCCCSCE
T ss_pred             CCCCChHHHHHHHHHHHcCCcccccchhheeccccc----cchHHHHHH-HHHhhhhhhh-----hhHHHHhhccccCce
Confidence            479999999999999753322  1112222122221    333222222 2211111100     111222233344455


Q ss_pred             EEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhH
Q 040234           79 LVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEY  154 (377)
Q Consensus        79 LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~  154 (377)
                      ++|+|+++..  .....+...+.......++|+|+... .+.... .....+.+.+++.++..+++...+....-..  .
T Consensus       111 viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i~i--~  188 (237)
T d1sxjd2         111 IIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKC--D  188 (237)
T ss_dssp             EEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCC--C
T ss_pred             EEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhccccccccccchhhhhhhhhhcCcC--C
Confidence            7999998763  23333222222223455666665542 221111 2246789999999999999988775432221  2


Q ss_pred             HHHHHHHHHHhCC
Q 040234          155 VELAESVVRICHC  167 (377)
Q Consensus       155 ~~~~~~I~~~c~G  167 (377)
                      .+..+.|++.++|
T Consensus       189 ~~~l~~ia~~s~g  201 (237)
T d1sxjd2         189 DGVLERILDISAG  201 (237)
T ss_dssp             HHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHcCC
Confidence            4668899999988

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.79  E-value=2.1e-05  Score=67.24  Aligned_cols=93  Identities=13%  Similarity=0.054  Sum_probs=59.6

Q ss_pred             ceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCCc
Q 040234           76 KKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKPL  151 (377)
Q Consensus        76 k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~  151 (377)
                      +.-++|||+++..  +....|+..+....+.+++|++|.+. .+.... +....+.+.+++.++..+.+...+.......
T Consensus       115 ~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~  194 (239)
T d1njfa_         115 RFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAH  194 (239)
T ss_dssp             SSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB
T ss_pred             CCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccCC
Confidence            4568999999873  33334443333224567777777653 222222 3467899999999999988877764322222


Q ss_pred             hhHHHHHHHHHHHhCCCCchh
Q 040234          152 EEYVELAESVVRICHCQKSTL  172 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G~~lpl  172 (377)
                        .++.+..|++.++|  .+-
T Consensus       195 --~~~~l~~i~~~s~G--d~R  211 (239)
T d1njfa_         195 --EPRALQLLARAAEG--SLR  211 (239)
T ss_dssp             --CHHHHHHHHHHTTT--CHH
T ss_pred             --CHHHHHHHHHHcCC--CHH
Confidence              24567889999999  664

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.78  E-value=6.8e-05  Score=62.70  Aligned_cols=139  Identities=16%  Similarity=0.163  Sum_probs=77.1

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      +|+|||.|++.++++........+++.           ..+....+...+...      .    ...+.+.+++ .=+|+
T Consensus        45 ~G~GKTHLl~A~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~------~----~~~~~~~~~~-~dll~  102 (213)
T d1l8qa2          45 VGTGKTHLLQAAGNEAKKRGYRVIYSS-----------ADDFAQAMVEHLKKG------T----INEFRNMYKS-VDLLL  102 (213)
T ss_dssp             SSSSHHHHHHHHHHHHHHTTCCEEEEE-----------HHHHHHHHHHHHHHT------C----HHHHHHHHHT-CSEEE
T ss_pred             CCCcHHHHHHHHHHHhccCccceEEec-----------hHHHHHHHHHHHHcc------c----hhhHHHHHhh-ccchh
Confidence            799999999999997766655555543           334444444443221      1    1222333332 45899


Q ss_pred             EeCCCCh---hhhhH-hhCCCCC-CCCCCeEEEEecch---------hHHhhCCCCCeeecCCCChhhhHHHHHHHhcCC
Q 040234           82 IDDAAHP---DHLRR-LVGEPDW-FGPGSRIIITTRNE---------HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDT  147 (377)
Q Consensus        82 LDdv~~~---~~~~~-l~~~l~~-~~~gs~IIvTTR~~---------~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~  147 (377)
                      |||++..   ..|+. +...+.. ...|.+||+||+..         ++..++....+++++ ++.++-.+++++++-..
T Consensus       103 iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~r  181 (213)
T d1l8qa2         103 LDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLKEF  181 (213)
T ss_dssp             EECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHHHT
T ss_pred             hhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHHHHc
Confidence            9999642   23332 1111111 03577899999853         233334456677785 46666777777776332


Q ss_pred             CCCchhHHHHHHHHHHHh
Q 040234          148 HKPLEEYVELAESVVRIC  165 (377)
Q Consensus       148 ~~~~~~~~~~~~~I~~~c  165 (377)
                      .-..+  ++++.-|+++.
T Consensus       182 gl~l~--~~v~~yl~~~~  197 (213)
T d1l8qa2         182 NLELR--KEVIDYLLENT  197 (213)
T ss_dssp             TCCCC--HHHHHHHHHHC
T ss_pred             CCCCC--HHHHHHHHHhc
Confidence            22211  34555566655

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.65  E-value=0.00044  Score=59.51  Aligned_cols=160  Identities=14%  Similarity=0.087  Sum_probs=81.9

Q ss_pred             CCCCcHHHHHHHHHchhccccc------cceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-
Q 040234            1 MGGLGKTTLARVVYDLISHEFD------GSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~------~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-   73 (377)
                      ++|+|||++|+.+++++.+...      ...++. .....    ............+...............+.+.... 
T Consensus        54 ppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~-~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  128 (287)
T d1w5sa2          54 RVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN-AFNAP----NLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLY  128 (287)
T ss_dssp             CCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE-GGGCC----SHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhhcccccCCceeeeec-ccccc----chhhHHHHHhhhcccccccccchHHHHHHHHHHHHH
Confidence            4799999999999996644321      122333 22221    55566666666654433222333344444444444 


Q ss_pred             -cCceEEEEEeCCCChh--------hhhH---h---hCCCCCCCCCCeEEEEecchhHH--------hhCCCCCeeecCC
Q 040234           74 -RRKKVLVVIDDAAHPD--------HLRR---L---VGEPDWFGPGSRIIITTRNEHLL--------KLHPVKKVYKLEA  130 (377)
Q Consensus        74 -~~k~~LLVLDdv~~~~--------~~~~---l---~~~l~~~~~gs~IIvTTR~~~v~--------~~~~~~~~~~l~~  130 (377)
                       .+...++++|.++...        ....   +   .........-..|++++......        ........+.+++
T Consensus       129 ~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~  208 (287)
T d1w5sa2         129 VENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPA  208 (287)
T ss_dssp             HHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCC
T ss_pred             hccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceeeeccC
Confidence             3457788888875321        1111   1   11211112222344444433211        1112346788999


Q ss_pred             CChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHh
Q 040234          131 LTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRIC  165 (377)
Q Consensus       131 L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c  165 (377)
                      ++.++..+++..++-.......-.++..+.|++..
T Consensus       209 y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~  243 (287)
T d1w5sa2         209 YKSRELYTILEQRAELGLRDTVWEPRHLELISDVY  243 (287)
T ss_dssp             CCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHH
T ss_pred             CcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHH
Confidence            99999999998876321111111134455566554

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.65  E-value=5e-05  Score=64.23  Aligned_cols=91  Identities=13%  Similarity=0.174  Sum_probs=55.5

Q ss_pred             CceEEEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      .++.++++|+++.  ......++..+........+|.||... .+.... .....+.+.+.+.++....+.+.+....-.
T Consensus       108 ~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i~  187 (231)
T d1iqpa2         108 ASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE  187 (231)
T ss_dssp             CSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE
T ss_pred             CCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccccccchhhHHHHHHHHHHHhCCC
Confidence            4567899999875  233333333332223344556665443 222221 234678999999999999998877543321


Q ss_pred             chhHHHHHHHHHHHhCC
Q 040234          151 LEEYVELAESVVRICHC  167 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G  167 (377)
                        -..+..+.|++.++|
T Consensus       188 --i~~~~l~~I~~~~~g  202 (231)
T d1iqpa2         188 --LTEEGLQAILYIAEG  202 (231)
T ss_dssp             --ECHHHHHHHHHHHTT
T ss_pred             --CCHHHHHHHHHHcCC
Confidence              124567889999998

>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=97.48  E-value=2.1e-05  Score=67.37  Aligned_cols=92  Identities=12%  Similarity=0.114  Sum_probs=53.6

Q ss_pred             CceEEEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecchh-HHhh-CCCCCeeecCCCChhhhHHHHHHHhcCCCCC
Q 040234           75 RKKVLVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNEH-LLKL-HPVKKVYKLEALTYDEAFRLLCLKAFDTHKP  150 (377)
Q Consensus        75 ~k~~LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~~-v~~~-~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~  150 (377)
                      .+.-++|||+++..  +....++..+......+++|+||.+.. +... .+....+++.+++.++..+++...+-...-.
T Consensus       130 ~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~  209 (252)
T d1sxje2         130 HRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQ  209 (252)
T ss_dssp             -CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCE
T ss_pred             CCceEEEeccccccccccchhhhcccccccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCC
Confidence            34558999999873  233333222222245567777766532 2111 1224578899999999999987665221111


