Citrus Sinensis ID: 043252

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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-------
Protein Sequence
MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQD
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccEEEEEEccccccHHHHHHHHHccHHHHHcccccEEEEEcccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccEEEEEEccccccccccHHHHHHHHHccccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEcccccccccHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEcccccccccEccccEEccccHHHHHHHHHHccccccccccEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEcccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccEEEEEEEccccccHHHHHHHHcHHHccccccEEEEEEcccc
Coil and Loop (DISEMBL)
MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDdaeekkttdDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLlgngepaaahdqpsssrtstkskfrkliptccptftlqsIQFDYSMMSKIKKINDRFRDIEEEIGSLKLikssaggskkarqrrdTTSLVEEAKVYGRETEKKEIVELLLkddsrndggfsvipiigmgglgkTTLAQLVYndkqvedhfdlkawtcvsddfdvIRLTKSILLSIasdqnvdnhdLNKLQEELKKQLFGKKFLLVLDDVwnenytdwvhlslpfqagaqgsKIIVTTRNQD
Flexible Loop (DISEMBL)
MSIIGEAILTASVELLVNKLASEGIRlfarqgrikddlvkWKKKLVTIkavlddaeekkttddsvKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNgepaaahdqpsssrtstkskfrkLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGslklikssaggskkarqrrdttslveeakvygretekkeivelllkddsrndgGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIasdqnvdnHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSlpfqagaqgskiIVTTRNQD
Low Complexity Region (SEG)
MSIIGEAILTASVELLVNKLASEGIRLFARQGRIkddlvkwkkklvTIKAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPsssrtstkskfrkLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNklqeelkkqlfgkkfllVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQD
Disordered region (IsUnstruct)
**IIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLL**********************FRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIG**************************************EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIV******
Disordered Region (DISOPRED)
MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLL***********************FRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLK********************LVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIA************LQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKI*VTTRN**
Disordered Region (DISEMBL)
MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDD********DSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNG*******************FRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIK*****************LVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQD
Disordered Region (DISPRO)
MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLI********KAR***DTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDxxxxxxxxxxxxxxxxxxxxxKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQD
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	337	2.2.26 [Sep-21-2011]
Q9LRR4	1054	Putative disease resistan	yes	no	0.925	0.296	0.375	2e-51
Q7XBQ9	970	Disease resistance protei	N/A	no	0.869	0.302	0.350	7e-48
Q7XA40	992	Putative disease resistan	N/A	no	0.744	0.253	0.385	1e-46
Q7XA42	979	Putative disease resistan	N/A	no	0.866	0.298	0.338	8e-44
Q7XA39	988	Putative disease resistan	N/A	no	0.866	0.295	0.345	6e-43
Q9LRR5	1424	Putative disease resistan	no	no	0.919	0.217	0.310	2e-37
Q38834	852	Disease resistance RPP13-	no	no	0.872	0.345	0.278	6e-29
Q9M667	835	Disease resistance protei	no	no	0.869	0.350	0.3	3e-26
Q9FJK8	908	Probable disease resistan	no	no	0.872	0.323	0.289	1e-23
Q8W3K3	910	Putative disease resistan	no	no	0.866	0.320	0.281	3e-23

>sp|Q9LRR4|R13L1_ARATH Putative disease resistance RPP13-like protein 1 OS=Arabidopsis thaliana GN=RPPL1 PE=3 SV=1

 Score =  202 bits (515), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 128/341 (37%), Positives = 202/341 (59%), Gaps = 29/341 (8%)

Query: 1   MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLV-KWKKKLVTIKAVLDDAEEKK 59
           M+ IGE  L A ++ L   L SE  R F ++  + ++L+ +    L+TI AVL DAEEK+
Sbjct: 1   MTGIGEMFLAAFLQALFQTLVSEPFRSFFKRRELNENLLERLSTALLTITAVLIDAEEKQ 60

Query: 60  TTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSK 119
            T+  V+ W+ EL+++ Y  ED LD+  TEA R  +                + +S+ ++
Sbjct: 61  ITNPVVEKWVNELRDVVYHAEDALDDIATEALRLNI---------------GAESSSSNR 105

Query: 120 FRKLIPTCCPTFTLQSIQFDYS--MMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKAR 177
            R+L        +L       S  + ++++K+  R   +  +   L L + +A   K   
Sbjct: 106 LRQLRGR----MSLGDFLDGNSEHLETRLEKVTIRLERLASQRNILGLKELTAMIPK--- 158

Query: 178 QRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVY 237
           QR  TTSLV+E++V+GR+ +K EI+  L+ ++ + D G +V+ I+G+GG+GKTTL+QL+Y
Sbjct: 159 QRLPTTSLVDESEVFGRDDDKDEIMRFLIPENGK-DNGITVVAIVGIGGVGKTTLSQLLY 217

Query: 238 NDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK- 296
           ND+ V  +F  K W  VS++FDV ++TK +  S+ S +  +  DL+ LQ +LK++L G  
Sbjct: 218 NDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTS-RPCEFTDLDVLQVKLKERLTGTG 276

Query: 297 -KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
             FLLVLDD+WNEN+ DW  L  PF   AQGS+I+VTTR+Q
Sbjct: 277 LPFLLVLDDLWNENFADWDLLRQPFIHAAQGSQILVTTRSQ 317

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

>sp|Q7XBQ9|RGA2_SOLBU Disease resistance protein RGA2 OS=Solanum bulbocastanum GN=RGA2 PE=1 SV=1

 Score =  191 bits (485), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 116/331 (35%), Positives = 188/331 (56%), Gaps = 38/331 (11%)

Query: 4   IGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDD 63
           + EA +   ++ L + L  E + LF  Q    D+  +      TI+AVL+DA+EK+  + 
Sbjct: 1   MAEAFIQVLLDNLTSFLKGELVLLFGFQ----DEFQRLSSMFSTIQAVLEDAQEKQLNNK 56

Query: 64  SVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKL 123
            ++ WL +L    Y+V+D+LDE++T+A R                       ++S++ + 
Sbjct: 57  PLENWLQKLNAATYEVDDILDEYKTKATR----------------------FSQSEYGRY 94

Query: 124 IPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTT 183
            P   P        F + +  ++ ++  + + I EE  +  L +      ++   RR+T 
Sbjct: 95  HPKVIP--------FRHKVGKRMDQVMKKLKAIAEERKNFHLHEKIV---ERQAVRRETG 143

Query: 184 SLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVE 243
           S++ E +VYGR+ EK EIV++L+ + S +    SV+PI+GMGGLGKTTLAQ+V+ND++V 
Sbjct: 144 SVLTEPQVYGRDKEKDEIVKILINNVS-DAQHLSVLPILGMGGLGKTTLAQMVFNDQRVT 202

Query: 244 DHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLD 303
           +HF  K W CVS+DFD  RL K+I+ SI     +   DL  LQ++L++ L GK++LLVLD
Sbjct: 203 EHFHSKIWICVSEDFDEKRLIKAIVESIEGRPLLGEMDLAPLQKKLQELLNGKRYLLVLD 262

Query: 304 DVWNENYTDWVHLSLPFQAGAQGSKIIVTTR 334
           DVWNE+   W +L    + GA G+ ++ TTR
Sbjct: 263 DVWNEDQQKWANLRAVLKVGASGASVLTTTR 293

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 which restricts the pathogen growth. Confers a broad resistance to all known races of P.infestans.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA40|RGA3_SOLBU Putative disease resistance protein RGA3 OS=Solanum bulbocastanum GN=RGA3 PE=2 SV=2

 Score =  187 bits (474), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 111/288 (38%), Positives = 175/288 (60%), Gaps = 37/288 (12%)

Query: 48  IKAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFR-RKLLLGNGEPAAAH 106
           I+AVL+DA+EK+    ++K WL +L   AY+V+D+LD+ +TEA R ++ +LG   P    
Sbjct: 41  IQAVLEDAQEKQLKYKAIKNWLQKLNVAAYEVDDILDDCKTEAARFKQAVLGRYHP---- 96

Query: 107 DQPSSSRTSTKSKFRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLI 166
                                      ++I F Y +  ++K++ ++   I EE  +  L 
Sbjct: 97  ---------------------------RTITFCYKVGKRMKEMMEKLDAIAEERRNFHLD 129

Query: 167 KSSAGGSKKARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGG 226
           +      ++   RR T  ++ E KVYGRE E+ EIV++L+ + S ++    V+PI+GMGG
Sbjct: 130 ERII---ERQAARRQTGFVLTEPKVYGREKEEDEIVKILINNVSYSEE-VPVLPILGMGG 185

Query: 227 LGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQ 286
           LGKTTLAQ+V+ND+++ +HF+LK W CVSDDFD  RL K+I+ SI   +++ + DL  LQ
Sbjct: 186 LGKTTLAQMVFNDQRITEHFNLKIWVCVSDDFDEKRLIKAIVESIEG-KSLGDMDLAPLQ 244

Query: 287 EELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR 334
           ++L++ L GK++ LVLDDVWNE+   W +L    + GA G+ I++TTR
Sbjct: 245 KKLQELLNGKRYFLVLDDVWNEDQEKWDNLRAVLKIGASGASILITTR 292

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 which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA42|RGA1_SOLBU Putative disease resistance protein RGA1 OS=Solanum bulbocastanum GN=RGA1 PE=2 SV=2

 Score =  177 bits (450), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 112/331 (33%), Positives = 184/331 (55%), Gaps = 39/331 (11%)

Query: 4   IGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDD 63
           + EA +   ++ L + L  E + LF  Q    D+  +      TI+AVL+DA+EK+  D 
Sbjct: 1   MAEAFIQVVLDNLTSFLKGELVLLFGFQ----DEFQRLSSMFSTIQAVLEDAQEKQLNDK 56

Query: 64  SVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKL 123
            ++ WL +L    Y+V+D+LDE++T+A R                        +S++ + 
Sbjct: 57  PLENWLQKLNAATYEVDDILDEYKTKATR----------------------FLQSEYGRY 94

Query: 124 IPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTT 183
            P   P        F + +  ++ ++  +   I EE     L +      ++    R+T 
Sbjct: 95  HPKVIP--------FRHKVGKRMDQVMKKLNAIAEERKKFHLQEKII---ERQAATRETG 143

Query: 184 SLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVE 243
           S++ E +VYGR+ EK EIV++L+   S +    SV+PI+GMGGLGKTTL+Q+V+ND++V 
Sbjct: 144 SVLTEPQVYGRDKEKDEIVKILINTAS-DAQKLSVLPILGMGGLGKTTLSQMVFNDQRVT 202

Query: 244 DHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLD 303
           + F  K W C+SDDF+  RL K+I+ SI   +++ + DL  LQ++L++ L GK++ LVLD
Sbjct: 203 ERFYPKIWICISDDFNEKRLIKAIVESIEG-KSLSDMDLAPLQKKLQELLNGKRYFLVLD 261

Query: 304 DVWNENYTDWVHLSLPFQAGAQGSKIIVTTR 334
           DVWNE+   W +L    + GA G+ ++ TTR
Sbjct: 262 DVWNEDQHKWANLRAVLKVGASGAFVLTTTR 292

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 which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA39|RGA4_SOLBU Putative disease resistance protein RGA4 OS=Solanum bulbocastanum GN=RGA4 PE=2 SV=1

 Score =  174 bits (442), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 115/333 (34%), Positives = 180/333 (54%), Gaps = 41/333 (12%)

Query: 4   IGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDD 63
           + EA L   +E L + +  + + +F      + +  K      TI+AVL DA+EK+  D 
Sbjct: 1   MAEAFLQVLLENLTSFIGDKLVLIFG----FEKECEKLSSVFSTIQAVLQDAQEKQLKDK 56

Query: 64  SVKLWLGELQNLAYDVEDLLDEFQTEAFR-RKLLLGNGEPAAAHDQPSSSRTSTKSKFRK 122
           +++ WL +L + AY+V+D+L E + EA R  +  LG   P                    
Sbjct: 57  AIENWLQKLNSAAYEVDDILGECKNEAIRFEQSRLGFYHPGI------------------ 98

Query: 123 LIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDT 182
                        I F + +  ++K+I ++   I EE      ++      + A   R+T
Sbjct: 99  -------------INFRHKIGRRMKEIMEKLDAISEERRKFHFLEKITE-RQAAAATRET 144

Query: 183 TSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV 242
             ++ E KVYGR+ E+ EIV++L+ + +  +    V PIIGMGGLGKTTLAQ+++ND++V
Sbjct: 145 GFVLTEPKVYGRDKEEDEIVKILINNVNVAEE-LPVFPIIGMGGLGKTTLAQMIFNDERV 203

Query: 243 EDHFDLKAWTCVSDDFDVIRLTKSILLSIA-SDQNVDNHDLNKLQEELKKQLFGKKFLLV 301
             HF+ K W CVSDDFD  RL K+I+ +I  S  +V+  DL   Q++L++ L GK++LLV
Sbjct: 204 TKHFNPKIWVCVSDDFDEKRLIKTIIGNIERSSPHVE--DLASFQKKLQELLNGKRYLLV 261

Query: 302 LDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR 334
           LDDVWN++   W  L      GA+G+ I+ TTR
Sbjct: 262 LDDVWNDDLEKWAKLRAVLTVGARGASILATTR 294

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 which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q9LRR5|DRL21_ARATH Putative disease resistance protein At3g14460 OS=Arabidopsis thaliana GN=At3g14460 PE=3 SV=1

 Score =  156 bits (394), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 104/335 (31%), Positives = 176/335 (52%), Gaps = 25/335 (7%)

Query: 4   IGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVK-WKKKLVTIKAVLDDAEEKKTTD 62
           +  + L++   ++V ++ +    +   +G+    L+K  K  LVT   VL DA+++    
Sbjct: 1   MANSYLSSCANVMVERINTSQELVELCKGKSSSALLKRLKVALVTANPVLADADQRAEHV 60

Query: 63  DSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRK 122
             VK WL  +++  +  ED+LDE QTEA RR+++   G          + R + + K   
Sbjct: 61  REVKHWLTGIKDAFFQAEDILDELQTEALRRRVVAEAGGLGGLFQNLMAGREAIQKKIEP 120

Query: 123 LIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKA-RQRRD 181
                               M K+ ++ +      E IG  +  ++     ++A R R D
Sbjct: 121 -------------------KMEKVVRLLEHHVKHIEVIGLKEYSETREPQWRQASRSRPD 161

Query: 182 TTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ 241
               + + ++ GR  +K  +V LLL DD  + G  +VI ++GM G+GKTTL ++V+ND +
Sbjct: 162 D---LPQGRLVGRVEDKLALVNLLLSDDEISIGKPAVISVVGMPGVGKTTLTEIVFNDYR 218

Query: 242 VEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLV 301
           V +HF++K W     +F+V  +TK++L  I S   V+  DL  LQ +LKK L GK+FLLV
Sbjct: 219 VTEHFEVKMWISAGINFNVFTVTKAVLQDITSSA-VNTEDLPSLQIQLKKTLSGKRFLLV 277

Query: 302 LDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
           LDD W+E+ ++W    + F    +GSKI++TTR++
Sbjct: 278 LDDFWSESDSEWESFQVAFTDAEEGSKIVLTTRSE 312

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q38834|R13L4_ARATH Disease resistance RPP13-like protein 4 OS=Arabidopsis thaliana GN=RPP13L4 PE=2 SV=2

 Score =  128 bits (321), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 93/334 (27%), Positives = 179/334 (53%), Gaps = 40/334 (11%)

Query: 6   EAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSV 65
           +A++T  +E  +N L  +G  +   + +++D     + +L  +++ L DAE +K T++++
Sbjct: 3   DAVVTVFLEKTLNILEEKGRTVSDYRKQLED----LQSELKYMQSFLKDAERQKRTNETL 58

Query: 66  KLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKLIP 125
           +  + +L+ L Y+ ED+L + Q         L +G+         + + S+ +   +L P
Sbjct: 59  RTLVADLRELVYEAEDILVDCQ---------LADGDDG-------NEQRSSNAWLSRLHP 102

Query: 126 TCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGS-LKLIKSSAGGSKKARQRRDTTS 184
              P          Y    ++++IN+R   I+ ++    + I  S  G      R  ++ 
Sbjct: 103 ARVP--------LQYKKSKRLQEINERITKIKSQVEPYFEFITPSNVGRDNGTDRW-SSP 153

Query: 185 LVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED 244
           + +  +V G E +K++I E L +    ND    ++  +GMGGLGKTT+AQ V+NDK++E 
Sbjct: 154 VYDHTQVVGLEGDKRKIKEWLFRS---NDSQLLIMAFVGMGGLGKTTIAQEVFNDKEIEH 210

Query: 245 HFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDD 304
            F+ + W  VS  F   ++ +SIL ++  D +V + D+  L  ++++ L GK++L+V+DD
Sbjct: 211 RFERRIWVSVSQTFTEEQIMRSILRNLG-DASVGD-DIGTLLRKIQQYLLGKRYLIVMDD 268

Query: 305 VWNENYTDW--VHLSLPFQAGAQGSKIIVTTRNQ 336
           VW++N + W  ++  LP     QG  +IVTTR++
Sbjct: 269 VWDKNLSWWDKIYQGLP---RGQGGSVIVTTRSE 299

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M667|RPP13_ARATH Disease resistance protein RPP13 OS=Arabidopsis thaliana GN=RPP13 PE=2 SV=2

 Score =  119 bits (298), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 102/340 (30%), Positives = 163/340 (47%), Gaps = 47/340 (13%)

Query: 8   ILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSVKL 67
           ++ A  E +V K+ +  I   +    +K+DL + K +L  I   L D E ++  D+  K 
Sbjct: 1   MVDAITEFVVGKIGNYLIEEASMFMAVKEDLEELKTELTCIHGYLKDVEAREREDEVSKE 60

Query: 68  WLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKLIPTC 127
           W   + + AYDVED+LD +  +   R              Q    R  T    RK+    
Sbjct: 61  WSKLVLDFAYDVEDVLDTYHLKLEER-------------SQRRGLRRLTNKIGRKMDA-- 105

Query: 128 CPTFTLQSIQFDYSMMSKIKKINDRFRDIEEE-----IGSLKLIKSSAGG---SKKARQR 179
                       YS++  I+ +  R  DI  +     IG LK  +   GG   S + RQ 
Sbjct: 106 ------------YSIVDDIRILKRRILDITRKRETYGIGGLK--EPQGGGNTSSLRVRQL 151

Query: 180 RDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND 239
           R   S+ +E  V G E + K ++E LL  + +N     +I I GMGGLGKT LA+ +YN 
Sbjct: 152 RRARSVDQEEVVVGLEDDAKILLEKLLDYEEKNR---FIISIFGMGGLGKTALARKLYNS 208

Query: 240 KQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKL-QEELKKQLF---- 294
           + V++ F+ +AWT VS ++    +   I+ S+      +   + K  +EEL+  L+    
Sbjct: 209 RDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGEELEKIRKFAEEELEVYLYGLLE 268

Query: 295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR 334
           GKK+L+V+DD+W     D +  +LP     +GS++I+TTR
Sbjct: 269 GKKYLVVVDDIWEREAWDSLKRALP--CNHEGSRVIITTR 306

Disease resistance protein. 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. In contrast to other resistance proteins, it works independently of ESD1 and NSD1 proteins and does not require the accumulation of salicylic acid, suggesting the existence of an independent signaling pathway. The specificity to avirulence proteins differs in the different cultivars.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJK8|RP8L4_ARATH Probable disease resistance RPP8-like protein 4 OS=Arabidopsis thaliana GN=RPP8L4 PE=2 SV=1

 Score =  110 bits (276), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 99/342 (28%), Positives = 168/342 (49%), Gaps = 48/342 (14%)

Query: 4   IGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDD 63
           + E  ++  +E L + L+ E  RL   QG I + L   K++L +++++L DA+ KK   D
Sbjct: 1   MAEGFVSFGLEKLWDLLSRESERL---QG-IDEQLDGLKRQLRSLQSLLKDADAKKHGSD 56

Query: 64  SVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKL 123
            V+ +L ++++L +D ED+++ +     R     G G+    H +  +   + + K    
Sbjct: 57  RVRNFLEDVKDLVFDAEDIIESYVLNKLR-----GEGKGVKKHVRRLARFLTDRHK---- 107

Query: 124 IPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSL---KLIKSSAGGSKKARQR- 179
                             + S I+ I  R  D+  E+ S    ++I      S + RQR 
Sbjct: 108 ------------------VASDIEGITKRISDVIGEMQSFGIQQIIDGVRSLSLQERQRV 149

Query: 180 ----RDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQL 235
               R T     E+ + G E   +E+V  L+++D      + V+ I GMGG+GKTTLA+ 
Sbjct: 150 QREIRQTYPDSSESDLVGVEQSVEELVGHLVENDI-----YQVVSIAGMGGIGKTTLARQ 204

Query: 236 VYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSI-ASDQNVDNHDLNKLQEELKKQLF 294
           V++   V  HFD  AW CVS  F +  + + IL  +   D N+   D + LQ +L + L 
Sbjct: 205 VFHHDLVRRHFDGFAWVCVSQQFTLKHVWQRILQELQPHDGNILQMDESALQPKLFQLLE 264

Query: 295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
             ++LLVLDDVW +   DW  +   F    +G K+++T+RN+
Sbjct: 265 TGRYLLVLDDVWKKE--DWDRIKAVFPR-KRGWKMLLTSRNE 303

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W3K3|DRL8_ARATH Putative disease resistance protein At1g58400 OS=Arabidopsis thaliana GN=At1g58400 PE=3 SV=1

 Score =  109 bits (273), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 96/341 (28%), Positives = 164/341 (48%), Gaps = 49/341 (14%)

Query: 6   EAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSV 65
           EAI++  VE L ++L  E  +    QG ++D + + K  L  +K+ L DAE KK T   V
Sbjct: 3   EAIVSFGVEKLWDRLTQEYEQF---QG-VEDRIAELKSNLNLLKSFLKDAEAKKNTSQMV 58

Query: 66  KLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKLIP 125
           +  + E++ + YD E++++ F  +   RK                  R+    +  KL  
Sbjct: 59  RHCVEEIKEIVYDTENMIETFILKEAARK------------------RSGIIRRITKL-- 98

Query: 126 TCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSK-------KARQ 178
           TC            +   S I  I+ R   + +++ S  + +  + GS+       + R+
Sbjct: 99  TCIKVHR-------WEFASDIGGISKRISKVIQDMHSFGVQQMISDGSQSSHLLQERERE 151

Query: 179 RRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN 238
            R T S   E+   G E   K++V  L+++D        ++ + GMGGLGKTTLA+ V+N
Sbjct: 152 MRQTFSRGYESDFVGLEVNVKKLVGYLVEEDD-----IQIVSVTGMGGLGKTTLARQVFN 206

Query: 239 DKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVD---NHDLNKLQEELKKQLFG 295
            + V+  FD  AW CVS +F    + + IL ++ S +  D     +  +L +EL + L  
Sbjct: 207 HEDVKHQFDRLAWVCVSQEFTRKNVWQMILQNLTSRETKDEILQMEEAELHDELFQLLET 266

Query: 296 KKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
            K L+V DD+W E   DW  ++ P     +G K+++T+R +
Sbjct: 267 SKSLIVFDDIWKEE--DWGLIN-PIFPPKKGWKVLITSRTE 304

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	337
147862409	1466	hypothetical protein VITISV_042289 [Viti	0.949	0.218	0.535	1e-91
359487182	2283	PREDICTED: putative disease resistance p	0.949	0.140	0.532	5e-91
359487188	1292	PREDICTED: putative disease resistance R	0.952	0.248	0.522	9e-88
359487172	1310	PREDICTED: putative disease resistance R	0.958	0.246	0.501	1e-84
296087855	992	unnamed protein product [Vitis vinifera]	0.958	0.325	0.498	3e-83
359487170	1293	PREDICTED: putative disease resistance R	0.958	0.249	0.498	4e-83
359495026	2204	PREDICTED: uncharacterized protein LOC10	0.952	0.145	0.497	5e-83
225465831	1483	PREDICTED: putative disease resistance R	0.955	0.217	0.497	9e-83
147860511	1406	hypothetical protein VITISV_014536 [Viti	0.952	0.228	0.497	9e-83
359495024	1390	PREDICTED: putative disease resistance p	0.952	0.230	0.497	1e-82

>gi|147862409|emb|CAN81911.1| hypothetical protein VITISV_042289 [Vitis vinifera]

 Score =  342 bits (877), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 180/336 (53%), Positives = 240/336 (71%), Gaps = 16/336 (4%)

Query: 1   MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKT 60
           M+ +GEAIL+A  E L  KLAS  +  FARQ ++  +L KW+K L+ I AVLDDAEEK+ 
Sbjct: 1   MAFVGEAILSALFETLFFKLASSDLLKFARQEQVHAELKKWEKILLKIHAVLDDAEEKQM 60

Query: 61  TDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKF 120
           TD  VK+WL EL++LAYDVED+LDEF TEA RRKL+        A  +PS+S   +    
Sbjct: 61  TDRLVKIWLDELRDLAYDVEDILDEFGTEALRRKLM--------AETEPSTSMVCS---- 108

Query: 121 RKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRR 180
             LIP+CC +F   +++F+  M SKI++I  R ++I  +   L L +++ G S   + R 
Sbjct: 109 --LIPSCCTSFNPSTVRFNVKMGSKIEEITARLQEISGQKNDLHLRENAGGSSYTMKSRL 166

Query: 181 DTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK 240
            TTSLV+E++VYGRET+K+ I+ LLLKD+  +D    VIPI+GMGG+GKTTLAQL +ND 
Sbjct: 167 PTTSLVDESRVYGRETDKEAILNLLLKDEPSDD-EVCVIPIVGMGGIGKTTLAQLAFNDC 225

Query: 241 QVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLL 300
           +VEDHFDL+AW CVSDDFDV+R+TK+IL S++ D + D +DLN LQ  LK++L G KFLL
Sbjct: 226 KVEDHFDLRAWVCVSDDFDVVRVTKTILQSVSLDTH-DVNDLNLLQVMLKEKLSGNKFLL 284

Query: 301 VLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
           VLDDVWNEN  +W  L  P +AGA GSK+I+TTRN+
Sbjct: 285 VLDDVWNENCEEWDILCSPMRAGAPGSKVIITTRNK 320

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487182|ref|XP_003633528.1| PREDICTED: putative disease resistance protein At3g14460-like [Vitis vinifera]

 Score =  340 bits (873), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 179/336 (53%), Positives = 240/336 (71%), Gaps = 16/336 (4%)

Query: 1    MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKT 60
            M+ +GEAIL+A  E L  KLAS  +  FARQ ++  +L KW+K L+ I AVLDDAEEK+ 
Sbjct: 1012 MAFVGEAILSALFETLFFKLASSDLLKFARQEQVHAELKKWEKILLKIHAVLDDAEEKQM 1071

Query: 61   TDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKF 120
            TD  VK+WL EL++LAYDVED+LDEF TEA RRKL+        A  +PS+S   +    
Sbjct: 1072 TDRLVKIWLDELRDLAYDVEDILDEFGTEALRRKLM--------AETEPSTSMVCS---- 1119

Query: 121  RKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRR 180
              LIP+CC +F   +++F+  M SKI++I  R ++I  +   L L +++ G S   + R 
Sbjct: 1120 --LIPSCCTSFNPSTVRFNVKMGSKIEEITARLQEISGQKNDLHLRENAGGSSYTMKSRL 1177

Query: 181  DTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK 240
             TTSLV+E++VYGRET+K+ I+ LLLKD+  +D    VIPI+GMGG+GKTTLAQL +ND 
Sbjct: 1178 PTTSLVDESRVYGRETDKEAILNLLLKDEPSDD-EVCVIPIVGMGGIGKTTLAQLAFNDC 1236

Query: 241  QVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLL 300
            +V+DHFDL+AW CVSDDFDV+R+TK+IL S++ D + D +DLN LQ  LK++L G KFLL
Sbjct: 1237 KVKDHFDLRAWVCVSDDFDVVRVTKTILQSVSLDTH-DVNDLNLLQVMLKEKLSGNKFLL 1295

Query: 301  VLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
            VLDDVWNEN  +W  L  P +AGA GSK+I+TTRN+
Sbjct: 1296 VLDDVWNENCEEWDILCSPMRAGAPGSKVIITTRNK 1331

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487188|ref|XP_003633529.1| PREDICTED: putative disease resistance RPP13-like protein 1-like, partial [Vitis vinifera]

 Score =  329 bits (844), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 176/337 (52%), Positives = 236/337 (70%), Gaps = 16/337 (4%)

Query: 1   MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKT 60
           M+ +GEA L++  + L+++L S  +  +ARQ ++  +L KW+K L  I AVL+DAEEK+ 
Sbjct: 4   MAFVGEAFLSSFFKTLLDELISSDLLDYARQVQVHAELNKWEKTLKKIHAVLEDAEEKQM 63

Query: 61  TDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKF 120
            +  VK+WL +L++LAYDVED+LDE  TEA  RKL+        A  QPS+S      KF
Sbjct: 64  ENQVVKIWLDDLRDLAYDVEDILDELATEALGRKLM--------AETQPSTS------KF 109