Q ss_pred             chhHHHHHHHHHHHhCC
Q 040234          151 LEEYVELAESVVRICHC  167 (377)
Q Consensus       151 ~~~~~~~~~~I~~~c~G  167 (377)
                       ...++....|++.+.|
T Consensus       210 -~~~~~~l~~i~~~s~G  225 (252)
T d1sxje2         210 -LETKDILKRIAQASNG  225 (252)
T ss_dssp             -ECCSHHHHHHHHHHTT
T ss_pred             -CCcHHHHHHHHHHcCC
Confidence             1113566789999988

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.42  E-value=0.00094  Score=57.35  Aligned_cols=123  Identities=13%  Similarity=0.105  Sum_probs=74.1

Q ss_pred             CCCCcHHHHHHHHHchhcc-----cc-ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-
Q 040234            1 MGGLGKTTLARVVYDLISH-----EF-DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~-----~f-~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-   73 (377)
                      .+|+|||+|+..+++++..     .. ...+|..+++.--                 .+  .......+++...+...+ 
T Consensus        47 ~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~li-----------------ag--~~~~g~~e~r~~~i~~~~~  107 (268)
T d1r6bx2          47 ESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLL-----------------AG--TKYRGDFEKRFKALLKQLE  107 (268)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC--------------------CC--CCCSSCHHHHHHHHHHHHS
T ss_pred             CCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHh-----------------cc--CccchhHHHHHHHHHHHhh
Confidence            4799999999999985432     22 2456665433321                 00  111223444444444444 


Q ss_pred             cCceEEEEEeCCCCh----------hhhh-HhhCCCCCCCCCCeEEEEecchhHHhhCC-------CCCeeecCCCChhh
Q 040234           74 RRKKVLVVIDDAAHP----------DHLR-RLVGEPDWFGPGSRIIITTRNEHLLKLHP-------VKKVYKLEALTYDE  135 (377)
Q Consensus        74 ~~k~~LLVLDdv~~~----------~~~~-~l~~~l~~~~~gs~IIvTTR~~~v~~~~~-------~~~~~~l~~L~~~e  135 (377)
                      +..+.+|++|++...          .... .|.|.+.  ...-++|.||..+.......       ..+.+.+++++.++
T Consensus       108 ~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~  185 (268)
T d1r6bx2         108 QDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEE  185 (268)
T ss_dssp             SSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHH
T ss_pred             ccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCHHH
Confidence            346789999997432          1233 4445554  34568888888776654432       24678999999999


Q ss_pred             hHHHHHHHh
Q 040234          136 AFRLLCLKA  144 (377)
Q Consensus       136 a~~L~~~~~  144 (377)
                      +.+++....
T Consensus       186 t~~IL~~~~  194 (268)
T d1r6bx2         186 TVQIINGLK  194 (268)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhh
Confidence            999997644

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=97.28  E-value=0.0007  Score=57.62  Aligned_cols=139  Identities=15%  Similarity=0.106  Sum_probs=72.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.++++..-.    ++..+.++          +..    ...      ..+.....+.+...-...+.+|
T Consensus        50 ppGtGKT~la~aia~~~~~~----~~~i~~~~----------l~~----~~~------g~~~~~l~~~f~~a~~~~p~Ii  105 (247)
T d1ixza_          50 PPGVGKTHLARAVAGEARVP----FITASGSD----------FVE----MFV------GVGAARVRDLFETAKRHAPCIV  105 (247)
T ss_dssp             CTTSSHHHHHHHHHHHTTCC----EEEEEHHH----------HHH----SCT------THHHHHHHHHHHHHTTSSSEEE
T ss_pred             CCCCChhHHHHHHHHHcCCC----EEEEEhHH----------hhh----ccc------cHHHHHHHHHHHHHHHcCCEEE
Confidence            47999999999999865432    22221221          111    000      0011112222333334568899


Q ss_pred             EEeCCCCh------------h----hhhHhhC---CCCCCCCCCeEEEEecchhHH-hhC----CCCCeeecCCCChhhh
Q 040234           81 VIDDAAHP------------D----HLRRLVG---EPDWFGPGSRIIITTRNEHLL-KLH----PVKKVYKLEALTYDEA  136 (377)
Q Consensus        81 VLDdv~~~------------~----~~~~l~~---~l~~~~~gs~IIvTTR~~~v~-~~~----~~~~~~~l~~L~~~ea  136 (377)
                      +|||++..            .    .+..|+.   .+.. ..+.-||.||....-. ..+    .-...+++++.+.++-
T Consensus       106 ~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~-~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR  184 (247)
T d1ixza_         106 FIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK-DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  184 (247)
T ss_dssp             EEETHHHHHC---------CHHHHHHHHHHHHHHHTCCT-TCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHH
T ss_pred             EEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCC-CCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHH
Confidence            99997521            0    1222322   2211 2232334466654321 111    2346889999999999


Q ss_pred             HHHHHHHhcCCCCCchhHHHHHHHHHHHhCC
Q 040234          137 FRLLCLKAFDTHKPLEEYVELAESVVRICHC  167 (377)
Q Consensus       137 ~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G  167 (377)
                      .++|............   .....+++.+.|
T Consensus       185 ~~il~~~l~~~~~~~~---~~~~~la~~t~g  212 (247)
T d1ixza_         185 EQILRIHARGKPLAED---VDLALLAKRTPG  212 (247)
T ss_dssp             HHHHHHHHTTSCBCTT---CCHHHHHHTCTT
T ss_pred             HHHHHHHhcccCCccc---cCHHHHHHHCCC
Confidence            9999887743322111   124567788888

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.25  E-value=0.00064  Score=58.29  Aligned_cols=143  Identities=15%  Similarity=0.092  Sum_probs=78.2

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||+||+.+++....+|    +..+.+.....                    ............+...-..++.+|
T Consensus        46 ppGtGKT~l~~ala~~~~~~~----~~i~~~~l~~~--------------------~~g~~~~~l~~~f~~A~~~~p~il  101 (258)
T d1e32a2          46 PPGTGKTLIARAVANETGAFF----FLINGPEIMSK--------------------LAGESESNLRKAFEEAEKNAPAII  101 (258)
T ss_dssp             CTTSSHHHHHHHHHHHTTCEE----EEECHHHHTTS--------------------CTTHHHHHHHHHHHHHHHTCSEEE
T ss_pred             CCCCCchHHHHHHHHHhCCeE----EEEEchhhccc--------------------ccccHHHHHHHHHHHHHhcCCeEE
Confidence            479999999999999655442    22212211100                    000111122233333345678999


Q ss_pred             EEeCCCChh----------------hhhHhhCCCCCCCCCCeEEEEecchhHHh-hC----CCCCeeecCCCChhhhHHH
Q 040234           81 VIDDAAHPD----------------HLRRLVGEPDWFGPGSRIIITTRNEHLLK-LH----PVKKVYKLEALTYDEAFRL  139 (377)
Q Consensus        81 VLDdv~~~~----------------~~~~l~~~l~~~~~gs~IIvTTR~~~v~~-~~----~~~~~~~l~~L~~~ea~~L  139 (377)
                      +|||++...                .+....... ....+.-||.||....-.. ..    .-...++++..+.++-.++
T Consensus       102 ~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~-~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~i  180 (258)
T d1e32a2         102 FIDELDAIAPKREKTHGEVERRIVSQLLTLMDGL-KQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEI  180 (258)
T ss_dssp             EESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTC-CCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHH
T ss_pred             EehhhhhhccCCCCCCCchHHHHHHHhccccccc-cccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHH
Confidence            999987521                111111111 1133444566887653321 11    2367889999999999999


Q ss_pred             HHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          140 LCLKAFDTHKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      |......... .++  ....+|++.+.|  ...|
T Consensus       181 l~~~l~~~~~-~~~--~~~~~la~~t~G--~s~a  209 (258)
T d1e32a2         181 LQIHTKNMKL-ADD--VDLEQVANETHG--HVGA  209 (258)
T ss_dssp             HHHTTTTSCB-CTT--CCHHHHHHHCTT--CCHH
T ss_pred             hhhhccCccc-ccc--cchhhhhhcccC--CCHH
Confidence            9877633221 111  124678999988  6544

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.12  E-value=0.00028  Score=57.51  Aligned_cols=119  Identities=12%  Similarity=0.068  Sum_probs=66.0