Query: 121 RKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGG-SKKARQR 179
           R LIP+CC +FT  +I+F+  M SKI+KI +R +DI  +  +L L +   G  S KA + 
Sbjct: 110 RSLIPSCCTSFTPSAIKFNVKMRSKIEKITERLQDISSQQNNLLLTEKVTGKRSAKATEI 169

Query: 180 RDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND 239
             TTSLV+E++V GRET+K  I++LLL D   +D    VIPIIGMGG+GKTTLAQL YND
Sbjct: 170 LPTTSLVDESRVCGRETDKAAILDLLLHDHEPSDDAVRVIPIIGMGGVGKTTLAQLAYND 229

Query: 240 KQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFL 299
            +VE HFDL+ W CVSDDFDV+R+TK+I+ S+ASD + D +DLN LQ +LK++L G KFL
Sbjct: 230 DKVESHFDLRVWACVSDDFDVLRVTKTIVQSVASDMS-DFNDLNLLQVKLKEKLSGTKFL 288

Query: 300 LVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
           LVLDDVWN+N   W  L  P + GAQGS++IVTTRNQ
Sbjct: 289 LVLDDVWNQNCDKWDTLYAPMRTGAQGSRVIVTTRNQ 325

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487172|ref|XP_002264364.2| PREDICTED: putative disease resistance RPP13-like protein 1-like [Vitis vinifera]

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 168/335 (50%), Positives = 229/335 (68%), Gaps = 12/335 (3%)

Query: 3   IIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTD 62
            +GEAIL+  ++ L++ +    +  FA +G +  +L KWKK L+ I AVL DAEEK+ TD
Sbjct: 4   FVGEAILSGFIQKLIDMVNPPELWNFASEGHVHSELNKWKKILMKIYAVLHDAEEKQMTD 63

Query: 63  DSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRK 122
             VK+WL EL +LAYDVED+LD F T+A RR L+        A   PS ++ ST SK R 
Sbjct: 64  PLVKMWLDELGDLAYDVEDILDGFVTQALRRNLM--------AETHPSGTQPST-SKLRS 114

Query: 123 LIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAG-GSKKARQRRD 181
           LIP+CC +FT  +I+F+  M SKIKKI  R ++I  +   L L ++ AG  S K R+   
Sbjct: 115 LIPSCCTSFTPNAIKFNAEMWSKIKKITARLQEISAQKNDLHLRENIAGESSTKTREILP 174

Query: 182 TTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ 241
           TTSLV+E++VYGRET+K  I  LLL+DD   D    VIP++GM G+GKTTLAQL +ND +
Sbjct: 175 TTSLVDESRVYGRETDKAAIANLLLRDDPCTD-EVCVIPVVGMAGIGKTTLAQLAFNDDE 233

Query: 242 VEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLV 301
           ++ HFDL+ W  VSDDFDV+++TK+IL S++ +   D +DLN LQ  L++ L GKKFLL+
Sbjct: 234 IKAHFDLRVWVYVSDDFDVLKITKTILQSVSPNTQ-DVNDLNLLQMTLREGLSGKKFLLI 292

Query: 302 LDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
           LDDVWNEN+  W  L +P ++G  GSK+IVTTRN+
Sbjct: 293 LDDVWNENFDSWDFLCMPMRSGEPGSKLIVTTRNE 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087855|emb|CBI35111.3| unnamed protein product [Vitis vinifera]

 Score =  315 bits (806), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 167/335 (49%), Positives = 225/335 (67%), Gaps = 12/335 (3%)

Query: 3   IIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTD 62
            +GEA+L+  ++ L++ + S  +  FA +  +  +L KWKK L  I  VL DAEEK  TD
Sbjct: 4   FVGEAVLSGLIQKLIDMVTSPELWNFASEEHVHSELNKWKKILTKIYVVLHDAEEKHMTD 63

Query: 63  DSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRK 122
             VK+WL EL +LAYDVED+LD F TEA RR L+        A   PS ++ ST SK R 
Sbjct: 64  PLVKMWLDELGDLAYDVEDILDSFATEALRRNLM--------AETLPSGTQPST-SKLRS 114

Query: 123 LIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGG-SKKARQRRD 181
           LIP+CC +FT  SI+F+  M SK KKI    ++I  +   L L ++ AG  S K R+   
Sbjct: 115 LIPSCCTSFTPNSIKFNAEMWSKFKKITAGLQEISAQKNDLHLTENIAGKRSTKTREILP 174

Query: 182 TTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ 241
           TTSLV+E++VYGRET+K  I  LLL+DDS  D    VIP++GM G+GKTTLAQL +ND +
Sbjct: 175 TTSLVDESRVYGRETDKAAIANLLLRDDSCTD-EVCVIPVVGMAGIGKTTLAQLAFNDDE 233

Query: 242 VEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLV 301
           V+ HFDL+ W  VSDD+DV+++TK+IL S++ +   D +DLN LQ  L++ L GKKFLL+
Sbjct: 234 VKAHFDLRVWVYVSDDYDVLKITKTILQSVSPNTQ-DVNDLNLLQMALRENLSGKKFLLI 292

Query: 302 LDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
           LDDVWNEN+  W  L +P ++G  GSK+IVTTRN+
Sbjct: 293 LDDVWNENHDSWEFLCMPMRSGTPGSKLIVTTRNE 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487170|ref|XP_002264316.2| PREDICTED: putative disease resistance RPP13-like protein 1-like [Vitis vinifera]

 Score =  314 bits (804), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 167/335 (49%), Positives = 225/335 (67%), Gaps = 12/335 (3%)

Query: 3   IIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTD 62
            +GEA+L+  ++ L++ + S  +  FA +  +  +L KWKK L  I  VL DAEEK  TD
Sbjct: 4   FVGEAVLSGLIQKLIDMVTSPELWNFASEEHVHSELNKWKKILTKIYVVLHDAEEKHMTD 63

Query: 63  DSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRK 122
             VK+WL EL +LAYDVED+LD F TEA RR L+        A   PS ++ ST SK R 
Sbjct: 64  PLVKMWLDELGDLAYDVEDILDSFATEALRRNLM--------AETLPSGTQPST-SKLRS 114

Query: 123 LIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGG-SKKARQRRD 181
           LIP+CC +FT  SI+F+  M SK KKI    ++I  +   L L ++ AG  S K R+   
Sbjct: 115 LIPSCCTSFTPNSIKFNAEMWSKFKKITAGLQEISAQKNDLHLTENIAGKRSTKTREILP 174

Query: 182 TTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ 241
           TTSLV+E++VYGRET+K  I  LLL+DDS  D    VIP++GM G+GKTTLAQL +ND +
Sbjct: 175 TTSLVDESRVYGRETDKAAIANLLLRDDSCTD-EVCVIPVVGMAGIGKTTLAQLAFNDDE 233

Query: 242 VEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLV 301
           V+ HFDL+ W  VSDD+DV+++TK+IL S++ +   D +DLN LQ  L++ L GKKFLL+
Sbjct: 234 VKAHFDLRVWVYVSDDYDVLKITKTILQSVSPNTQ-DVNDLNLLQMALRENLSGKKFLLI 292

Query: 302 LDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
           LDDVWNEN+  W  L +P ++G  GSK+IVTTRN+
Sbjct: 293 LDDVWNENHDSWEFLCMPMRSGTPGSKLIVTTRNE 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495026|ref|XP_003634900.1| PREDICTED: uncharacterized protein LOC100854556 [Vitis vinifera]

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 167/336 (49%), Positives = 233/336 (69%), Gaps = 15/336 (4%)

Query: 1   MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKT 60
           M+ +GEA L+AS++ LV+ LA   +R FAR+ ++  +L KW+  L+ I AVL DAEEK+ 
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKF 120
           T+  V++WL EL++LAYDVED+LD+F TEA RRKL+  +        QPS+S   +    
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRKLITDD-------PQPSTSTVRSIISS 113

Query: 121 RKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQR- 179
                     F   ++ ++ +M SK+++I  R  +I  + G L L ++    S + R+R 
Sbjct: 114 LSS------RFNPNALVYNLNMGSKLEEITARLHEISTQKGDLDLRENVEERSNRKRKRV 167

Query: 180 RDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND 239
            +TTSLV E++VYGRET+K+ I+E+LL+D+S +D    VIPI+GMGG+GKTTLAQL Y+D
Sbjct: 168 PETTSLVVESRVYGRETDKEAILEVLLRDESIHDNEVCVIPIVGMGGVGKTTLAQLAYHD 227

Query: 240 KQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFL 299
            +V++HFDL+AW CVSDDFDV+R+TK++L SIAS     N DLN LQ +LK++L GKKFL
Sbjct: 228 DRVKNHFDLRAWVCVSDDFDVLRITKTLLQSIASYAREIN-DLNLLQVKLKEKLSGKKFL 286

Query: 300 LVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN 335
           LVLDDVWNENY  W  L  P +AG  GSK+I+TTRN
Sbjct: 287 LVLDDVWNENYDKWDRLCTPLRAGGPGSKVIITTRN 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225465831|ref|XP_002264750.1| PREDICTED: putative disease resistance RPP13-like protein 1-like [Vitis vinifera]

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 167/336 (49%), Positives = 230/336 (68%), Gaps = 14/336 (4%)

Query: 3   IIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTD 62
            +GEA+L+  +E L + + S  +  FA +  +  +L KWK  L+ I AVL DAEEK+ T+
Sbjct: 4   FVGEAVLSVFIEKLADMVTSPELWNFASEELVHSELNKWKTILMKIYAVLHDAEEKQMTN 63

Query: 63  DSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRK 122
             VK+WL EL +LAYDVED+LD F TE+ RR L+        A   PS +  ST SK   
Sbjct: 64  PRVKMWLDELGDLAYDVEDILDGFATESLRRNLM--------AETHPSGTERST-SKLWS 114

Query: 123 LIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAG-GSKKARQRRD 181
           LIP+CC +FT  +I+F+  M+SKIK I    ++I  +   L L ++ +G  S K R+   
Sbjct: 115 LIPSCCTSFTPNAIKFNAEMLSKIKMITTSLQEISAQKSDLHLTENISGERSTKTREILP 174

Query: 182 TTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ 241
           TTSLV+E++VYGRET+K+ I  LLL+DD   D    VIP++GM G+GKTTL QL +ND +
Sbjct: 175 TTSLVDESRVYGRETDKEAIANLLLRDDPSTD-EICVIPVVGMAGIGKTTLTQLAFNDDE 233

Query: 242 VEDHFDLKAWTCVSDDFDVIRLTKSILLSIA-SDQNVDNHDLNKLQEELKKQLFGKKFLL 300
           V+DHFDL+ W  VSDDFDV+++TK+IL S++ + QNVD  DLN LQ EL+++L G+KFLL
Sbjct: 234 VKDHFDLRVWVYVSDDFDVLKITKTILQSVSLATQNVD--DLNLLQMELREKLSGQKFLL 291

Query: 301 VLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
           +LDDVWNE+Y  W  L +P ++GA GSK+IVTTRN+
Sbjct: 292 ILDDVWNESYDSWDLLCMPMRSGAPGSKLIVTTRNE 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860511|emb|CAN79726.1| hypothetical protein VITISV_014536 [Vitis vinifera]

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 167/336 (49%), Positives = 232/336 (69%), Gaps = 15/336 (4%)

Query: 1   MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKT 60
           M+ +GEA L+AS++ LV+ LA   +R FAR+ ++  +L KW+  L+ I AVL DAEEK+ 
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKF 120
           T+  V++WL EL++LAYDVED+LD+F TEA RR L+    +P     QPS+S   +    
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRNLI--KDDP-----QPSTSTVRSLISS 113

Query: 121 RKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQR- 179
                     F   ++ ++ +M SKI++I  R  +I  + G L L ++  G S + R+R 
Sbjct: 114 LSS------RFNPNALVYNLNMGSKIEEITARLHEISTQKGDLDLRENVEGRSHRKRKRV 167

Query: 180 RDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND 239
            +T SLV E++VYGRET+K+ I+E+LL+D+  +D    VIPI+GMGG+GKTTLAQL YND
Sbjct: 168 PETASLVVESRVYGRETDKEAILEVLLRDELIHDNEVCVIPIVGMGGVGKTTLAQLAYND 227

Query: 240 KQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFL 299
            +V++HFDL+AW CVSDDFDV+R+TK++L SIAS     N DLN LQ ++K++L GKKFL
Sbjct: 228 DRVKNHFDLRAWVCVSDDFDVLRITKTLLQSIASYTREIN-DLNLLQVKMKEKLSGKKFL 286

Query: 300 LVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN 335
           LVLDDVWNENY  W  L  P +AG  GSK+I+TTRN
Sbjct: 287 LVLDDVWNENYDKWDSLCTPLRAGGPGSKVIITTRN 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495024|ref|XP_002267933.2| PREDICTED: putative disease resistance protein At3g14460-like [Vitis vinifera]

 Score =  313 bits (801), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 167/336 (49%), Positives = 232/336 (69%), Gaps = 15/336 (4%)

Query: 1   MSIIGEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKT 60
           M+ +GEA L+AS++ LV+ LA   +R FAR+ ++  +L KW+  L+ I AVL DAEEK+ 
Sbjct: 1   MAFVGEAFLSASIQKLVDMLACPDLRKFAREEQVHAELKKWEGILLKIHAVLHDAEEKQM 60

Query: 61  TDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKF 120
           T+  V++WL EL++LAYDVED+LD+F TEA RR L+    +P     QPS+S   +    
Sbjct: 61  TNRFVQIWLAELRDLAYDVEDILDDFATEALRRNLI--KDDP-----QPSTSTVRSLISS 113

Query: 121 RKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQR- 179
                     F   ++ ++ +M SKI++I  R  +I  + G L L ++  G S + R+R 
Sbjct: 114 LSS------RFNPNALVYNLNMGSKIEEITARLHEISTQKGDLDLRENVEGRSHRKRKRV 167

Query: 180 RDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND 239
            +T SLV E++VYGRET+K+ I+E+LL+D+  +D    VIPI+GMGG+GKTTLAQL YND
Sbjct: 168 PETASLVVESRVYGRETDKEAILEVLLRDELIHDNEVCVIPIVGMGGVGKTTLAQLAYND 227

Query: 240 KQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFL 299
            +V++HFDL+AW CVSDDFDV+R+TK++L SIAS     N DLN LQ ++K++L GKKFL
Sbjct: 228 DRVKNHFDLRAWVCVSDDFDVLRITKTLLQSIASYTREIN-DLNLLQVKMKEKLSGKKFL 286

Query: 300 LVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN 335
           LVLDDVWNENY  W  L  P +AG  GSK+I+TTRN
Sbjct: 287 LVLDDVWNENYDKWDSLCTPLRAGGPGSKVIITTRN 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	337
TAIR|locus:2091672	1054	AT3G14470 [Arabidopsis thalian	0.560	0.179	0.386	3.6e-43
TAIR|locus:2091662	1424	AT3G14460 [Arabidopsis thalian	0.465	0.110	0.347	6.5e-29
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.569	0.225	0.303	3e-25
UNIPROTKB|O48647	1802	O48647 "XA1" [Oryza sativa (ta	0.522	0.097	0.345	1.6e-23
TAIR|locus:2075170	835	RPP13 "RECOGNITION OF PERONOSP	0.557	0.225	0.307	1.2e-21
TAIR|locus:2152536	908	AT5G48620 [Arabidopsis thalian	0.560	0.208	0.305	8e-18
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.566	0.225	0.296	1.4e-17
TAIR|locus:2037623	899	AT1G58410 [Arabidopsis thalian	0.537	0.201	0.299	2e-17
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.545	0.203	0.292	5.8e-17
TAIR|locus:2011982	857	AT1G50180 [Arabidopsis thalian	0.563	0.221	0.300	1e-16

TAIR|locus:2091672 AT3G14470 [Arabidopsis thaliana (taxid:3702)]

 Score = 349 (127.9 bits), Expect = 3.6e-43, Sum P(2) = 3.6e-43
 Identities = 75/194 (38%), Positives = 117/194 (60%)

Query:   144 SKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTTSLVEEAKVYGRETEKKEIVE 203
             ++++K+  R   +  +   L L + +A   K   QR  TTSLV+E++V+GR+ +K EI+ 
Sbjct:   128 TRLEKVTIRLERLASQRNILGLKELTAMIPK---QRLPTTSLVDESEVFGRDDDKDEIMR 184

Query:   204 LLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRL 263
              L+ ++ + D G +V+ I+G+GG+GKTTL+QL+YND+ V  +F  K W  VS++FDV ++
Sbjct:   185 FLIPENGK-DNGITVVAIVGIGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKI 243

Query:   264 TKSILLSIASDQ-NVDNHDLNXXXXXXXXXXXXXXXXXVLDDVWNENYTDWVHLSLPFQA 322
             TK +  S+ S      + D+                  VLDD+WNEN+ DW  L  PF  
Sbjct:   244 TKKVYESVTSRPCEFTDLDVLQVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQPFIH 303

Query:   323 GAQGSKIIVTTRNQ 336
              AQGS+I+VTTR+Q
Sbjct:   304 AAQGSQILVTTRSQ 317

GO:0005576 "extracellular region" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

TAIR|locus:2091662 AT3G14460 [Arabidopsis thaliana (taxid:3702)]

 Score = 266 (98.7 bits), Expect = 6.5e-29, Sum P(2) = 6.5e-29
 Identities = 56/161 (34%), Positives = 91/161 (56%)

Query:   176 ARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQL 235
             +R R D    + + ++ GR  +K  +V LLL DD  + G  +VI ++GM G+GKTTL ++
Sbjct:   156 SRSRPDD---LPQGRLVGRVEDKLALVNLLLSDDEISIGKPAVISVVGMPGVGKTTLTEI 212

Query:   236 VYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNXXXXXXXXXXXX 295
             V+ND +V +HF++K W     +F+V  +TK++L  I S   V+  DL             
Sbjct:   213 VFNDYRVTEHFEVKMWISAGINFNVFTVTKAVLQDITSSA-VNTEDLPSLQIQLKKTLSG 271

Query:   296 XXXXXVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ 336
                  VLDD W+E+ ++W    + F    +GSKI++TTR++
Sbjct:   272 KRFLLVLDDFWSESDSEWESFQVAFTDAEEGSKIVLTTRSE 312

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2078012 ZAR1 "HOPZ-ACTIVATED RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 250 (93.1 bits), Expect = 3.0e-25, Sum P(2) = 3.0e-25
 Identities = 62/204 (30%), Positives = 107/204 (52%)

Query:   136 IQFDYSMMSKIKKINDRFRDIEEEIGS-LKLIKSSAGGSKKARQRRDTTSLVEEAKVYGR 194
             +   Y    ++++IN+R   I+ ++    + I  S  G      R  ++ + +  +V G 
Sbjct:   105 VPLQYKKSKRLQEINERITKIKSQVEPYFEFITPSNVGRDNGTDRW-SSPVYDHTQVVGL 163

Query:   195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV 254
             E +K++I E L +    ND    ++  +GMGGLGKTT+AQ V+NDK++E  F+ + W  V
Sbjct:   164 EGDKRKIKEWLFRS---NDSQLLIMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSV 220

Query:   255 SDDFDVIRLTKSILLSIASDQNVDNHDLNXXXXXXXXXXXXXXXXXVLDDVWNENYTDW- 313
             S  F   ++ +SIL ++  D +V + D+                  V+DDVW++N + W 
Sbjct:   221 SQTFTEEQIMRSILRNLG-DASVGD-DIGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWD 278

Query:   314 -VHLSLPFQAGAQGSKIIVTTRNQ 336
              ++  LP   G QG  +IVTTR++
Sbjct:   279 KIYQGLP--RG-QGGSVIVTTRSE 299

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

UNIPROTKB|O48647 O48647 "XA1" [Oryza sativa (taxid:4530)]

 Score = 256 (95.2 bits), Expect = 1.6e-23, Sum P(2) = 1.6e-23
 Identities = 68/197 (34%), Positives = 102/197 (51%)

Query:   156 IEEEIGS-LKLIKSSAGGSKKARQ------RRDTTSLVEEAKVYGRETEKKEIVELLLKD 208
             +EE +   ++L +SS+  S ++RQ         T+S + E  VYGR  E + I +L++  
Sbjct:   257 LEEAVNEVMRLCRSSS--SNQSRQGTPPATNATTSSYLPEPIVYGRAAEMETIKQLIM-- 312

Query:   209 DSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL 268
              S    G +V+PI+G GG+GKTTLAQLV  D  ++  F++K W  VSD FDV+++T+ IL
Sbjct:   313 -SNRSNGITVLPIVGNGGIGKTTLAQLVCKDLVIKSQFNVKIWVYVSDKFDVVKITRQIL 371

Query:   269 LSIASDQNVDNHDLNXXXXXXXXXXXXXXXXXVLDDVWNENYTDWVHLSLPF-------- 320
               +++  +    +L+                 VLDDVW     DW  L  P         
Sbjct:   372 DHVSNQSHEGISNLDTLQQDLEEQMKSKKFLIVLDDVWEIRTDDWKKLLAPLRPNDQVNS 431

Query:   321 -QAGAQGSKIIVTTRNQ 336
              Q  A G+ II+TTR Q
Sbjct:   432 SQEEATGNMIILTTRIQ 448

GO:0006915 "apoptotic process" evidence=IGI

GO:0006952 "defense response" evidence=IGI

TAIR|locus:2075170 RPP13 "RECOGNITION OF PERONOSPORA PARASITICA 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 218 (81.8 bits), Expect = 1.2e-21, Sum P(2) = 1.2e-21
 Identities = 64/208 (30%), Positives = 106/208 (50%)

Query:   140 YSMMSKIKKINDRFRDIEEE-----IGSLKLIKSSAGG---SKKARQRRDTTSLVEEAKV 191
             YS++  I+ +  R  DI  +     IG LK  +   GG   S + RQ R   S+ +E  V
Sbjct:   106 YSIVDDIRILKRRILDITRKRETYGIGGLK--EPQGGGNTSSLRVRQLRRARSVDQEEVV 163

Query:   192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAW 251
              G E + K ++E LL  + +N   F +I I GMGGLGKT LA+ +YN + V++ F+ +AW
Sbjct:   164 VGLEDDAKILLEKLLDYEEKNR--F-IISIFGMGGLGKTALARKLYNSRDVKERFEYRAW 220

Query:   252 TCVSDDF---DVI-RLTKSILLSIASD-QNVDNHDLNXXXXXXXXXXXXXXXXXVLDDVW 306
             T VS ++   D++ R+ +S+ ++   + + +                       V+DD+W
Sbjct:   221 TYVSQEYKTGDILMRIIRSLGMTSGEELEKIRKFAEEELEVYLYGLLEGKKYLVVVDDIW 280

Query:   307 NENYTDWVHLSLPFQAGAQGSKIIVTTR 334
                  D +  +LP     +GS++I+TTR
Sbjct:   281 EREAWDSLKRALP--CNHEGSRVIITTR 306

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=TAS

GO:0009814 "defense response, incompatible interaction" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

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

TAIR|locus:2152536 AT5G48620 [Arabidopsis thaliana (taxid:3702)]

 Score = 199 (75.1 bits), Expect = 8.0e-18, Sum P(2) = 8.0e-18
 Identities = 63/206 (30%), Positives = 98/206 (47%)

Query:   140 YSMMSKIKKINDRFRDIEEEIGSL---KLIKSSAGGSKKARQR-----RDTTSLVEEAKV 191
             + + S I+ I  R  D+  E+ S    ++I      S + RQR     R T     E+ +
Sbjct:   106 HKVASDIEGITKRISDVIGEMQSFGIQQIIDGVRSLSLQERQRVQREIRQTYPDSSESDL 165

Query:   192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAW 251
              G E   +E+V  L+++D      + V+ I GMGG+GKTTLA+ V++   V  HFD  AW
Sbjct:   166 VGVEQSVEELVGHLVENDI-----YQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAW 220

Query:   252 TCVSDDFDVIRLTKSILLSIAS-DQNVDNHDLNXXXXXXXXXXXXXXXXXVLDDVWNENY 310
              CVS  F +  + + IL  +   D N+   D +                 VLDDVW +  
Sbjct:   221 VCVSQQFTLKHVWQRILQELQPHDGNILQMDESALQPKLFQLLETGRYLLVLDDVWKKE- 279

Query:   311 TDWVHLSLPFQAGAQGSKIIVTTRNQ 336
              DW  +   F    +G K+++T+RN+
Sbjct:   280 -DWDRIKAVFPR-KRGWKMLLTSRNE 303

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:504956483 AT3G46730 [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 1.4e-17, Sum P(2) = 1.4e-17
 Identities = 61/206 (29%), Positives = 101/206 (49%)

Query:   140 YSMMSKIKKINDRFRDIEEE-----IGSLKLIKSSAGGSKKARQRRDTTSLVEEAKVYGR 194
             Y+++  I+ +  R  DI  +     IGS    +     + + RQ R    + +E  V G 
Sbjct:   106 YNIVEDIRTLKRRILDITRKRETFGIGSFNEPRGENITNVRVRQLRRAPPVDQEELVVGL 165

Query:   195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV 254
             E + K ++  LL D+ + D  + +I I GMGGLGKT LA+ +YN   V+  FD +AWT V
Sbjct:   166 EDDVKILLVKLLSDNEK-DKSY-IISIFGMGGLGKTALARKLYNSGDVKRRFDCRAWTYV 223

Query:   255 SDDF---DV-IRLTKSI-LLSIASDQNVDNHDLNXXXXXXXXXXXXXXXXXVL-DDVWNE 308
             S ++   D+ IR+ +S+ ++S    + +   + +                 V+ DDVW+ 
Sbjct:   224 SQEYKTRDILIRIIRSLGIVSAEEMEKIKMFEEDEELEVYLYGLLEGKNYMVVVDDVWDP 283

Query:   309 NYTDWVHLSLPFQAGAQGSKIIVTTR 334
             +   W  L        +GSK+I+TTR
Sbjct:   284 DA--WESLKRALPCDHRGSKVIITTR 307

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037623 AT1G58410 [Arabidopsis thaliana (taxid:3702)]

 Score = 201 (75.8 bits), Expect = 2.0e-17, Sum P(2) = 2.0e-17
 Identities = 59/197 (29%), Positives = 95/197 (48%)

Query:   147 KKINDRFRDIEEEIGSLKLIKSSAGGS----KKARQRRDTTSLVEEAKVYGRETEKKEIV 202
             K+I+   +D++   G  ++I   +  S    ++ R+ R T S   E    G E   K++V
Sbjct:   115 KRISKVIQDMQS-FGVQQIITDGSRSSHPLQERQREMRHTFSRDSENDFVGMEANVKKLV 173

Query:   203 ELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIR 262
               L++ D      + ++ + GMGGLGKTTLA+ V+N   V+D FD  AW  VS +F  I 
Sbjct:   174 GYLVEKDD-----YQIVSLTGMGGLGKTTLARQVFNHDVVKDRFDGFAWVSVSQEFTRIS 228

Query:   263 LTKSILLSIASDQNVD---NHDLNXXXXXXXXXXXXXXXXXVLDDVWNENYTDWVHLSLP 319
             + ++IL ++ S +  D   N                     VLDD+W E   DW  L  P
Sbjct:   229 VWQTILQNLTSKERKDEIQNMKEADLHDDLFRLLESSKTLIVLDDIWKEE--DW-DLIKP 285

Query:   320 FQAGAQGSKIIVTTRNQ 336
                  +G K+++T+R +
Sbjct:   286 IFPPKKGWKVLLTSRTE 302

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2025916 AT1G59780 "AT1G59780" [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 5.8e-17, Sum P(2) = 5.8e-17
 Identities = 58/198 (29%), Positives = 100/198 (50%)

Query:   141 SMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTTSLVEEAKVYGRETEKKE 200
             S+  +I K+    +++  +   +  + S A   +K R+ R T S   E+ + G E   ++
Sbjct:   111 SISKRISKVIQVMQNLGIKSDIMDGVDSHAQLERK-RELRHTFSSESESNLVGLEKNVEK 169

Query:   201 IVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDV 260
             +VE L+ +DS +  G S   I G+GGLGKTTLA+ +++  +V+ HFD  AW CVS +F  
Sbjct:   170 LVEELVGNDSSH--GVS---ITGLGGLGKTTLARQIFDHDKVKSHFDGLAWVCVSQEFTR 224

Query:   261 IRLTKSILLSIA---SDQNVDNHDLNXXXXXXXXXXXXXXXXXVLDDVWNENYTDWVHLS 317
               + K+IL +++    D ++   D+                  V DD+W     DW  ++
Sbjct:   225 KDVWKTILGNLSPKYKDSDLPEDDIQKKLFQLLETKKALI---VFDDLWKRE--DWYRIA 279

Query:   318 LPFQAGAQGSKIIVTTRN 335
               F     G K+++T+RN
Sbjct:   280 PMFPERKAGWKVLLTSRN 297

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2011982 AT1G50180 [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 1.0e-16, Sum P(2) = 1.0e-16
 Identities = 62/206 (30%), Positives = 97/206 (47%)