Q ss_pred             CCCCcHHHHHHHHHchhcc-----cc-ccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-
Q 040234            1 MGGLGKTTLARVVYDLISH-----EF-DGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~-----~f-~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-   73 (377)
                      .+|+|||+|+..+++++..     .. ...+|..          +...++..         .....+.+++...+.+.+ 
T Consensus        51 ~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~l----------d~~~LiAg---------~~~rG~~E~rl~~il~e~~  111 (195)
T d1jbka_          51 EPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL----------DMGALVAG---------AKYRGEFEERLKGVLNDLA  111 (195)
T ss_dssp             CTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE----------CHHHHHTT---------TCSHHHHHHHHHHHHHHHH
T ss_pred             cCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEe----------eHHHHhcc---------CCccHHHHHHHHHHHHHHh
Confidence            3799999999999985432     22 3456655          33333210         001112233333333333 


Q ss_pred             c-CceEEEEEeCCCCh----------hhhhHhhCCCCCCCCCCeEEEEecchhHHhhC-------CCCCeeecCCCChhh
Q 040234           74 R-RKKVLVVIDDAAHP----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH-------PVKKVYKLEALTYDE  135 (377)
Q Consensus        74 ~-~k~~LLVLDdv~~~----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~-------~~~~~~~l~~L~~~e  135 (377)
                      + ..+.+|++|++...          +.-+.|.+.+.  ...-++|.||..+......       ...+.+.++..+.++
T Consensus       112 ~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~--rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~  189 (195)
T d1jbka_         112 KQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVED  189 (195)
T ss_dssp             HSTTTEEEEEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHH
T ss_pred             cCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHh--CCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCCHHH
Confidence            2 34799999997431          11233333332  2345788888766554433       224678888999888


Q ss_pred             hHHHH
Q 040234          136 AFRLL  140 (377)
Q Consensus       136 a~~L~  140 (377)
                      +.+++
T Consensus       190 t~~IL  194 (195)
T d1jbka_         190 TIAIL  194 (195)
T ss_dssp             HHTTC
T ss_pred             HHHHh
Confidence            87654

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.08  E-value=0.00094  Score=57.46  Aligned_cols=144  Identities=12%  Similarity=0.047  Sum_probs=77.4

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      .+|+|||+||+.+++...-+|    +..+.+.          +.        ..  ............+...-...+.+|
T Consensus        49 p~GtGKT~l~~ala~~~~~~~----~~~~~~~----------l~--------~~--~~~~~~~~l~~~f~~A~~~~p~il  104 (265)
T d1r7ra3          49 PPGCGKTLLAKAIANECQANF----ISIKGPE----------LL--------TM--WFGESEANVREIFDKARQAAPCVL  104 (265)
T ss_dssp             CTTSSHHHHHHHHHHHTTCEE----EEECHHH----------HH--------TS--CTTTHHHHHHHHHHHHHHTCSEEE
T ss_pred             CCCCcchhHHHHHHHHhCCcE----EEEEHHH----------hh--------hc--cccchHHHHHHHHHHHHhcCCcce
Confidence            479999999999999775442    3221211          11        00  001112222233333334678999


Q ss_pred             EEeCCCChh----------------hhhHhhCCCCCC--CCCCeEEEEecchhHH-hhC----CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHPD----------------HLRRLVGEPDWF--GPGSRIIITTRNEHLL-KLH----PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~~----------------~~~~l~~~l~~~--~~gs~IIvTTR~~~v~-~~~----~~~~~~~l~~L~~~ea~  137 (377)
                      +|||++...                ....++..+...  .++--||.||....-. ..+    .-...++++..+.++-.
T Consensus       105 ~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~  184 (265)
T d1r7ra3         105 FFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRV  184 (265)
T ss_dssp             EESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHH
T ss_pred             eHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHH
Confidence            999986310                123344444321  2334566677654321 111    23567899999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      ++|...........   .....+|++.+.|  ...+
T Consensus       185 ~il~~~l~~~~~~~---~~~l~~la~~t~g--~s~~  215 (265)
T d1r7ra3         185 AILKANLRKSPVAK---DVDLEFLAKMTNG--FSGA  215 (265)
T ss_dssp             HHHHHHTTCC-------CCCCHHHHHHHCS--SCCH
T ss_pred             HHHHHHhccCCchh---hhhHHHHHhcCCC--CCHH
Confidence            99987663221111   1124678888888  6544

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=97.05  E-value=0.0026  Score=54.22  Aligned_cols=144  Identities=15%  Similarity=0.062  Sum_probs=76.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+|||+||+.++++..-.+    +..+.++-.+.+                    ...+.....+.+...-+..+.+|
T Consensus        53 ppGtGKT~la~~iA~~~~~~~----~~i~~~~l~~~~--------------------~g~~~~~l~~~f~~A~~~~P~il  108 (256)
T d1lv7a_          53 PPGTGKTLLAKAIAGEAKVPF----FTISGSDFVEMF--------------------VGVGASRVRDMFEQAKKAAPCII  108 (256)
T ss_dssp             CTTSCHHHHHHHHHHHHTCCE----EEECSCSSTTSC--------------------CCCCHHHHHHHHHHHHTTCSEEE
T ss_pred             CCCCCccHHHHHHHHHcCCCE----EEEEhHHhhhcc--------------------hhHHHHHHHHHHHHHHHcCCEEE
Confidence            479999999999998764332    222222211100                    00112222233333335667899


Q ss_pred             EEeCCCCh------------h----hhhHhhCCCC--CCCCCCeEEEEecchhHH-hhC----CCCCeeecCCCChhhhH
Q 040234           81 VIDDAAHP------------D----HLRRLVGEPD--WFGPGSRIIITTRNEHLL-KLH----PVKKVYKLEALTYDEAF  137 (377)
Q Consensus        81 VLDdv~~~------------~----~~~~l~~~l~--~~~~gs~IIvTTR~~~v~-~~~----~~~~~~~l~~L~~~ea~  137 (377)
                      +|||++..            +    .+..++..+.  ....+--||.||...... ..+    .-.+.+.+++.+.++-.
T Consensus       109 ~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~  188 (256)
T d1lv7a_         109 FIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGRE  188 (256)
T ss_dssp             EETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHH
T ss_pred             EEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHH
Confidence            99998421            0    1222322221  112333455577754322 111    23578899999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhh
Q 040234          138 RLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLN  173 (377)
Q Consensus       138 ~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lpla  173 (377)
                      ++|............   .....+++.+.|  ..-+
T Consensus       189 ~il~~~l~~~~~~~~---~~~~~la~~t~G--~s~a  219 (256)
T d1lv7a_         189 QILKVHMRRVPLAPD---IDAAIIARGTPG--FSGA  219 (256)
T ss_dssp             HHHHHHHTTSCBCTT---CCHHHHHHTCTT--CCHH
T ss_pred             HHHHHhccCCCcCcc---cCHHHHHHhCCC--CCHH
Confidence            999887643321111   123567788888  6543

>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=96.80  E-value=0.0022  Score=54.34  Aligned_cols=20  Identities=25%  Similarity=0.149  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+|||+||+.++++..-.
T Consensus        48 ppGtGKT~la~alA~~~~~~   67 (246)
T d1d2na_          48 PPHSGKTALAAKIAEESNFP   67 (246)
T ss_dssp             STTSSHHHHHHHHHHHHTCS
T ss_pred             cCCCCHHHHHHHHhhccccc
Confidence            47999999999999976544

>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=96.73  E-value=0.00051  Score=58.38  Aligned_cols=150  Identities=13%  Similarity=0.077  Sum_probs=73.3

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLV   80 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LL   80 (377)
                      ++|+||||+|+.++++....+   .++. .+...    +. ..+.............. ...  ...........+..++
T Consensus        60 PpG~GKTt~a~~la~~~~~~~---~~~~-~~~~~----~~-~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~vi  127 (253)
T d1sxja2          60 PPGIGKTTAAHLVAQELGYDI---LEQN-ASDVR----SK-TLLNAGVKNALDNMSVV-GYF--KHNEEAQNLNGKHFVI  127 (253)
T ss_dssp             STTSSHHHHHHHHHHHTTCEE---EEEC-TTSCC----CH-HHHHHTGGGGTTBCCST-TTT--TC----CCSSTTSEEE
T ss_pred             CCCCCHHHHHHHHHHHHHhhh---hccc-cccch----hh-HHHHHHHHHHhhcchhh-hhh--hhhhhcccccccceEE
Confidence            479999999999998664332   2222 33221    11 22222111111110000 000  0011111224567789