Query:   140 YSMMSKIKKINDRFRDIEEEIGSLKLIKSSAG--G---SKKARQRRDTTSLVEEAKVYGR 194
             +S+ S+I++I  R   I   +     IK S G  G   S   R++R +   V E  + G 
Sbjct:   109 HSVGSEIREITSRLSKIAASMLDFG-IKESMGREGLSLSDSLREQRQSFPYVVEHNLVGL 167

Query:   195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV 254
             E   +++V  L+    +      V  I GMGGLGKTTLA+ +++  +V  HFD  AW  V
Sbjct:   168 EQSLEKLVNDLVSGGEK----LRVTSICGMGGLGKTTLAKQIFHHHKVRRHFDRFAWVYV 223

Query:   255 SDDFDVIRLTKSILLSIA-SDQNVDNHDLNXXXXXXXXXXXXXXXX--XVLDDVWNENYT 311
             S D     + + I L+++  D+N     L                    VLDD+W ++  
Sbjct:   224 SQDCRRRHVWQDIFLNLSYKDENQRILSLRDEQLGEELHRFLKRNKCLIVLDDIWGKDAW 283

Query:   312 DWVHLSLPFQAGAQGSKIIVTTRNQD 337
             D +    P + G   S+II+TTRN++
Sbjct:   284 DCLKHVFPHETG---SEIILTTRNKE 306

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

GO:0043531 "ADP binding" evidence=IEA

GO:0009506 "plasmodesma" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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: GSVIVG00030901001 SubName- Full=Chromosome undetermined scaffold_53, whole genome shotgun sequence; (1428 aa) (Vitis vinifera)

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	337
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-37
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	3e-05
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	3e-04

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

 Score =  135 bits (341), Expect = 2e-37
 Identities = 60/145 (41%), Positives = 86/145 (59%), Gaps = 7/145 (4%)

Query: 194 RETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC 253
           RE   + ++E LL+          V+ I+GMGG+GKTTLA+ +YND  V  HFD  AW  
Sbjct: 1   REDMIEALIEKLLEMS----DNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVV 56

Query: 254 VSDDFDVIRLTKSILLSIASDQN-VDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTD 312
           VS  +   RL K IL  +  D +     + ++L  ++K+ L  K+FLLVLDDVW +N  D
Sbjct: 57  VSKTYTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKN--D 114

Query: 313 WVHLSLPFQAGAQGSKIIVTTRNQD 337
           W  + +PF  G  GS++IVTTR++ 
Sbjct: 115 WDKIGVPFPDGENGSRVIVTTRSES 139

Length = 285

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

 Score = 43.3 bits (102), Expect = 3e-05
 Identities = 26/114 (22%), Positives = 43/114 (37%), Gaps = 21/114 (18%)

Query: 192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAW 251
            G+E   + + E L     +N      + + G  G GKTTLA+ +             A 
Sbjct: 1   VGQEEAIEALREALELPPPKN------LLLYGPPGTGKTTLARAI-------------AN 41

Query: 252 TCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDV 305
                    + L  S LL       +  H L +L  EL ++   K  +L +D++
Sbjct: 42  ELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEK--AKPGVLFIDEI 93

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

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

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 24/137 (17%), Positives = 46/137 (33%), Gaps = 30/137 (21%)

Query: 190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLK 249
           ++ GRE E + +++ L        GG   + + G  G GKT+L       +++ +   + 
Sbjct: 1   RLVGREEELERLLDAL---RRARSGGPPSVLLTGPSGTGKTSLL------RELLEGLLVA 51

Query: 250 AWTCVSDDFDVIRLTKSILLS------------IASDQNVDNHDLNKLQEELKKQLFG-- 295
           A  C   + +        L              +   +      L     E  + L    
Sbjct: 52  AGKCDQAERNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELL 111

Query: 296 -------KKFLLVLDDV 305
                  +  +LVLDD+
Sbjct: 112 ERLLARARPLVLVLDDL 128

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	337
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.92
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.74
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.19
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.11
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.96
PF05729	166	NACHT: NACHT domain	98.94
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.87
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.83
cd01128	249	rho_factor Transcription termination factor rho is	98.79
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.73
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.73
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.7
PF13173	128	AAA_14: AAA domain	98.66
PRK09376	416	rho transcription termination factor Rho; Provisio	98.65
PRK04841	903	transcriptional regulator MalT; Provisional	98.62
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.61
PTZ00202	550	tuzin; Provisional	98.59
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.51
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.5
PRK13342	413	recombination factor protein RarA; Reviewed	98.49
PRK12402	337	replication factor C small subunit 2; Reviewed	98.48
TIGR00767	415	rho transcription termination factor Rho. Members	98.47
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.46
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.35
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.33
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.32
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.32
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.3
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.3
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.29
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.28
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.28
PRK04195	482	replication factor C large subunit; Provisional	98.27
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.26
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.26
PHA02544	316	44 clamp loader, small subunit; Provisional	98.25
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.25
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.24
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.22
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.21
PLN03025	319	replication factor C subunit; Provisional	98.21
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.2
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.2
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.2
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.19
PRK13341	725	recombination factor protein RarA/unknown domain f	98.18
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.17
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.17
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.16
PRK06893	229	DNA replication initiation factor; Validated	98.16
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.15
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.14
KOG2028	554	consensus ATPase related to the helicase subunit o	98.12
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.12
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.09
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.07
PF00004	132	AAA: ATPase family associated with various cellula	98.06
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.04
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.03
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.02
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.0
smart00382	148	AAA ATPases associated with a variety of cellular	98.0
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.99
PRK08116	268	hypothetical protein; Validated	97.98
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.97
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.97
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.94
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.92
PRK10536	262	hypothetical protein; Provisional	97.89
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.88
PRK08118	167	topology modulation protein; Reviewed	97.87
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.85
PRK08727	233	hypothetical protein; Validated	97.84
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.84
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.84
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.84
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.83
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.82
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.81
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.8
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.8
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.79
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.79
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.78
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.77
PRK08939	306	primosomal protein DnaI; Reviewed	97.74
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.73
CHL00181	287	cbbX CbbX; Provisional	97.73
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.71
PRK08181	269	transposase; Validated	97.7
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.7
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.7
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.7
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.69
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.69
PRK08084	235	DNA replication initiation factor; Provisional	97.66
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.66
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.65
PRK05642	234	DNA replication initiation factor; Validated	97.65
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.65
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.64
PRK10865	857	protein disaggregation chaperone; Provisional	97.63
PRK09087	226	hypothetical protein; Validated	97.63
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.63
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.62
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.62
PRK12377	248	putative replication protein; Provisional	97.62
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.61
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.6
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.6
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.56
PRK06526	254	transposase; Provisional	97.56
PRK06921	266	hypothetical protein; Provisional	97.56
CHL00095	821	clpC Clp protease ATP binding subunit	97.56
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.56
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.55
PRK10865	857	protein disaggregation chaperone; Provisional	97.55
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.55
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.54
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.53
CHL00095	821	clpC Clp protease ATP binding subunit	97.52
PRK12608	380	transcription termination factor Rho; Provisional	97.49
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.49
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.48
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.48
PRK07952	244	DNA replication protein DnaC; Validated	97.48
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.47
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.46
PRK06835	329	DNA replication protein DnaC; Validated	97.45
PRK06620	214	hypothetical protein; Validated	97.44
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.44
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.44
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	97.43
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.43
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.41
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.41
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.4
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.38
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.38
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.36
PRK13531	498	regulatory ATPase RavA; Provisional	97.36
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.36
PRK07261	171	topology modulation protein; Provisional	97.36
PRK04296	190	thymidine kinase; Provisional	97.35
PRK09183	259	transposase/IS protein; Provisional	97.34
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	97.34
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.3
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.3
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.29
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.29
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.28
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.28
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.28
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.26
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.26
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.26
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.26
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	97.24
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.22
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	97.21
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.21
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	97.21
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.2
PRK12422	445	chromosomal replication initiation protein; Provis	97.2
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	97.2
PRK09354	349	recA recombinase A; Provisional	97.2
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.17
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.17
PRK05541	176	adenylylsulfate kinase; Provisional	97.17
PRK15455	644	PrkA family serine protein kinase; Provisional	97.16
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.13
CHL00176	638	ftsH cell division protein; Validated	97.13
PRK06696	223	uridine kinase; Validated	97.11
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	97.11
PRK08233	182	hypothetical protein; Provisional	97.11
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.08
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.06
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.05
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	97.05
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.04
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.03
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.03
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.03
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.01
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	97.01
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.0
TIGR02236	310	recomb_radA DNA repair and recombination protein R	97.0
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	97.0
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	96.99
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.95
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.94
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.93
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.92
PRK06067	234	flagellar accessory protein FlaH; Validated	96.92
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.92
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.91
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.91
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.9
PTZ00035	337	Rad51 protein; Provisional	96.89
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.89
PHA02244	383	ATPase-like protein	96.88
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.88
PRK13695	174	putative NTPase; Provisional	96.87
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.85
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.83
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.82
TIGR00959	428	ffh signal recognition particle protein. This mode	96.81
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.8
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.79
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.79
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.79
cd03246	173	ABCC_Protease_Secretion This family represents the	96.77
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.76
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.76
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.75
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	96.74
PRK05480	209	uridine/cytidine kinase; Provisional	96.73
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.72
PRK10867	433	signal recognition particle protein; Provisional	96.71
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.71
PTZ00301	210	uridine kinase; Provisional	96.71
PF00154	322	RecA: recA bacterial DNA recombination protein; In	96.7
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.68
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.67
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.67
PRK07667	193	uridine kinase; Provisional	96.66
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.66
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.66
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.64
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.64
PRK05439	311	pantothenate kinase; Provisional	96.62
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.62
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	96.61
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	96.61
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.6
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.6
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	96.6
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.6
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.59
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.57
cd03215	182	ABC_Carb_Monos_II This family represents domain II	96.56
COG0714	329	MoxR-like ATPases [General function prediction onl	96.55
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.55
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.54
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	96.5
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.49
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.49
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.48
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.48
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.46
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	96.45
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.45
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.45
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.45
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.44
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.44
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.43
PRK06762	166	hypothetical protein; Provisional	96.43
COG0488	530	Uup ATPase components of ABC transporters with dup	96.41
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	96.38
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.38
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	96.38
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.36
PRK14974	336	cell division protein FtsY; Provisional	96.36
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	96.35
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.35
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.35
PRK06547	172	hypothetical protein; Provisional	96.34
PTZ00088	229	adenylate kinase 1; Provisional	96.33
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.33
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.32
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.32
PRK03839	180	putative kinase; Provisional	96.29
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	96.28
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.26
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	96.25
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.23
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.21
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.19
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.19
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.18
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.18
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	96.18
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.17
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	96.17
PF14516	331	AAA_35: AAA-like domain	96.16
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	96.16
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.15
PRK04040	188	adenylate kinase; Provisional	96.15
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.13
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.12
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.12
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.12
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.12
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.11
PRK00131	175	aroK shikimate kinase; Reviewed	96.11
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.11
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.1
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	96.1
COG3903	414	Predicted ATPase [General function prediction only	96.09
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	96.09
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.08
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	96.08
PRK08149	428	ATP synthase SpaL; Validated	96.08
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.08
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.07
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	96.06
PRK05917	290	DNA polymerase III subunit delta'; Validated	96.06
PRK00625	173	shikimate kinase; Provisional	96.05
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	96.05
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	96.05
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.04
PRK00889	175	adenylylsulfate kinase; Provisional	96.04
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.02
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.01
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	96.01
PRK05922	434	type III secretion system ATPase; Validated	96.01
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	96.0
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.0
PHA00729	226	NTP-binding motif containing protein	95.99
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	95.98
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.97
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	95.97
PRK13765	637	ATP-dependent protease Lon; Provisional	95.96
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.96
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.95
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.95
PRK04328	249	hypothetical protein; Provisional	95.94
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	95.93
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	95.93
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.93
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	95.92
PRK00300	205	gmk guanylate kinase; Provisional	95.92
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	95.92
PRK07993	334	DNA polymerase III subunit delta'; Validated	95.91
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.91
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.91
COG3899	849	Predicted ATPase [General function prediction only	95.91
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.9
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	95.89
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.88
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.88
PRK00279	215	adk adenylate kinase; Reviewed	95.86
PRK06217	183	hypothetical protein; Validated	95.86
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	95.85
PF07726	131	AAA_3: ATPase family associated with various cellu	95.85
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.85
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.84
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.83
PRK03846	198	adenylylsulfate kinase; Provisional	95.83
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	95.83
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	95.82
PRK15064	530	ABC transporter ATP-binding protein; Provisional	95.81
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	95.81
PRK13949	169	shikimate kinase; Provisional	95.79
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	95.79
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.78
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.78
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	95.77
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.77
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.75
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.75
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.75
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.74
PRK15453	290	phosphoribulokinase; Provisional	95.73
KOG0066	807	consensus eIF2-interacting protein ABC50 (ABC supe	95.73
PRK09099	441	type III secretion system ATPase; Provisional	95.73
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	95.72
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.71
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.71
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.71
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	95.7
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	95.68
PRK13947	171	shikimate kinase; Provisional	95.68
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.68
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.67
PRK12678	672	transcription termination factor Rho; Provisional	95.67
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.66
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.65
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	95.65
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	95.65
PRK14530	215	adenylate kinase; Provisional	95.65
PTZ00185	574	ATPase alpha subunit; Provisional	95.64
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.64
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.64
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	95.63
PRK14738	206	gmk guanylate kinase; Provisional	95.63
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	95.62
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.61
PHA02774	613	E1; Provisional	95.61
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	95.6
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	95.6
PRK14737	186	gmk guanylate kinase; Provisional	95.59
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	95.59
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.59
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	95.57
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	95.57
PRK13975	196	thymidylate kinase; Provisional	95.56
PRK06936	439	type III secretion system ATPase; Provisional	95.56
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.55
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.54
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	95.54
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	95.53
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.51
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.5
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	95.49
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	95.48
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.47
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.47
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.47
CHL00195	489	ycf46 Ycf46; Provisional	95.46
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	95.46
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	95.46
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	95.45
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	95.45
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.45
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.45
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.44
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.44
smart00487	201	DEXDc DEAD-like helicases superfamily.	95.44
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	95.44
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	95.42
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.41
PRK05057	172	aroK shikimate kinase I; Reviewed	95.41
PRK14527	191	adenylate kinase; Provisional	95.41
PRK13409	590	putative ATPase RIL; Provisional	95.4
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	95.4
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	95.4
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.38
COG4133	209	CcmA ABC-type transport system involved in cytochr	95.35
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.34
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	95.32
PRK11823	446	DNA repair protein RadA; Provisional	95.32
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	95.31
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	95.3
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	95.27
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	95.25
PRK09825	176	idnK D-gluconate kinase; Provisional	95.24
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	95.23
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	95.2
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	95.2
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	95.2
PRK11147	635	ABC transporter ATPase component; Reviewed	95.2
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	95.2
COG1100	219	GTPase SAR1 and related small G proteins [General	95.19
PLN02348	395	phosphoribulokinase	95.19
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	95.18
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.18
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	95.17
KOG0927	614	consensus Predicted transporter (ABC superfamily)	95.17
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.16
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.14
PRK04182	180	cytidylate kinase; Provisional	95.14
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	95.13
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	95.11
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	95.11
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	95.1
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.1
PRK08356	195	hypothetical protein; Provisional	95.1
PLN02200	234	adenylate kinase family protein	95.09
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.09
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	95.09
TIGR01287	275	nifH nitrogenase iron protein. This model describe	95.08
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	95.07
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.05
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	95.04
PRK13946	184	shikimate kinase; Provisional	95.03
PRK14529	223	adenylate kinase; Provisional	95.03
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.03
PRK13236	296	nitrogenase reductase; Reviewed	95.02
PRK13948	182	shikimate kinase; Provisional	95.01
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	95.0
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.0
PRK10416	318	signal recognition particle-docking protein FtsY;	95.0
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	94.99
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	94.99
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	94.98
PRK14532	188	adenylate kinase; Provisional	94.98
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	94.96
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	94.96
PRK13889	988	conjugal transfer relaxase TraA; Provisional	94.94
cd03269	210	ABC_putative_ATPase This subfamily is involved in	94.94
PRK10875	615	recD exonuclease V subunit alpha; Provisional	94.94
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	94.93
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	94.93
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	94.93
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	94.92
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.91
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	94.91
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	94.91
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	94.9
PRK06820	440	type III secretion system ATPase; Validated	94.9
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	94.89
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	94.88
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	94.87
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	94.87
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	94.86
cd03116	159	MobB Molybdenum is an essential trace element in t	94.86
PRK03731	171	aroL shikimate kinase II; Reviewed	94.86

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.8e-35  Score=292.84  Aligned_cols=287  Identities=29%  Similarity=0.434  Sum_probs=222.4

Q ss_pred             HHHhhHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHccccCChHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHhh
Q 043252           18 NKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLL   97 (337)
Q Consensus        18 ~kl~s~~~~~~~~~~~v~~~~~~L~~~L~~i~~~L~~ae~~~~~~~~~~~Wl~~lr~~ayd~eD~lD~~~~~~~~~~~~~   97 (337)
                      +++.+.+..++....+.++.+..|++.|..++.+++++++++.....+..|.+.+++++|++||.++.+.......+..+
T Consensus        10 ~~~~~~l~~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~~   89 (889)
T KOG4658|consen   10 EKLDQLLNRESECLDGKDNYILELKENLKALQSALEDLDAKRDDLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKAND   89 (889)
T ss_pred             hhHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            34444455566677888999999999999999999999999999999999999999999999999999999887654332


Q ss_pred             CCCCCCccCCCCCCccccccccccccccccCCCCcccchhhhhHHHHHHHHHHHHHHHHHHHhhccccccccCCCC--cc
Q 043252           98 GNGEPAAAHDQPSSSRTSTKSKFRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSLKLIKSSAGGS--KK  175 (337)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~i~~~l~~i~~~~~~~~~~~~~~~~~--~~  175 (337)
                      .-      .         ......+.++.         ..++++....+..+..++..+.+..+.++.........  ..
T Consensus        90 ~l------~---------~~~~~~~~~c~---------~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~  145 (889)
T KOG4658|consen   90 LL------S---------TRSVERQRLCL---------CGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLD  145 (889)
T ss_pred             Hh------h---------hhHHHHHHHhh---------hhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceeccccccc
Confidence            00      0         00011111111         13456666777777777777777777776443211111  11


Q ss_pred             cccccccccCccccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc-ccccccceEEEEe
Q 043252          176 ARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHFDLKAWTCV  254 (337)
Q Consensus       176 ~~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~v  254 (337)
                      .....++.+..+... ||.+..++++.+.|..++.      .+++|+||||+||||||+.++|+.. ++.+|+.++||+|
T Consensus       146 ~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~------~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~V  218 (889)
T KOG4658|consen  146 PREKVETRPIQSESD-VGLETMLEKLWNRLMEDDV------GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVV  218 (889)
T ss_pred             chhhcccCCCCcccc-ccHHHHHHHHHHHhccCCC------CEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEE
Confidence            112233334344444 9999999999999987652      7999999999999999999999987 9999999999999


Q ss_pred             CCCCCHHHHHHHHHHHhhCCCCC-CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          255 SDDFDVIRLTKSILLSIASDQNV-DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       255 ~~~~~~~~~~~~il~~~~~~~~~-~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      |+.|+...+..+|+..++..... .....+.++..|.+.|.+|||||||||||+.  .+|+.+..++|...+||+|++||
T Consensus       219 Sk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~--~dw~~I~~~~p~~~~g~KvvlTT  296 (889)
T KOG4658|consen  219 SKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEE--VDWDKIGVPFPSRENGSKVVLTT  296 (889)
T ss_pred             cccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCceEEEEeccccc--ccHHhcCCCCCCccCCeEEEEEe
Confidence            99999999999999998774432 2233478999999999999999999999998  68999999999999999999999


Q ss_pred             cCCC
Q 043252          334 RNQD  337 (337)
Q Consensus       334 R~~~  337 (337)
                      |+++
T Consensus       297 Rs~~  300 (889)
T KOG4658|consen  297 RSEE  300 (889)
T ss_pred             ccHh
Confidence            9863

>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=99.92  E-value=1.1e-24  Score=195.73  Aligned_cols=137  Identities=39%  Similarity=0.654  Sum_probs=112.3

Q ss_pred             chhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhC
Q 043252          194 RETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIAS  273 (337)
Q Consensus       194 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~  273 (337)
                      ||.++++|.++|....    .+.++|+|+|+||+||||||+.+|++..++.+|+.++|+.++...+...++..|+.++..
T Consensus         1 re~~~~~l~~~L~~~~----~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~   76 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNS----NEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGE   76 (287)
T ss_dssp             -HHHHHHHHHHHHTTT----TSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHhhCCC----CCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccc
Confidence            7899999999998743    368999999999999999999999987789999999999999999999999999999987


Q ss_pred             CCCC--CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          274 DQNV--DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       274 ~~~~--~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      ....  ...+.+.+...+.+.|.+++|||||||||+.  ..|+.+...++....||+||||||+.
T Consensus        77 ~~~~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~kilvTTR~~  139 (287)
T PF00931_consen   77 PDSSISDPKDIEELQDQLRELLKDKRCLLVLDDVWDE--EDLEELREPLPSFSSGSKILVTTRDR  139 (287)
T ss_dssp             C-STSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SH--HHH-------HCHHSS-EEEEEESCG
T ss_pred             cccccccccccccccccchhhhccccceeeeeeeccc--cccccccccccccccccccccccccc
Confidence            7432  4567888999999999999999999999986  68888888888777899999999985

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=99.74  E-value=2.3e-17  Score=173.26  Aligned_cols=138  Identities=22%  Similarity=0.360  Sum_probs=100.5

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEe---CCC------
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV---SDD------  257 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v---~~~------  257 (337)
                      +...+||++..++++..+|.-.    .+..++|+||||||+||||||+.+|+.  +..+|+..+|+..   +..      
T Consensus       182 ~~~~~vG~~~~l~~l~~lL~l~----~~~~~vvgI~G~gGiGKTTLA~~l~~~--l~~~F~g~vfv~~~~v~~~~~~~~~  255 (1153)
T PLN03210        182 DFEDFVGIEDHIAKMSSLLHLE----SEEVRMVGIWGSSGIGKTTIARALFSR--LSRQFQSSVFIDRAFISKSMEIYSS  255 (1153)
T ss_pred             ccccccchHHHHHHHHHHHccc----cCceEEEEEEcCCCCchHHHHHHHHHH--HhhcCCeEEEeeccccccchhhccc
Confidence            3456999999999999988533    346899999999999999999999984  7778988877642   111      


Q ss_pred             -----CC-HHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEE
Q 043252          258 -----FD-VIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIV  331 (337)
Q Consensus       258 -----~~-~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iiv  331 (337)
                           ++ ...+..+++.++...........    ..+++.|.++|+||||||||+.  ..|+.+.......++||+|||
T Consensus       256 ~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~----~~~~~~L~~krvLLVLDdv~~~--~~l~~L~~~~~~~~~GsrIIi  329 (1153)
T PLN03210        256 ANPDDYNMKLHLQRAFLSEILDKKDIKIYHL----GAMEERLKHRKVLIFIDDLDDQ--DVLDALAGQTQWFGSGSRIIV  329 (1153)
T ss_pred             ccccccchhHHHHHHHHHHHhCCCCcccCCH----HHHHHHHhCCeEEEEEeCCCCH--HHHHHHHhhCccCCCCcEEEE
Confidence                 11 12344555555543322111122    4577889999999999999886  678888776655678999999


Q ss_pred             EecCC
Q 043252          332 TTRNQ  336 (337)
Q Consensus       332 TTR~~  336 (337)
                      |||+.
T Consensus       330 TTrd~  334 (1153)
T PLN03210        330 ITKDK  334 (1153)
T ss_pred             EeCcH
Confidence            99975

syringae 6; Provisional

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.19  E-value=3.1e-10  Score=106.64  Aligned_cols=120  Identities=16%  Similarity=0.123  Sum_probs=86.9

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~  266 (337)
                      .+..++||++++++|...|...-  .+.....+.|+|++|+|||++++.++++.......-..+++++....+...++..
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~--~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~  105 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPAL--RGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSE  105 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHh--CCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHH
Confidence            34679999999999999985432  1223446789999999999999999986432222234567777777788899999


Q ss_pred             HHHHhhCC-CCCCCCCHHHHHHHHHHHcC--CCeEEEEEeCCCCC
Q 043252          267 ILLSIASD-QNVDNHDLNKLQEELKKQLF--GKKFLLVLDDVWNE  308 (337)
Q Consensus       267 il~~~~~~-~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~  308 (337)
                      ++.++... .+....+...+...+.+.+.  ++..+||||+++.-
T Consensus       106 i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l  150 (394)
T PRK00411        106 IARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYL  150 (394)
T ss_pred             HHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHh
Confidence            99998763 22233456777777777774  45689999999763

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.11  E-value=1.7e-09  Score=100.60  Aligned_cols=118  Identities=15%  Similarity=0.181  Sum_probs=83.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccc-ccc---cceEEEEeCCCCCHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVE-DHF---DLKAWTCVSDDFDVIRLT  264 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F---~~~~wv~v~~~~~~~~~~  264 (337)
                      ..++||+.+++.|..+|...-  .+.....+.|+|++|+|||++++.+++..... ...   -..+|+++....+...++
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~--~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~   92 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPIL--RGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVL   92 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHH--cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHH
Confidence            479999999999999986422  12234578999999999999999999752110 111   135788887777788899


Q ss_pred             HHHHHHhhC---CCCCCCCCHHHHHHHHHHHc--CCCeEEEEEeCCCCC
Q 043252          265 KSILLSIAS---DQNVDNHDLNKLQEELKKQL--FGKKFLLVLDDVWNE  308 (337)
Q Consensus       265 ~~il~~~~~---~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  308 (337)
                      ..|+.++..   ..+....+..++...+.+.+  .+++++||||+++.-
T Consensus        93 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928        93 VELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             HHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhh
Confidence            999999842   22212234555666666666  356889999999764

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.

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

Probab=98.96  E-value=2.2e-09  Score=84.52  Aligned_cols=117  Identities=17%  Similarity=0.157  Sum_probs=80.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhccccc---ccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVE---DHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQ  292 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~  292 (337)
                      -+++.|+|.+|+|||++++.+.+.....   ..-...+|+.++...+...+...|+..+..... ...+...+.+.+.+.
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~~~l~~~~~~~   82 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLK-SRQTSDELRSLLIDA   82 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSS-STS-HHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCcccc-ccCCHHHHHHHHHHH
Confidence            4689999999999999999998752110   002346799998888999999999999987765 345677777888888


Q ss_pred             cCCC-eEEEEEeCCCCC-ChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          293 LFGK-KFLLVLDDVWNE-NYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       293 L~~k-r~LlVlDdv~~~-~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +... ..+||||++..- ....++.+...+ + ..+.+||++.+.
T Consensus        83 l~~~~~~~lviDe~~~l~~~~~l~~l~~l~-~-~~~~~vvl~G~~  125 (131)
T PF13401_consen   83 LDRRRVVLLVIDEADHLFSDEFLEFLRSLL-N-ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHCTEEEEEEETTHHHHTHHHHHHHHHHT-C-SCBEEEEEEESS
T ss_pred             HHhcCCeEEEEeChHhcCCHHHHHHHHHHH-h-CCCCeEEEEECh
Confidence            8544 459999999665 444555554433 3 556677776543

>PF05729 NACHT: NACHT domain

Probab=98.94  E-value=3.2e-09  Score=86.94  Aligned_cols=114  Identities=25%  Similarity=0.278  Sum_probs=64.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhccccccc----ccceEEEEeCCCCCHH---HHHHHHHHHhhCCCCCCCCCHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDH----FDLKAWTCVSDDFDVI---RLTKSILLSIASDQNVDNHDLNKLQEEL  289 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~v~~~~~~~---~~~~~il~~~~~~~~~~~~~~~~~~~~l  289 (337)
                      +++.|+|.+|+||||+++.++..-.....    +...+|++........   .+...|..+....    ..........+
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~----~~~~~~~~~~~   76 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPES----IAPIEELLQEL   76 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccc----hhhhHHHHHHH
Confidence            47899999999999999999875322222    4566777766543322   2333333332211    11111111111


Q ss_pred             HHHcCCCeEEEEEeCCCCCCh--h-----cHHHh-hccCCC-CCCCcEEEEEecCC
Q 043252          290 KKQLFGKKFLLVLDDVWNENY--T-----DWVHL-SLPFQA-GAQGSKIIVTTRNQ  336 (337)
Q Consensus       290 ~~~L~~kr~LlVlDdv~~~~~--~-----~~~~l-~~~l~~-~~~gs~iivTTR~~  336 (337)
                        ....++++||||++.+-..  .     .+..+ ...++. ..+++++|||+|..
T Consensus        77 --~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~  130 (166)
T PF05729_consen   77 --LEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPR  130 (166)
T ss_pred             --HHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCC
Confidence              1257899999999965422  1     12222 223332 35689999999975

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

Probab=98.87  E-value=3.2e-08  Score=78.79  Aligned_cols=124  Identities=16%  Similarity=0.082  Sum_probs=70.7

Q ss_pred             ccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHh
Q 043252          192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSI  271 (337)
Q Consensus       192 vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~  271 (337)
                      +|++..++.+...+...      ....+.|+|++|+|||+|++.+++...  ..-..++++..............+... 
T Consensus         1 ~~~~~~~~~i~~~~~~~------~~~~v~i~G~~G~GKT~l~~~i~~~~~--~~~~~v~~~~~~~~~~~~~~~~~~~~~-   71 (151)
T cd00009           1 VGQEEAIEALREALELP------PPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGHF-   71 (151)
T ss_pred             CchHHHHHHHHHHHhCC------CCCeEEEECCCCCCHHHHHHHHHHHhh--cCCCCeEEEehhhhhhhhHHHHHhhhh-
Confidence            47888888998888543      235889999999999999999998532  112345566655433322211111000 


Q ss_pred             hCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChh---cHHHhhccCCCC---CCCcEEEEEecCC
Q 043252          272 ASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYT---DWVHLSLPFQAG---AQGSKIIVTTRNQ  336 (337)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~---~~~~l~~~l~~~---~~gs~iivTTR~~  336 (337)
                                  ............+..+|++||++.....   .+..+...+...   ..+..||+||...
T Consensus        72 ------------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~  130 (151)
T cd00009          72 ------------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRP  130 (151)
T ss_pred             ------------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCcc
Confidence                        0111112223456789999999854222   222222222221   3577888888753

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.