Q ss_pred             EEeCCCCh-----hhhhHhhCCCCCCCCCCeEEEEecc--h-hHHhhCCCCCeeecCCCChhhhHHHHHHHhcCCC-CCc
Q 040234           81 VIDDAAHP-----DHLRRLVGEPDWFGPGSRIIITTRN--E-HLLKLHPVKKVYKLEALTYDEAFRLLCLKAFDTH-KPL  151 (377)
Q Consensus        81 VLDdv~~~-----~~~~~l~~~l~~~~~gs~IIvTTR~--~-~v~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~-~~~  151 (377)
                      ++|+++..     ..+..+.....  .....+++|+..  . .+.........+++.+++.++-...+....-... ..+
T Consensus       128 ~ide~~~~~~~~~~~~~~~~~~~~--~~~~~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~  205 (253)
T d1sxja2         128 IMDEVDGMSGGDRGGVGQLAQFCR--KTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLD  205 (253)
T ss_dssp             EECSGGGCCTTSTTHHHHHHHHHH--HCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             EeeeccccccchhhhhHHHhhhhc--ccccccccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCC
Confidence            99997642     11222221110  112235554432  2 2222234467899999999999998887653211 112


Q ss_pred             hhHHHHHHHHHHHhCC
Q 040234          152 EEYVELAESVVRICHC  167 (377)
Q Consensus       152 ~~~~~~~~~I~~~c~G  167 (377)
                         ++...+|++.++|
T Consensus       206 ---~~~l~~i~~~s~G  218 (253)
T d1sxja2         206 ---PNVIDRLIQTTRG  218 (253)
T ss_dssp             ---TTHHHHHHHHTTT
T ss_pred             ---HHHHHHHHHhCCC
Confidence               2356789999999

>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=96.73  E-value=0.0029  Score=53.04  Aligned_cols=67  Identities=13%  Similarity=-0.013  Sum_probs=41.7

Q ss_pred             CCeEEEEecch-hH--HhhCCCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhH
Q 040234          104 GSRIIITTRNE-HL--LKLHPVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       104 gs~IIvTTR~~-~v--~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                      ...+|.+|... ..  .........+.++..+.++...++...........  .++.+..|++.++|  -+-.+
T Consensus       134 ~~~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~l~~i~~~s~g--d~R~a  203 (238)
T d1in4a2         134 PFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEI--EDAAAEMIAKRSRG--TPRIA  203 (238)
T ss_dssp             CCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCB--CHHHHHHHHHTSTT--CHHHH
T ss_pred             CeEEEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccchh--hHHHHHHHHHhCCC--CHHHH
Confidence            34555555443 32  12223345678999999999999987774433222  24568889999998  54433

>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=96.72  E-value=0.0026  Score=57.61  Aligned_cols=123  Identities=14%  Similarity=0.080  Sum_probs=65.2

Q ss_pred             CCCCcHHHHHHHHHchhccc------cccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHh-
Q 040234            1 MGGLGKTTLARVVYDLISHE------FDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRL-   73 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~------f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l-   73 (377)
                      .+|+|||+|+..+++++...      .+..+|..+++.          ++...         ......+++...+...+ 
T Consensus        51 ~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~----------l~ag~---------~~~g~~e~r~~~i~~~~~  111 (387)
T d1qvra2          51 EPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS----------LLAGA---------KYRGEFEERLKAVIQEVV  111 (387)
T ss_dssp             CTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC------------------------------CHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh----------hhccc---------CcchhHHHHHHHHHHHhc
Confidence            37999999998888753221      235677764433          22110         00112333333333333 


Q ss_pred             cC-ceEEEEEeCCCCh----------hhhhHhhCCCCCCCCCCeEEEEecchhHHhhC------CCCCeeecCCCChhhh
Q 040234           74 RR-KKVLVVIDDAAHP----------DHLRRLVGEPDWFGPGSRIIITTRNEHLLKLH------PVKKVYKLEALTYDEA  136 (377)
Q Consensus        74 ~~-k~~LLVLDdv~~~----------~~~~~l~~~l~~~~~gs~IIvTTR~~~v~~~~------~~~~~~~l~~L~~~ea  136 (377)
                      .. .+.+|++|++...          +..+.|.|.+.  ...-++|.||.........      ...+.+.+++.+.+++
T Consensus       112 ~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~--rg~~~~I~~tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~  189 (387)
T d1qvra2         112 QSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEET  189 (387)
T ss_dssp             TTCSSEEEEECCC-------------------HHHHH--TTCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHH
T ss_pred             cCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHh--CCCcceeeecCHHHHHHhcccHHHHHhcccccCCCCcHHHH
Confidence            32 4789999998542          22233444442  2344677777655443221      2357789999999999


Q ss_pred             HHHHHHHh
Q 040234          137 FRLLCLKA  144 (377)
Q Consensus       137 ~~L~~~~~  144 (377)
                      .+++....
T Consensus       190 ~~il~~~~  197 (387)
T d1qvra2         190 ISILRGLK  197 (387)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99987544

>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=96.56  E-value=0.0085  Score=50.03  Aligned_cols=50  Identities=20%  Similarity=-0.087  Sum_probs=35.3

Q ss_pred             CCCCeeecCCCChhhhHHHHHHHhcCCCCCchhHHHHHHHHHHHhCCCCchhhH
Q 040234          121 PVKKVYKLEALTYDEAFRLLCLKAFDTHKPLEEYVELAESVVRICHCQKSTLNA  174 (377)
Q Consensus       121 ~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~I~~~c~G~~lplal  174 (377)
                      .....+.+...+.++..+++...+......  ...+....|++.++|  .+-.+
T Consensus       155 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~--~~~~~l~~ia~~s~g--d~R~a  204 (239)
T d1ixsb2         155 RFGIVEHLEYYTPEELAQGVMRDARLLGVR--ITEEAALEIGRRSRG--TMRVA  204 (239)
T ss_dssp             GCSEEEECCCCCHHHHHHHHHHHHGGGCCC--BCHHHHHHHHHHTTS--SHHHH
T ss_pred             ccceeeEeeccChhhhhHHHHHHHHHhCCc--cchHHHHHHHHHcCC--CHHHH
Confidence            346678889999999998888766433222  225678899999999  65443

>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=95.14  E-value=0.018  Score=46.74  Aligned_cols=108  Identities=8%  Similarity=-0.040  Sum_probs=57.3

Q ss_pred             CCCcHHHHHHHHHchhc---cccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceE
Q 040234            2 GGLGKTTLARVVYDLIS---HEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKV   78 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~---~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~   78 (377)
                      +|+|||++|..+++.+.   ...++...+..-+..-    .+.++ +.+.+.+....                 ..+++=
T Consensus        24 ~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I----~Id~I-R~i~~~~~~~~-----------------~~~~~K   81 (198)
T d2gnoa2          24 DLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENI----GIDDI-RTIKDFLNYSP-----------------ELYTRK   81 (198)
T ss_dssp             SSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCB----CHHHH-HHHHHHHTSCC-----------------SSSSSE
T ss_pred             CCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCC----CHHHH-HHHHHHHhhCc-----------------ccCCCE
Confidence            69999999999998442   2234555554211111    33333 23433332110                 023445


Q ss_pred             EEEEeCCCC--hhhhhHhhCCCCCCCCCCeEEEEecch-hHHhhC-CCCCeeecCCC
Q 040234           79 LVVIDDAAH--PDHLRRLVGEPDWFGPGSRIIITTRNE-HLLKLH-PVKKVYKLEAL  131 (377)
Q Consensus        79 LLVLDdv~~--~~~~~~l~~~l~~~~~gs~IIvTTR~~-~v~~~~-~~~~~~~l~~L  131 (377)
                      ++|+|+++.  .+..+.|+..+..-.+++.+|++|.+. .+.... +....+.+.+.
T Consensus        82 viIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p  138 (198)
T d2gnoa2          82 YVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVP  138 (198)
T ss_dssp             EEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCC
T ss_pred             EEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCc
Confidence            899999986  345555554443324567776666654 333322 33455666543

>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=94.80  E-value=0.0053  Score=47.50  Aligned_cols=19  Identities=26%  Similarity=0.371  Sum_probs=16.4

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||+|+.+++++.-
T Consensus        10 ~~GsGKSTvak~La~~L~~   28 (169)
T d1kaga_          10 PMGAGKSTIGRQLAQQLNM   28 (169)
T ss_dssp             CTTSCHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHhCC
Confidence            6899999999999997643

>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=94.58  E-value=0.0074  Score=47.47  Aligned_cols=21  Identities=19%  Similarity=0.197  Sum_probs=17.8

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      ++|+||||+|+.+++++...|
T Consensus        14 ~~GsGKTTia~~La~~L~~~~   34 (183)
T d1m8pa3          14 YMNSGKDAIARALQVTLNQQG   34 (183)
T ss_dssp             STTSSHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHhhcC
Confidence            689999999999999876543