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

Probab=98.83  E-value=1.4e-08  Score=84.80  Aligned_cols=48  Identities=27%  Similarity=0.404  Sum_probs=32.7

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      .|+||+++++++...|. ..  .....+.+.|+|.+|+|||+|.+.++...
T Consensus         1 ~fvgR~~e~~~l~~~l~-~~--~~~~~~~~ll~G~~G~GKT~ll~~~~~~~   48 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLD-AA--QSGSPRNLLLTGESGSGKTSLLRALLDRL   48 (185)
T ss_dssp             --TT-HHHHHHHHHTTG-GT--SS-----EEE-B-TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH-HH--HcCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999995 21  23456899999999999999999998753

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

Probab=98.79  E-value=9.5e-09  Score=89.63  Aligned_cols=90  Identities=21%  Similarity=0.198  Sum_probs=63.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC--CCHHHHHHHHHHHhhCCCCCCCCCH------HHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD--FDVIRLTKSILLSIASDQNVDNHDL------NKLQE  287 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~--~~~~~~~~~il~~~~~~~~~~~~~~------~~~~~  287 (337)
                      -..+.|+|++|+|||||++.+|++.... +|+..+|+++.+.  +++.+++..+...+-.... +....      ....+
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~-~~~~~~~~~~~~~~~~   93 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTF-DEPPERHVQVAEMVLE   93 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecC-CCCHHHHHHHHHHHHH
Confidence            3589999999999999999999975444 8999999998777  7899999988443332222 11111      11222


Q ss_pred             HHHHH-cCCCeEEEEEeCCCC
Q 043252          288 ELKKQ-LFGKKFLLVLDDVWN  307 (337)
Q Consensus       288 ~l~~~-L~~kr~LlVlDdv~~  307 (337)
                      ..... -.+++.+|++|++..
T Consensus        94 ~a~~~~~~G~~vll~iDei~r  114 (249)
T cd01128          94 KAKRLVEHGKDVVILLDSITR  114 (249)
T ss_pred             HHHHHHHCCCCEEEEEECHHH
Confidence            22222 258999999999953

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.

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

Probab=98.73  E-value=3.9e-07  Score=80.97  Aligned_cols=97  Identities=28%  Similarity=0.300  Sum_probs=63.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHH----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKK----Q  292 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~----~  292 (337)
                      ..+.|+|++|+|||||++.+++..... .+ ..+|+ +....+..+++..|+..++....  ..+...+...+..    .
T Consensus        44 ~~~~l~G~~G~GKTtl~~~l~~~l~~~-~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~--~~~~~~~~~~l~~~l~~~  118 (269)
T TIGR03015        44 GFILITGEVGAGKTTLIRNLLKRLDQE-RV-VAAKL-VNTRVDAEDLLRMVAADFGLETE--GRDKAALLRELEDFLIEQ  118 (269)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHhcCCC-Ce-EEeee-eCCCCCHHHHHHHHHHHcCCCCC--CCCHHHHHHHHHHHHHHH
Confidence            488999999999999999999863321 11 12233 33345777888888888765432  2232333333333    2


Q ss_pred             -cCCCeEEEEEeCCCCCChhcHHHhhc
Q 043252          293 -LFGKKFLLVLDDVWNENYTDWVHLSL  318 (337)
Q Consensus       293 -L~~kr~LlVlDdv~~~~~~~~~~l~~  318 (337)
                       ..+++++||+||++......++.+..
T Consensus       119 ~~~~~~~vliiDe~~~l~~~~~~~l~~  145 (269)
T TIGR03015       119 FAAGKRALLVVDEAQNLTPELLEELRM  145 (269)
T ss_pred             HhCCCCeEEEEECcccCCHHHHHHHHH
Confidence             26788999999999876666766653

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.

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

Probab=98.73  E-value=2e-07  Score=85.95  Aligned_cols=116  Identities=19%  Similarity=0.162  Sum_probs=86.3

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      .+.+|+.+++++...|...-.  +....-+.|+|..|.|||+.++.|.+..+....=...++|++-...+...++..|+.
T Consensus        18 ~l~~Re~ei~~l~~~l~~~~~--~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~   95 (366)
T COG1474          18 ELPHREEEINQLASFLAPALR--GERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILN   95 (366)
T ss_pred             cccccHHHHHHHHHHHHHHhc--CCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHH
Confidence            389999999999988865432  222334999999999999999999985322111111789999999999999999999


Q ss_pred             HhhCCCCCCCCCHHHHHHHHHHHc--CCCeEEEEEeCCCCC
Q 043252          270 SIASDQNVDNHDLNKLQEELKKQL--FGKKFLLVLDDVWNE  308 (337)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  308 (337)
                      .+..... ......+....+.+.+  .++.++||||++...
T Consensus        96 ~~~~~p~-~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L  135 (366)
T COG1474          96 KLGKVPL-TGDSSLEILKRLYDNLSKKGKTVIVILDEVDAL  135 (366)
T ss_pred             HcCCCCC-CCCchHHHHHHHHHHHHhcCCeEEEEEcchhhh
Confidence            9973332 4455666667777777  468999999999654

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.70  E-value=1.5e-07  Score=93.08  Aligned_cols=120  Identities=18%  Similarity=0.084  Sum_probs=80.9

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc---ccccc--ceEEEEeCCCCCHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV---EDHFD--LKAWTCVSDDFDVIR  262 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~F~--~~~wv~v~~~~~~~~  262 (337)
                      +..+.||++|+++|...|...-. +.....++.|+|++|.|||++++.|.+....   .....  .+++|++....+...
T Consensus       754 PD~LPhREeEIeeLasfL~paIk-gsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~s  832 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIK-QSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNA  832 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHh-cCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHH
Confidence            36789999999999988864321 1223357889999999999999999865311   11111  356788777777888


Q ss_pred             HHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC---CCeEEEEEeCCCCC
Q 043252          263 LTKSILLSIASDQNVDNHDLNKLQEELKKQLF---GKKFLLVLDDVWNE  308 (337)
Q Consensus       263 ~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~---~kr~LlVlDdv~~~  308 (337)
                      ++..|..++....+............+...+.   +...+||||+|...
T Consensus       833 IYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L  881 (1164)
T PTZ00112        833 AYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYL  881 (1164)
T ss_pred             HHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhh
Confidence            99999988855443333333444555555442   23458999999653

>PF13173 AAA_14: AAA domain

Probab=98.66  E-value=5.6e-08  Score=76.36  Aligned_cols=96  Identities=23%  Similarity=0.228  Sum_probs=62.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      +++.|.|+.|+|||||++.++.+..   ....+++++..+.......                 ..+ +.+.+.+....+
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~-----------------~~~-~~~~~~~~~~~~   61 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLA-----------------DPD-LLEYFLELIKPG   61 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHh-----------------hhh-hHHHHHHhhccC
Confidence            5899999999999999999987532   2345667766553221100                 000 223333334347


Q ss_pred             eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          297 KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..+|+||++...  ..|......+.+..+..+|++|+.+
T Consensus        62 ~~~i~iDEiq~~--~~~~~~lk~l~d~~~~~~ii~tgS~   98 (128)
T PF13173_consen   62 KKYIFIDEIQYL--PDWEDALKFLVDNGPNIKIILTGSS   98 (128)
T ss_pred             CcEEEEehhhhh--ccHHHHHHHHHHhccCceEEEEccc
Confidence            788999999665  5787776666665556789999865

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.65  E-value=6.9e-08  Score=88.17  Aligned_cols=89  Identities=20%  Similarity=0.238  Sum_probs=60.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC--CHHHHHHHHHHHhhCCCCCCCCCHHH------HHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF--DVIRLTKSILLSIASDQNVDNHDLNK------LQEE  288 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~--~~~~~~~~il~~~~~~~~~~~~~~~~------~~~~  288 (337)
                      .-..|+|++|+||||||+.+|++.... +|++++||.+.+.+  ++.+++..+...+-.... +.....+      ..+.
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~-d~~~~~~~~~a~~~ie~  247 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTF-DEPAERHVQVAEMVIEK  247 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECC-CCCHHHHHHHHHHHHHH
Confidence            478899999999999999999975444 89999999999887  677777777632222221 1111111      1111


Q ss_pred             HHHH-cCCCeEEEEEeCCCC
Q 043252          289 LKKQ-LFGKKFLLVLDDVWN  307 (337)
Q Consensus       289 l~~~-L~~kr~LlVlDdv~~  307 (337)
                      -... ..|++.||++|++..
T Consensus       248 Ae~~~e~G~dVlL~iDsItR  267 (416)
T PRK09376        248 AKRLVEHGKDVVILLDSITR  267 (416)
T ss_pred             HHHHHHcCCCEEEEEEChHH
Confidence            1121 368999999999943

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.62  E-value=4.4e-07  Score=94.33  Aligned_cols=133  Identities=18%  Similarity=0.232  Sum_probs=83.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC-CCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD-DFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~-~~~~~~~~~~i  267 (337)
                      ..++-|+.-.+.    |..     ....+++.|+|++|.||||++..+...      +..++|+++.. ..++..++..+
T Consensus        14 ~~~~~R~rl~~~----l~~-----~~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l   78 (903)
T PRK04841         14 HNTVVRERLLAK----LSG-----ANNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYL   78 (903)
T ss_pred             cccCcchHHHHH----Hhc-----ccCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHH
Confidence            345666544444    432     124679999999999999999998752      23689999964 44667777888


Q ss_pred             HHHhhCCCCC------------CCCCHHHHHHHHHHHcC--CCeEEEEEeCCCCCChhcHHH-hhccCCCCCCCcEEEEE
Q 043252          268 LLSIASDQNV------------DNHDLNKLQEELKKQLF--GKKFLLVLDDVWNENYTDWVH-LSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       268 l~~~~~~~~~------------~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~~~~~~~~-l~~~l~~~~~gs~iivT  332 (337)
                      +..+......            ...+...+...+...+.  +.+++|||||+...+...... +...++....+.++|||
T Consensus        79 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~  158 (903)
T PRK04841         79 IAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVL  158 (903)
T ss_pred             HHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEE
Confidence            8777522111            11223334444444442  678999999997654333333 33333334556788899


Q ss_pred             ecCC
Q 043252          333 TRNQ  336 (337)
Q Consensus       333 TR~~  336 (337)
                      ||..
T Consensus       159 sR~~  162 (903)
T PRK04841        159 SRNL  162 (903)
T ss_pred             eCCC
Confidence            9973

>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=98.61  E-value=3.6e-08  Score=85.34  Aligned_cols=44  Identities=34%  Similarity=0.452  Sum_probs=35.7

Q ss_pred             cccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          191 VYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       191 ~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      |+||+.+++.|.+++....      ...+.|+|+.|+|||+|++.+.+..
T Consensus         1 F~gR~~el~~l~~~l~~~~------~~~~~l~G~rg~GKTsLl~~~~~~~   44 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGP------SQHILLYGPRGSGKTSLLKEFINEL   44 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--------SSEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHhhc------CcEEEEEcCCcCCHHHHHHHHHHHh
Confidence            6899999999999997542      3589999999999999999998853

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

>PTZ00202 tuzin; Provisional

Probab=98.59  E-value=1.2e-06  Score=80.86  Aligned_cols=105  Identities=18%  Similarity=0.223  Sum_probs=72.0

Q ss_pred             CccccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHH
Q 043252          185 LVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLT  264 (337)
Q Consensus       185 ~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~  264 (337)
                      +.+...|+||+.+...|...|...+.   ....++.|.|++|+|||||++.+.....    +  ..+  +....+..+++
T Consensus       258 Pa~~~~FVGReaEla~Lr~VL~~~d~---~~privvLtG~~G~GKTTLlR~~~~~l~----~--~qL--~vNprg~eElL  326 (550)
T PTZ00202        258 PAVIRQFVSREAEESWVRQVLRRLDT---AHPRIVVFTGFRGCGKSSLCRSAVRKEG----M--PAV--FVDVRGTEDTL  326 (550)
T ss_pred             CCCccCCCCcHHHHHHHHHHHhccCC---CCceEEEEECCCCCCHHHHHHHHHhcCC----c--eEE--EECCCCHHHHH
Confidence            34567899999999999999965432   2346999999999999999999986422    1  122  22233679999


Q ss_pred             HHHHHHhhCCCCCCCCCHHHHHHHHHHHc-----C-CCeEEEEEe
Q 043252          265 KSILLSIASDQNVDNHDLNKLQEELKKQL-----F-GKKFLLVLD  303 (337)
Q Consensus       265 ~~il~~~~~~~~~~~~~~~~~~~~l~~~L-----~-~kr~LlVlD  303 (337)
                      ..++.+|+....   .....+...|.+.|     . |++-+|||-
T Consensus       327 r~LL~ALGV~p~---~~k~dLLrqIqeaLl~~~~e~GrtPVLII~  368 (550)
T PTZ00202        327 RSVVKALGVPNV---EACGDLLDFISEACRRAKKMNGETPLLVLK  368 (550)
T ss_pred             HHHHHHcCCCCc---ccHHHHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            999999986322   22233434443333     3 677788775