>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=94.28  E-value=0.02  Score=48.75  Aligned_cols=75  Identities=20%  Similarity=0.183  Sum_probs=43.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhcccc----CccchhhhHHHHHHHhcC-c
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADN----NIRNVYDGINMLRVRLRR-K   76 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~----~~~~~~~~~~~l~~~l~~-k   76 (377)
                      +|+|||+||.+++...+..=...+|+. .-..+    +.     +++++++...+.    .+.+.++..+.+...++. +
T Consensus        66 ~~sGKT~l~l~~~~~aqk~g~~v~yiD-tE~~~----~~-----~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~~~  135 (268)
T d1xp8a1          66 ESGGKTTLALAIVAQAQKAGGTCAFID-AEHAL----DP-----VYARALGVNTDELLVSQPDNGEQALEIMELLVRSGA  135 (268)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEEE-SSCCC----CH-----HHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTC
T ss_pred             CccchHHHHHHHHHHHHhCCCEEEEEE-CCccC----CH-----HHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhcCC
Confidence            689999999998885544323456776 32222    33     245555443221    234555566666655544 3


Q ss_pred             eEEEEEeCCC
Q 040234           77 KVLVVIDDAA   86 (377)
Q Consensus        77 ~~LLVLDdv~   86 (377)
                      .-|+|+|.+.
T Consensus       136 ~~liIiDSi~  145 (268)
T d1xp8a1         136 IDVVVVDSVA  145 (268)
T ss_dssp             CSEEEEECTT
T ss_pred             CcEEEEeccc
Confidence            5588888874

>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=94.23  E-value=0.013  Score=49.85  Aligned_cols=75  Identities=20%  Similarity=0.158  Sum_probs=40.9

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc----cCccchhhhHHHHHHHhc-Cc
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD----NNIRNVYDGINMLRVRLR-RK   76 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~k   76 (377)
                      +|+||||||.+++......-...+|+. .-..+    +..     .++.++...+    ....+.++..+.+....+ ++
T Consensus        63 ~gsGKTtl~l~~~~~~q~~g~~~vyid-tE~~~----~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~~~~  132 (263)
T d1u94a1          63 ESSGKTTLTLQVIAAAQREGKTCAFID-AEHAL----DPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGA  132 (263)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEEE-SSCCC----CHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTC
T ss_pred             CCcHHHHHHHHHHHHHHcCCCEEEEEc-ccccc----CHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHHHHhcCC
Confidence            689999999999986555444567776 33222    322     2344433211    112334444555544443 23


Q ss_pred             eEEEEEeCCC
Q 040234           77 KVLVVIDDAA   86 (377)
Q Consensus        77 ~~LLVLDdv~   86 (377)
                      .-|+|+|.+.
T Consensus       133 ~~liViDSi~  142 (263)
T d1u94a1         133 VDVIVVDSVA  142 (263)
T ss_dssp             CSEEEEECGG
T ss_pred             CCEEEEECcc
Confidence            4477777763

>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=94.16  E-value=0.043  Score=46.62  Aligned_cols=44  Identities=23%  Similarity=0.319  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEecchhhcccccCHHHHHHHHHH
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLADVREKCDKEGSVISLQKQLLS   49 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~~~~~~~~~~~~~~~~~~~i~~   49 (377)
                      +|+|||+|+..+++...+.-. ..+++ .+++..+   ...++.+++.+
T Consensus        77 ~g~GKt~l~~~i~~~~~~~~~~v~V~~-~iGer~~---ev~~~~~~~~~  121 (276)
T d2jdid3          77 AGVGKTVLIMELINNVAKAHGGYSVFA-GVGERTR---EGNDLYHEMIE  121 (276)
T ss_dssp             TTSSHHHHHHHHHHHHTTTCSSEEEEE-EESCCHH---HHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhhCCCeEEEE-EeccChH---HHHHHHHHHHh
Confidence            699999999999986433323 34444 3665431   44555555554

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.15  E-value=0.024  Score=48.30  Aligned_cols=76  Identities=18%  Similarity=0.097  Sum_probs=45.2

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccc----cCccchhhhHHHHHHHhcC-c
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLAD----NNIRNVYDGINMLRVRLRR-K   76 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~----~~~~~~~~~~~~l~~~l~~-k   76 (377)
                      +|+|||+||.+++...+..-...+|+. .-..+    +...     +++++...+    ..+.+.++..+.+...+.. +
T Consensus        69 ~~~GKT~l~l~~~~~~q~~g~~~vyID-tE~~~----~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~~~~  138 (269)
T d1mo6a1          69 ESSGKTTVALHAVANAQAAGGVAAFID-AEHAL----DPDY-----AKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGA  138 (269)
T ss_dssp             SSSSHHHHHHHHHHHHHHTTCEEEEEE-SSCCC----CHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTTC
T ss_pred             CCcHHHHHHHHHHHHHhcCCCEEEEEE-CCccC----CHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHHHHHhcCC
Confidence            689999999888875544444567776 33322    3322     444443322    1234555666665555544 4


Q ss_pred             eEEEEEeCCCC
Q 040234           77 KVLVVIDDAAH   87 (377)
Q Consensus        77 ~~LLVLDdv~~   87 (377)
                      .-|+|+|.+-.
T Consensus       139 ~~liIiDSi~a  149 (269)
T d1mo6a1         139 LDIVVIDSVAA  149 (269)
T ss_dssp             EEEEEEECSTT
T ss_pred             CCEEEEecccc
Confidence            67889998854

>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=93.95  E-value=0.0074  Score=48.35  Aligned_cols=27  Identities=22%  Similarity=0.209  Sum_probs=20.7

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEE
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      ++|+||||||+.++.++...+....++
T Consensus        27 ~pGSGKTTiAk~La~~l~~~~~~~~~~   53 (195)
T d1x6va3          27 LSGAGKTTVSMALEEYLVCHGIPCYTL   53 (195)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCCccch
Confidence            589999999999999776655544443

>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=93.93  E-value=0.01  Score=46.31  Aligned_cols=18  Identities=33%  Similarity=0.425  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+++++.
T Consensus        12 ~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_          12 TPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            589999999999998653

>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=93.73  E-value=0.012  Score=45.97  Aligned_cols=20  Identities=25%  Similarity=0.415  Sum_probs=17.2

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      |+|+||||+|+.+++++.-.
T Consensus         9 ~~G~GKSTig~~La~~l~~~   28 (165)
T d2iyva1           9 LPGSGKSTIGRRLAKALGVG   28 (165)
T ss_dssp             STTSSHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHhCCC
Confidence            68999999999999977544

>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=93.60  E-value=0.012  Score=46.38  Aligned_cols=18  Identities=17%  Similarity=0.206  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      +.|+||||||+.++++..
T Consensus        15 ~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2          15 GESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CTTSHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998654

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=93.24  E-value=0.14  Score=44.32  Aligned_cols=17  Identities=35%  Similarity=0.530  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ..|+|||.||+.+++.+
T Consensus        61 p~G~GKt~lak~la~~l   77 (315)
T d1qvra3          61 PTGVGKTELAKTLAATL   77 (315)
T ss_dssp             CSSSSHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHHHh
Confidence            47999999999999866

>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=93.15  E-value=0.016  Score=45.01  Aligned_cols=18  Identities=22%  Similarity=0.394  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.++.+..
T Consensus        10 ~~GsGKTTva~~L~~~~~   27 (176)
T d2bdta1          10 PAGVGKSTTCKRLAAQLD   27 (176)
T ss_dssp             STTSSHHHHHHHHHHHSS
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            589999999999997543

>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=92.98  E-value=0.019  Score=44.76  Aligned_cols=18  Identities=39%  Similarity=0.501  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      |+|+||||+|+.+++++.
T Consensus         8 ~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           8 FMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            689999999999999763

>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=92.68  E-value=0.022  Score=44.72  Aligned_cols=18  Identities=28%  Similarity=0.372  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      |+|+||||+|+.+++++.
T Consensus        10 ~~GsGKSTia~~LA~~Lg   27 (170)
T d1e6ca_          10 ARGCGMTTVGRELARALG   27 (170)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            689999999999998764

>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=92.63  E-value=0.022  Score=43.50  Aligned_cols=16  Identities=38%  Similarity=0.362  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      ++|+||||||+++..+
T Consensus        10 ~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_          10 CPGSGKSTWAREFIAK   25 (152)
T ss_dssp             CTTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHh
Confidence            5899999999988753

>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=92.57  E-value=0.02  Score=44.39  Aligned_cols=20  Identities=30%  Similarity=0.418  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ..|+|||||+.++.++...+
T Consensus        10 ~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_          10 WSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             CTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            37999999999999876554

>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=92.49  E-value=0.032  Score=43.69  Aligned_cols=20  Identities=30%  Similarity=0.449  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      .+|+|||||++++++.+...
T Consensus         9 ~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           9 PPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCSSCHHHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHHHHHHHHC
Confidence            48999999999999866544

>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=92.19  E-value=0.028  Score=43.75  Aligned_cols=19  Identities=16%  Similarity=0.350  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||+|+.+++++..
T Consensus        11 ~~GsGKsTva~~L~~~l~~   29 (178)
T d1qhxa_          11 GSSAGKSGIVRCLQSVLPE   29 (178)
T ss_dssp             CTTSSHHHHHHHHHHHSSS
T ss_pred             CCCCCHHHHHHHHHHHcCC
Confidence            4799999999999987643

>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=91.79  E-value=0.12  Score=42.49  Aligned_cols=27  Identities=22%  Similarity=0.240  Sum_probs=22.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +|+|||+||.+++.....+....+|+.
T Consensus        35 pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          35 TGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             TTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHHhccccceee
Confidence            799999999999997767766777776

>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=91.74  E-value=0.031  Score=43.50  Aligned_cols=17  Identities=29%  Similarity=0.485  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.+++++
T Consensus        13 ~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_          13 TPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999999865

>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=91.74  E-value=0.034  Score=43.32  Aligned_cols=17  Identities=35%  Similarity=0.477  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        12 ~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1          12 HPGSGKSTIAEALANLP   28 (176)
T ss_dssp             CTTSCHHHHHHHHHTCS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999998754

>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=91.59  E-value=0.034  Score=43.13  Aligned_cols=18  Identities=28%  Similarity=0.429  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+++++.
T Consensus        14 ~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_          14 VSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             STTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998663

>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=91.58  E-value=0.028  Score=45.93  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+||||||+.+.+++...
T Consensus        32 lsGsGKTTia~~L~~~l~~~   51 (208)
T d1m7ga_          32 LSASGKSTLAVELEHQLVRD   51 (208)
T ss_dssp             STTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHh
Confidence            58999999999999876443

>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=91.41  E-value=0.035  Score=44.79  Aligned_cols=19  Identities=16%  Similarity=0.317  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+||||||+++++....
T Consensus        10 lpgsGKSTla~~L~~~l~~   28 (213)
T d1bifa1          10 LPARGKTYISKKLTRYLNF   28 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            5899999999999985543

>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=91.33  E-value=0.19  Score=42.47  Aligned_cols=30  Identities=17%  Similarity=0.039  Sum_probs=18.7

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchh
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVRE   32 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~   32 (377)
                      .|+|||+|+.........+-...++.. +++
T Consensus        76 ~g~GKt~l~~~~~~~~~~~~~v~V~~~-iGe  105 (276)
T d1fx0a3          76 RQTGKTAVATDTILNQQGQNVICVYVA-IGQ  105 (276)
T ss_dssp             SSSSHHHHHHHHHHTCCTTTCEEEEEE-ESC
T ss_pred             CCCChHHHHHHHHhhhcccCceeeeee-ecc
Confidence            599999999886654444433444443 444

>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=90.93  E-value=0.041  Score=46.25  Aligned_cols=20  Identities=25%  Similarity=0.438  Sum_probs=16.9

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+|||+||+.++......
T Consensus        40 pPGtGKT~la~~la~~~~~~   59 (273)
T d1gvnb_          40 QPGSGKTSLRSAIFEETQGN   59 (273)
T ss_dssp             CTTSCTHHHHHHHHHHTTTC
T ss_pred             CCCCCHHHHHHHHHHHhhcc
Confidence            48999999999999876544

>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=90.71  E-value=0.32  Score=39.31  Aligned_cols=27  Identities=30%  Similarity=0.377  Sum_probs=18.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccceEEe
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGSSFLA   28 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~~w~~   28 (377)
                      +.|+||||.+.+++.+.+.+ ...+.+.
T Consensus        17 ptGvGKTTTiAKLA~~~~~~-g~kV~li   43 (211)
T d2qy9a2          17 VNGVGKTTTIGKLARQFEQQ-GKSVMLA   43 (211)
T ss_dssp             CTTSCHHHHHHHHHHHHHTT-TCCEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHC-CCcEEEE
Confidence            46999999888888766533 3445554

>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=90.46  E-value=0.14  Score=43.56  Aligned_cols=27  Identities=19%  Similarity=0.122  Sum_probs=18.7

Q ss_pred             CCCcHHHHHHHHHchhccccc-cceEEe
Q 040234            2 GGLGKTTLARVVYDLISHEFD-GSSFLA   28 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~-~~~w~~   28 (377)
                      .|+|||+|+.++++....... ..+++.
T Consensus        52 ~g~GKT~l~~~i~~~~~~~~~~~v~~~~   79 (289)
T d1xpua3          52 PKAGKTMLLQNIAQSIAYNHPDCVLMVL   79 (289)
T ss_dssp             SSSSHHHHHHHHHHHHHHHCTTSEEEEE
T ss_pred             CCCCHHHHHHHHHHHHhhcCCCeEEEEE
Confidence            699999999999985544433 333433

>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=90.14  E-value=0.068  Score=43.75  Aligned_cols=26  Identities=23%  Similarity=0.282  Sum_probs=19.3

Q ss_pred             CCCcHHHHHHHHHchhccccccceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      ||+||||+|..++..+.++-..++.+
T Consensus        11 GGvGKTtia~nlA~~la~~g~~Vlli   36 (232)
T d1hyqa_          11 GGTGKTTITANLGVALAQLGHDVTIV   36 (232)
T ss_dssp             SCSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCChHHHHHHHHHHHHHhCCCCEEEE
Confidence            89999999999998665543334444

>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=90.02  E-value=0.087  Score=41.32  Aligned_cols=20  Identities=25%  Similarity=0.574  Sum_probs=17.1

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      ++|+||||+|+.+++++..+
T Consensus         9 ~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           9 IPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             CTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHHc
Confidence            57999999999999877654

>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=90.00  E-value=0.088  Score=41.07  Aligned_cols=21  Identities=29%  Similarity=0.408  Sum_probs=17.6

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      +.|+||||+++.+++++....
T Consensus         9 ~~GsGKsT~~~~L~~~l~~~~   29 (190)
T d1khta_           9 VPGVGSTTSSQLAMDNLRKEG   29 (190)
T ss_dssp             CTTSCHHHHHHHHHHHHHTTT
T ss_pred             CCCCCHHHHHHHHHHHHHHcC
Confidence            579999999999999776553

>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=89.90  E-value=0.45  Score=38.30  Aligned_cols=20  Identities=25%  Similarity=0.272  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      +.|+||||.+.+++...+.+
T Consensus        14 ptGvGKTTTiaKLA~~~~~~   33 (207)
T d1okkd2          14 VNGVGKTTTIAKLGRYYQNL   33 (207)
T ss_dssp             STTSSHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            46999999888888755433

>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=89.26  E-value=0.07  Score=41.90  Aligned_cols=16  Identities=25%  Similarity=0.272  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHHch
Q 040234            1 MGGLGKTTLARVVYDL   16 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (377)
                      ++|+||||+|++++..
T Consensus        22 ~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          22 FPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             CTTSSHHHHHHHHTGG
T ss_pred             CCCCCHHHHHHHHHHh
Confidence            5899999999988764

>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=89.25  E-value=0.073  Score=46.13  Aligned_cols=19  Identities=37%  Similarity=0.499  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ++|+|||.||+.+++....
T Consensus        57 PpG~GKT~lAkalA~~~~~   75 (309)
T d1ofha_          57 PTGVGKTEIARRLAKLANA   75 (309)
T ss_dssp             CTTSSHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHhhcccc
Confidence            5899999999999986543

>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=89.24  E-value=0.096  Score=41.36  Aligned_cols=21  Identities=29%  Similarity=0.305  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      .+|+||||||+.+.+......
T Consensus        30 ~~GSGKSTla~~L~~~l~~~~   50 (198)
T d1rz3a_          30 LSRSGKTTLANQLSQTLREQG   50 (198)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhcccc
Confidence            379999999999998665543

>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=89.24  E-value=0.24  Score=42.87  Aligned_cols=21  Identities=24%  Similarity=0.295  Sum_probs=17.7

Q ss_pred             CCCCcHHHHHHHHHchhcccc
Q 040234            1 MGGLGKTTLARVVYDLISHEF   21 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f   21 (377)
                      .+|+|||.||+.++.++..++
T Consensus       131 ~pG~GKT~la~ala~~~~~~~  151 (321)
T d1w44a_         131 KGNSGKTPLVHALGEALGGKD  151 (321)
T ss_dssp             SSSSCHHHHHHHHHHHHHTTS
T ss_pred             CCCccHHHHHHHHHHHhcCCC
Confidence            489999999999999876543

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=88.92  E-value=0.096  Score=42.85  Aligned_cols=26  Identities=23%  Similarity=0.206  Sum_probs=19.0

Q ss_pred             CCCcHHHHHHHHHchhccccccceEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFL   27 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~   27 (377)
                      ||+||||+|..++....++-..++.+
T Consensus        12 GGvGKTtia~nLA~~la~~g~~Vlli   37 (237)
T d1g3qa_          12 GGTGKTTVTANLSVALGDRGRKVLAV   37 (237)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCcHHHHHHHHHHHHHhCCCCEEEE
Confidence            89999999999998665543334444

>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=88.91  E-value=0.087  Score=41.01  Aligned_cols=19  Identities=32%  Similarity=0.545  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      ..|+|||||++.++..+..
T Consensus         8 ~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           8 EPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             CTTSSHHHHHHHHHHHHGG
T ss_pred             CCCcHHHHHHHHHHhcCCC
Confidence            3799999999999985543

>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=88.74  E-value=0.071  Score=41.28  Aligned_cols=25  Identities=24%  Similarity=0.154  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHchhccc-cccceE
Q 040234            2 GGLGKTTLARVVYDLISHE-FDGSSF   26 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-f~~~~w   26 (377)
                      .|+|||||+.++..+++.+ +...+.
T Consensus        10 ~gSGKTTli~~l~~~L~~~g~~v~vi   35 (165)
T d1xjca_          10 KHSGKTTLMEKWVAAAVREGWRVGTV   35 (165)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            6999999999999977655 444443

>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=88.38  E-value=0.12  Score=43.44  Aligned_cols=19  Identities=26%  Similarity=0.426  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+...
T Consensus        10 GGvGKTT~a~nLA~~LA~~   28 (269)
T d1cp2a_          10 GGIGKSTTTQNLTSGLHAM   28 (269)
T ss_dssp             TTSSHHHHHHHHHHHHHTT
T ss_pred             CcCCHHHHHHHHHHHHHhC
Confidence            8999999999999866544

>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=88.27  E-value=0.84  Score=37.65  Aligned_cols=14  Identities=36%  Similarity=0.729  Sum_probs=12.7

Q ss_pred             CCCcHHHHHHHHHc
Q 040234            2 GGLGKTTLARVVYD   15 (377)
Q Consensus         2 gGiGKTtLA~~v~~   15 (377)
                      .|+|||++|+.+.+
T Consensus        32 ~GtGK~~~A~~ih~   45 (247)
T d1ny5a2          32 SGVGKEVVARLIHK   45 (247)
T ss_dssp             TTSSHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHH
Confidence            59999999999986

>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=88.12  E-value=0.51  Score=37.94  Aligned_cols=20  Identities=30%  Similarity=0.247  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      +.|+||||.+.+++.+.+.+
T Consensus        18 p~GvGKTTTiaKLA~~~~~~   37 (207)
T d1ls1a2          18 LQGSGKTTTAAKLALYYKGK   37 (207)
T ss_dssp             CTTTTHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            47999999888888755544

>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=88.07  E-value=0.54  Score=37.90  Aligned_cols=19  Identities=26%  Similarity=0.282  Sum_probs=10.6

Q ss_pred             CCCCcHHHHHHHHHchhcc
Q 040234            1 MGGLGKTTLARVVYDLISH   19 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (377)
                      +.|+||||.+.+++.+.+.
T Consensus        20 ptGvGKTTTiAKLA~~~~~   38 (211)
T d1j8yf2          20 VQGTGKATTAGKLAYFYKK   38 (211)
T ss_dssp             SCCC----HHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3699999988888775543

>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=87.95  E-value=0.66  Score=37.42  Aligned_cols=20  Identities=30%  Similarity=0.413  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      +.|+||||.+.+++.+.+.+
T Consensus        19 ptGvGKTTTiAKLAa~~~~~   38 (213)
T d1vmaa2          19 VNGTGKTTSCGKLAKMFVDE   38 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            46999999887777755443

>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=87.62  E-value=0.33  Score=41.16  Aligned_cols=15  Identities=27%  Similarity=0.067  Sum_probs=12.7

Q ss_pred             CCCcHHHHHHHHHch
Q 040234            2 GGLGKTTLARVVYDL   16 (377)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (377)
                      +|+|||+|+..+...
T Consensus        77 ~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          77 RQTGKTSIAIDTIIN   91 (285)
T ss_dssp             TTSSHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHh
Confidence            699999999888763

>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=87.59  E-value=0.13  Score=43.72  Aligned_cols=19  Identities=26%  Similarity=0.499  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+.++
T Consensus        17 GGVGKTTvaa~lA~~lA~~   35 (296)
T d1ihua1          17 GGVGKTSISCATAIRLAEQ   35 (296)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CcChHHHHHHHHHHHHHHC
Confidence            8999999998888755443

>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=87.56  E-value=0.11  Score=40.69  Aligned_cols=17  Identities=29%  Similarity=0.337  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         8 ~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           8 LPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            58999999999998865

>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=87.54  E-value=0.11  Score=41.20  Aligned_cols=17  Identities=18%  Similarity=0.132  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        11 ppGsGKsT~a~~La~~~   27 (189)
T d1zaka1          11 APASGKGTQCELIKTKY   27 (189)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            57999999999998865

>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=87.41  E-value=0.13  Score=43.72  Aligned_cols=19  Identities=26%  Similarity=0.525  Sum_probs=15.8

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+.+.
T Consensus        11 GGVGKTT~a~NLA~~LA~~   29 (289)
T d2afhe1          11 GGIGKSTTTQNLVAALAEM   29 (289)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            8999999999998855544

>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=87.33  E-value=0.11  Score=41.30  Aligned_cols=17  Identities=24%  Similarity=0.294  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        14 ~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1          14 APGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CTTSSHHHHHHHHHHHB
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            68999999999999854

>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=87.14  E-value=0.12  Score=40.51  Aligned_cols=17  Identities=29%  Similarity=0.251  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         8 ~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           8 PPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            58999999999999865

>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=86.95  E-value=0.12  Score=41.00  Aligned_cols=17  Identities=24%  Similarity=0.108  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        14 ~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_          14 GPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            58999999999999854

>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=86.92  E-value=0.12  Score=40.55  Aligned_cols=17  Identities=29%  Similarity=0.358  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         8 ~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           8 LPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            58999999999999865

>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=86.83  E-value=0.15  Score=42.96  Aligned_cols=19  Identities=37%  Similarity=0.573  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHchhccc
Q 040234            2 GGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (377)
                      ||+||||+|..++..+..+
T Consensus        29 GGVGKTT~a~nLA~~lA~~   47 (279)
T d1ihua2          29 GGVGKTTMAAAIAVRLADM   47 (279)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            8999999988888754433

>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=86.50  E-value=0.14  Score=40.21  Aligned_cols=17  Identities=29%  Similarity=0.235  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        10 ~pGSGKtT~a~~La~~~   26 (180)
T d1akya1          10 PPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999999864

>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=85.86  E-value=1.4  Score=36.30  Aligned_cols=17  Identities=41%  Similarity=0.485  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      .+|+|||+||.+++..+
T Consensus        37 ~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          37 PGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            37999999999888744

>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=85.47  E-value=0.16  Score=40.40  Aligned_cols=17  Identities=24%  Similarity=0.112  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        16 ppGSGKsT~a~~La~~~   32 (196)
T d1ukza_          16 GPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999855

>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=85.23  E-value=0.36  Score=38.89  Aligned_cols=20  Identities=20%  Similarity=0.336  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHchhccc
Q 040234            1 MGGLGKTTLARVVYDLISHE   20 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (377)
                      +-|+||||+|+.+.+.+..+
T Consensus        11 ~dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_          11 VDRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             STTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            46999999999999977554

>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=84.83  E-value=0.18  Score=40.82  Aligned_cols=17  Identities=24%  Similarity=0.366  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++.++
T Consensus        11 p~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_          11 PASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             SSCSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999865

>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=84.81  E-value=0.18  Score=39.75  Aligned_cols=17  Identities=29%  Similarity=0.176  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus        11 ~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1          11 PPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999999754

>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=84.59  E-value=0.19  Score=39.74  Aligned_cols=24  Identities=29%  Similarity=0.405  Sum_probs=18.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGS   24 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~   24 (377)
                      ++|+|||||++.++++....|...
T Consensus         9 psG~GK~tl~~~L~~~~~~~~~~~   32 (186)
T d1gkya_           9 PSGTGKSTLLKKLFAEYPDSFGFS   32 (186)
T ss_dssp             CTTSSHHHHHHHHHHHCTTTEEEC
T ss_pred             CCCCCHHHHHHHHHHhCCcceeEE
Confidence            479999999999988766555433

>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=84.58  E-value=1  Score=37.46  Aligned_cols=43  Identities=19%  Similarity=0.131  Sum_probs=26.0

Q ss_pred             CCCcHHHHHHHHHchh--ccccccceEEecchhhcccccCHHHHHHHHHHHHh
Q 040234            2 GGLGKTTLARVVYDLI--SHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLL   52 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~--~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~   52 (377)
                      +|+|||+||.+++...  .+..+. +++. .- .     +...+...++....
T Consensus        44 ~G~GKT~~~~~la~~~a~~~g~~v-~~~s-~E-~-----~~~~~~~r~~~~~~   88 (277)
T d1cr2a_          44 SGMGKSTFVRQQALQWGTAMGKKV-GLAM-LE-E-----SVEETAEDLIGLHN   88 (277)
T ss_dssp             TTSSHHHHHHHHHHHHHHTSCCCE-EEEE-SS-S-----CHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHhhhhhcccce-eEee-ec-c-----chhhHHhHHHHHhh
Confidence            7999999999998754  233332 2322 21 1     55666666666544

>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=84.28  E-value=0.21  Score=39.59  Aligned_cols=22  Identities=32%  Similarity=0.459  Sum_probs=17.3

Q ss_pred             CCCCcHHHHHHHHHchhccccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFD   22 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~   22 (377)
                      ++|+|||||+++++++....|.
T Consensus         8 PsGsGK~tl~~~L~~~~~~~~~   29 (190)
T d1lvga_           8 PSGAGKSTLLKKLFQEHSSIFG   29 (190)
T ss_dssp             CTTSSHHHHHHHHHHHHTTTEE
T ss_pred             CCCCCHHHHHHHHHHhCCCcee
Confidence            4799999999999886555443

>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=84.23  E-value=0.2  Score=39.58  Aligned_cols=17  Identities=24%  Similarity=0.192  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         9 ppGSGKsT~a~~La~~~   25 (194)
T d1teva_           9 GPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            48999999999999854

>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=84.18  E-value=0.21  Score=38.88  Aligned_cols=17  Identities=24%  Similarity=0.190  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|+.++++.
T Consensus         8 ~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           8 APVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999999754

>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=84.12  E-value=0.19  Score=38.73  Aligned_cols=14  Identities=50%  Similarity=0.579  Sum_probs=13.0

Q ss_pred             CCcHHHHHHHHHch
Q 040234            3 GLGKTTLARVVYDL   16 (377)
Q Consensus         3 GiGKTtLA~~v~~~   16 (377)
                      |+||||+++.+++.
T Consensus        43 GaGKTtfvr~~~~~   56 (158)
T d1htwa_          43 GAGKTTLTRGMLQG   56 (158)
T ss_dssp             TSSHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHhh
Confidence            89999999999984

>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=84.03  E-value=0.71  Score=39.03  Aligned_cols=21  Identities=19%  Similarity=0.444  Sum_probs=17.1

Q ss_pred             CCCcHHHHHHHHHchhccccc
Q 040234            2 GGLGKTTLARVVYDLISHEFD   22 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~   22 (377)
                      .|+||||||..+...+.+.+.
T Consensus        36 qGSGKSTl~~~l~~~L~~~~~   56 (286)
T d1odfa_          36 QGSGKSFTSIQIYNHLMEKYG   56 (286)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHG
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            699999999999887666543

>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=83.89  E-value=0.53  Score=41.36  Aligned_cols=33  Identities=21%  Similarity=0.383  Sum_probs=21.1

Q ss_pred             EEEEeCCCCh--hhhhHhhCCCCCCCCCCeEEEEecch
Q 040234           79 LVVIDDAAHP--DHLRRLVGEPDWFGPGSRIIITTRNE  114 (377)
Q Consensus        79 LLVLDdv~~~--~~~~~l~~~l~~~~~gs~IIvTTR~~  114 (377)
                      ++|+|++...  .....+...+   .++++||+.--..
T Consensus       264 ~lIIDEaSmv~~~l~~~ll~~~---~~~~~lILvGD~~  298 (359)
T d1w36d1         264 VLVVDEASMIDLPMMSRLIDAL---PDHARVIFLGDRD  298 (359)
T ss_dssp             EEEECSGGGCBHHHHHHHHHTC---CTTCEEEEEECTT
T ss_pred             eeeehhhhccCHHHHHHHHHHh---cCCCEEEEECChh
Confidence            9999998653  3445555554   3567888765443

>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=83.75  E-value=0.22  Score=40.11  Aligned_cols=18  Identities=17%  Similarity=0.397  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHchhcc
Q 040234            2 GGLGKTTLARVVYDLISH   19 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (377)
                      .|+||||||+.+.+.+..
T Consensus        11 ~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_          11 TASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             TTSSHHHHHHHHHHHTTG
T ss_pred             CCCCHHHHHHHHHHHhch
Confidence            699999999999886543

>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=83.39  E-value=0.23  Score=39.96  Aligned_cols=18  Identities=28%  Similarity=0.479  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHchhc
Q 040234            1 MGGLGKTTLARVVYDLIS   18 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (377)
                      ++|+||||+|+.+++++.
T Consensus        11 ppGSGKgT~ak~La~~~g   28 (225)
T d1ckea_          11 PSGAGKGTLCKAMAEALQ   28 (225)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            589999999999998663

>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=81.84  E-value=0.22  Score=39.44  Aligned_cols=16  Identities=31%  Similarity=0.162  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHchh
Q 040234            2 GGLGKTTLARVVYDLI   17 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (377)
                      -|+||||+|+.+.+..
T Consensus        18 ~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1          18 IGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             TTSCHHHHHHTTGGGT
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            5999999999988754

>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=81.39  E-value=0.31  Score=38.54  Aligned_cols=17  Identities=24%  Similarity=0.165  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHchh
Q 040234            1 MGGLGKTTLARVVYDLI   17 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (377)
                      ++|+||||+|..++++.
T Consensus        16 ~pGSGKsT~a~~La~~~   32 (194)
T d3adka_          16 GPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             CTTSSHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            58999999999999854

>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=81.28  E-value=0.32  Score=38.12  Aligned_cols=24  Identities=13%  Similarity=0.264  Sum_probs=18.6

Q ss_pred             CCCCcHHHHHHHHHchhccccccc
Q 040234            1 MGGLGKTTLARVVYDLISHEFDGS   24 (377)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~f~~~   24 (377)
                      ++|+|||||++++.++..+.|...
T Consensus        11 psg~GK~tl~~~L~~~~~~~~~~~   34 (178)
T d1kgda_          11 AHGVGRRHIKNTLITKHPDRFAYP   34 (178)
T ss_dssp             CTTSSHHHHHHHHHHHCTTTEECC
T ss_pred             CCCCCHHHHHHHHHHhCCcCeeec
Confidence            479999999999987666655543

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=81.26  E-value=1.1  Score=39.90  Aligned_cols=82  Identities=17%  Similarity=0.058  Sum_probs=45.8

Q ss_pred             CCCcHHHHHHHHHchhccccccceEEecchhhcccccCHHHHHHHHHHHHhhccccCccchhhhHHHHHHHhcCceEEEE
Q 040234            2 GGLGKTTLARVVYDLISHEFDGSSFLADVREKCDKEGSVISLQKQLLSDLLKLADNNIRNVYDGINMLRVRLRRKKVLVV   81 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~f~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~k~~LLV   81 (377)
                      .|+||||....+.+.+...-...+=+-+--+..-.  +.            .+......+.....+.++..|+..+=+|+
T Consensus       167 TGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~~--~~------------~q~~v~~~~~~~~~~~l~~~lR~dPDvi~  232 (401)
T d1p9ra_         167 TGSGKSTTLYAGLQELNSSERNILTVEDPIEFDID--GI------------GQTQVNPRVDMTFARGLRAILRQDPDVVM  232 (401)
T ss_dssp             TTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCCS--SS------------EEEECBGGGTBCHHHHHHHHGGGCCSEEE
T ss_pred             CCCCccHHHHHHhhhhcCCCceEEEeccCcccccC--CC------------CeeeecCCcCCCHHHHHHHHHhhcCCEEE
Confidence            59999999988888653322222222211110000  00            00011112233457788888888888999


Q ss_pred             EeCCCChhhhhHhhCC
Q 040234           82 IDDAAHPDHLRRLVGE   97 (377)
Q Consensus        82 LDdv~~~~~~~~l~~~   97 (377)
                      +.++.|.+.......+
T Consensus       233 igEiRd~~ta~~a~~a  248 (401)
T d1p9ra_         233 VGEIRDLETAQIAVQA  248 (401)
T ss_dssp             ESCCCSHHHHHHHHHH
T ss_pred             ecCcCChHHHHHHHHH
Confidence            9999997766554433

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=81.03  E-value=4.3  Score=31.85  Aligned_cols=17  Identities=35%  Similarity=0.429  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHchhc
Q 040234            2 GGLGKTTLARVVYDLIS   18 (377)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (377)
                      .|.|||.+|..++.+..
T Consensus        94 tG~GKT~~a~~~~~~~~  110 (206)
T d2fz4a1          94 TGSGKTHVAMAAINELS  110 (206)
T ss_dssp             SSTTHHHHHHHHHHHSC
T ss_pred             CCCCceehHHhHHHHhc
Confidence            59999999988887553