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.51  E-value=1.4e-06  Score=79.30  Aligned_cols=124  Identities=18%  Similarity=0.225  Sum_probs=83.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc----cccccccceEEEEe-CCCCCHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK----QVEDHFDLKAWTCV-SDDFDVIRL  263 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~----~~~~~F~~~~wv~v-~~~~~~~~~  263 (337)
                      .+++|.+.-++.|..++....     -.+...++|+.|+||||+|+.++..-    ....|++...|... +.....++ 
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~-----~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~-   77 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR-----FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD-   77 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-----CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH-
Confidence            457899999999999996443     34588899999999999999887631    12345665555442 22233333 


Q ss_pred             HHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          264 TKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       264 ~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      .+++.+.+....                 ..+++-++|+|++...+...++.|...|.....++.+|++|.+
T Consensus        78 ir~~~~~~~~~p-----------------~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~  132 (313)
T PRK05564         78 IRNIIEEVNKKP-----------------YEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCEN  132 (313)
T ss_pred             HHHHHHHHhcCc-----------------ccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCC
Confidence            223333332111                 1245567778877666667899999999887889999988864

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

Probab=98.50  E-value=1.5e-06  Score=81.21  Aligned_cols=117  Identities=14%  Similarity=0.132  Sum_probs=76.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..+++.+...+.+...|...        +.|.++|++|+|||++|+.+++.......|..+.||.+++.++..+++..+ 
T Consensus       175 ~d~~i~e~~le~l~~~L~~~--------~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~-  245 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK--------KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGY-  245 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC--------CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhccc-
Confidence            45788899999999999743        367889999999999999998865445567888899999988866654321 


Q ss_pred             HHhhCCCCCCCC-CHHHHHHHHHHHc--CCCeEEEEEeCCCCCChhc-HHHhhc
Q 043252          269 LSIASDQNVDNH-DLNKLQEELKKQL--FGKKFLLVLDDVWNENYTD-WVHLSL  318 (337)
Q Consensus       269 ~~~~~~~~~~~~-~~~~~~~~l~~~L--~~kr~LlVlDdv~~~~~~~-~~~l~~  318 (337)
                         ..... ... ...-+.+.+....  .+++++||||++...+... +..+..
T Consensus       246 ---rP~~v-gy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani~kiFGel~~  295 (459)
T PRK11331        246 ---RPNGV-GFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMM  295 (459)
T ss_pred             ---CCCCC-CeEecCchHHHHHHHHHhcccCCcEEEEehhhccCHHHhhhhhhh
Confidence               11110 110 0011222222222  2468999999997665433 334433

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.49  E-value=5.8e-07  Score=84.88  Aligned_cols=109  Identities=19%  Similarity=0.301  Sum_probs=64.7

Q ss_pred             cccccchhHHHH---HHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKE---IVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~---l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..+..   |..++...      ....+.++|++|+||||||+.+++..  ...|     +.++.......-++
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~------~~~~ilL~GppGtGKTtLA~~ia~~~--~~~~-----~~l~a~~~~~~~ir   78 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAG------RLSSMILWGPPGTGKTTLARIIAGAT--DAPF-----EALSAVTSGVKDLR   78 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcC------CCceEEEECCCCCCHHHHHHHHHHHh--CCCE-----EEEecccccHHHHH
Confidence            458888777555   77776432      34578889999999999999998752  2222     22222111111122


Q ss_pred             HHHHHhhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEE
Q 043252          266 SILLSIASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIV  331 (337)
Q Consensus       266 ~il~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iiv  331 (337)
                      .++.                  ..... ..+++.+|+||+++.......+.|...+..   |+.+++
T Consensus        79 ~ii~------------------~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~---~~iilI  124 (413)
T PRK13342         79 EVIE------------------EARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED---GTITLI  124 (413)
T ss_pred             HHHH------------------HHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhc---CcEEEE
Confidence            2222                  22111 146788999999987765566666655543   444444

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.48  E-value=1e-06  Score=81.02  Aligned_cols=45  Identities=13%  Similarity=0.259  Sum_probs=37.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|++..++.|..++..+      ..+.+.++|+.|+||||+|+.+.+.
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~------~~~~lll~Gp~GtGKT~la~~~~~~   59 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSP------NLPHLLVQGPPGSGKTAAVRALARE   59 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCC------CCceEEEECCCCCCHHHHHHHHHHH
Confidence            56889999999999988543      2346789999999999999998874

>TIGR00767 rho transcription termination factor Rho

Probab=98.47  E-value=3.5e-07  Score=84.03  Aligned_cols=91  Identities=16%  Similarity=0.148  Sum_probs=63.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC--CCHHHHHHHHHHHhhCCCCCCCCCH-----HHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD--FDVIRLTKSILLSIASDQNVDNHDL-----NKLQEE  288 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~--~~~~~~~~~il~~~~~~~~~~~~~~-----~~~~~~  288 (337)
                      -..++|+|++|+|||||++.+++.... ++|+..+|+.+.+.  .++.+++..++..+-..........     ....+.
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~-nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~  246 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITR-NHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEK  246 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhcc-cCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHH
Confidence            358999999999999999999986433 37999999999866  7889999988655433332111111     112222


Q ss_pred             HHHH-cCCCeEEEEEeCCCC
Q 043252          289 LKKQ-LFGKKFLLVLDDVWN  307 (337)
Q Consensus       289 l~~~-L~~kr~LlVlDdv~~  307 (337)
                      .... -+|++.+|++|++..
T Consensus       247 Ae~~~~~GkdVVLlIDEitR  266 (415)
T TIGR00767       247 AKRLVEHKKDVVILLDSITR  266 (415)
T ss_pred             HHHHHHcCCCeEEEEEChhH
Confidence            2222 268999999999953

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

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.46  E-value=1.7e-06  Score=85.15  Aligned_cols=135  Identities=18%  Similarity=0.231  Sum_probs=76.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+..++.|.+++....     -...+.++|..|+||||+|+.+.+.......+.       +.++..-.....|.
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR-----L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~-------~~PCG~C~sCr~I~   83 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR-----LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVT-------SQPCGVCRACREID   83 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC-----CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCC-------CCCCcccHHHHHHh
Confidence            568999999999999986443     245667999999999999998876422111110       00111001111111


Q ss_pred             HH-----hhCCCCCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          269 LS-----IASDQNVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       269 ~~-----~~~~~~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      ..     +..+.. .....+++.+.+...    ..++.-++|||++...+...|+.|+..|..-....++|+||.+.
T Consensus        84 ~G~h~DviEIDAa-s~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~  159 (830)
T PRK07003         84 EGRFVDYVEMDAA-SNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDP  159 (830)
T ss_pred             cCCCceEEEeccc-ccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECCh
Confidence            00     000000 111122222222211    12445588999998877778888888776656677888887653

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.35  E-value=6.5e-06  Score=76.40  Aligned_cols=135  Identities=16%  Similarity=0.193  Sum_probs=73.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+.-++.+...+....     -...+.++|+.|+||||+|+.+.+.-.....+.       ..++..-....++.
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~~-----~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~-------~~pc~~c~~c~~~~   83 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLGR-----IHHAWLLSGTRGVGKTTIARLLAKSLNCQNGIT-------SNPCRKCIICKEIE   83 (363)
T ss_pred             hhccChHHHHHHHHHHHHcCC-----CCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCCCHHHHHHh
Confidence            568999999999999886433     245789999999999999999976421111000       00000000011111


Q ss_pred             HHhhCC----CCCCCCCHHH---HHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASD----QNVDNHDLNK---LQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~----~~~~~~~~~~---~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ......    ........+.   +.+.+... ..+++-++|+|++.......++.+...+.......++|++|.+
T Consensus        84 ~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~  158 (363)
T PRK14961         84 KGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTD  158 (363)
T ss_pred             cCCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCC
Confidence            100000    0000011222   11111111 1245569999999877656777887777765666777777643

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.33  E-value=6.2e-06  Score=80.17  Aligned_cols=136  Identities=16%  Similarity=0.223  Sum_probs=76.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc---cccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED---HFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      .++||.+.-++.|.+++....     -.+.+.++|+.|+||||+|+.+.+......   ....     .+.++..-....
T Consensus        16 ddVIGQe~vv~~L~~al~~gR-----LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~-----~~~PCG~C~sC~   85 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR-----LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGI-----TAQPCGQCRACT   85 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC-----CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccC-----CCCCCcccHHHH
Confidence            568999999999999997544     245778999999999999998876421100   0000     000000000111


Q ss_pred             HHHHHh-----hCCCCCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          266 SILLSI-----ASDQNVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       266 ~il~~~-----~~~~~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      .|...-     ..+.. .....+++.+.+...    ..++.-++|||++...+...++.|+..|..-..+.++|++|.+
T Consensus        86 ~I~aG~hpDviEIdAa-s~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323         86 EIDAGRFVDYIEMDAA-SNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             HHHcCCCCcceEeccc-ccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCC
Confidence            111000     00000 111222222222221    1356669999999888778888888888765556676666643

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

Probab=98.32  E-value=4.9e-06  Score=76.77  Aligned_cols=118  Identities=19%  Similarity=0.174  Sum_probs=83.6

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~  266 (337)
                      .+..++||+.|++.+.+|+...-  +.+...-+.|.|-+|.|||.+...++.+......=.+++++++..-.....++..
T Consensus       148 ~p~~l~gRe~e~~~v~~F~~~hl--e~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~k  225 (529)
T KOG2227|consen  148 PPGTLKGRELEMDIVREFFSLHL--ELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKK  225 (529)
T ss_pred             CCCCccchHHHHHHHHHHHHhhh--hcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHH
Confidence            45789999999999999987543  2345668899999999999999999986432222124577777766677888888


Q ss_pred             HHHHhhCCCCCCCCCHHHHHHHHHHHcCCC--eEEEEEeCCCC
Q 043252          267 ILLSIASDQNVDNHDLNKLQEELKKQLFGK--KFLLVLDDVWN  307 (337)
Q Consensus       267 il~~~~~~~~~~~~~~~~~~~~l~~~L~~k--r~LlVlDdv~~  307 (337)
                      |...+..... ......+.+..+.++....  -||+|||..+.
T Consensus       226 I~~~~~q~~~-s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~  267 (529)
T KOG2227|consen  226 IFSSLLQDLV-SPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDH  267 (529)
T ss_pred             HHHHHHHHhc-CCchhHHHHHHHHHHHhcccceEEEEechhhH
Confidence            8888733322 1222255666666666544  58999999854

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.32  E-value=6.9e-06  Score=81.14  Aligned_cols=141  Identities=21%  Similarity=0.212  Sum_probs=85.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccc---cceEEEEeCCC---CCHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF---DLKAWTCVSDD---FDVIR  262 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~v~~~---~~~~~  262 (337)
                      +.++|++..+..+...+...      ....+.|+|++|+||||||+.+++.......+   ...-|+.+...   .+...
T Consensus       154 ~~iiGqs~~~~~l~~~ia~~------~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~  227 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVASP------FPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPRE  227 (615)
T ss_pred             HhceeCcHHHHHHHHHHhcC------CCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHH
Confidence            45889999999888877432      23479999999999999999998764332222   12345544321   12222


Q ss_pred             HHHHH---------------HHHhhCCCC---------------CCCCC-HHHHHHHHHHHcCCCeEEEEEeCCCCCChh
Q 043252          263 LTKSI---------------LLSIASDQN---------------VDNHD-LNKLQEELKKQLFGKKFLLVLDDVWNENYT  311 (337)
Q Consensus       263 ~~~~i---------------l~~~~~~~~---------------~~~~~-~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~  311 (337)
                      +...+               +...+....               .+... ....+..+.+.+.+++++++-|+.|..+..
T Consensus       228 i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~  307 (615)
T TIGR02903       228 VTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDDPN  307 (615)
T ss_pred             HhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecceeccCCcc
Confidence            21111               111110000               00111 134678899999999999998888877667


Q ss_pred             cHHHhhccCCCCCCCcEEEE--EecC
Q 043252          312 DWVHLSLPFQAGAQGSKIIV--TTRN  335 (337)
Q Consensus       312 ~~~~l~~~l~~~~~gs~iiv--TTR~  335 (337)
                      .|..+...+....+...|++  ||++
T Consensus       308 ~~~~ik~~~~~~~~~~~VLI~aTt~~  333 (615)
T TIGR02903       308 VPKYIKKLFEEGAPADFVLIGATTRD  333 (615)
T ss_pred             cchhhhhhcccCccceEEEEEecccc
Confidence            78888777766555554555  4553

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.30  E-value=2.4e-06  Score=77.47  Aligned_cols=50  Identities=28%  Similarity=0.452  Sum_probs=39.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|+|++..++.|..++..... .......+.++|++|+|||+||+.+.+.
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~-~~~~~~~~ll~Gp~G~GKT~la~~ia~~   53 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKM-RQEALDHLLLYGPPGLGKTTLAHIIANE   53 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHh-cCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999998864321 1223456889999999999999999875

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.30  E-value=1.4e-05  Score=78.80  Aligned_cols=130  Identities=20%  Similarity=0.273  Sum_probs=87.1

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC-CCHHHHHHHHHHHhhCCCCC
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD-FDVIRLTKSILLSIASDQNV  277 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~-~~~~~~~~~il~~~~~~~~~  277 (337)
                      ..|++.|..     ..+.+.+.|..|+|.|||||+-.....   ...=..+.|.++.+. .++..++..++..+..-.+.
T Consensus        25 ~rL~~~L~~-----~~~~RL~li~APAGfGKttl~aq~~~~---~~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~   96 (894)
T COG2909          25 PRLLDRLRR-----ANDYRLILISAPAGFGKTTLLAQWREL---AADGAAVAWLSLDESDNDPARFLSYLIAALQQATPT   96 (894)
T ss_pred             HHHHHHHhc-----CCCceEEEEeCCCCCcHHHHHHHHHHh---cCcccceeEeecCCccCCHHHHHHHHHHHHHHhCcc
Confidence            345555543     336899999999999999999988741   112235899998764 56788999998888743321


Q ss_pred             ------------CCCCHHHHHHHHHHHcC--CCeEEEEEeCCCCCChhcHHH-hhccCCCCCCCcEEEEEecCC
Q 043252          278 ------------DNHDLNKLQEELKKQLF--GKKFLLVLDDVWNENYTDWVH-LSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       278 ------------~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~~~~~~~~-l~~~l~~~~~gs~iivTTR~~  336 (337)
                                  ...+...+.+.+..-|.  .+.+++||||..--....... +.-.+...+.+-.+|||||++
T Consensus        97 ~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~r  170 (894)
T COG2909          97 LGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSR  170 (894)
T ss_pred             ccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccC
Confidence                        23344555555555543  467899999986543334443 333344556778999999985

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.29  E-value=7.7e-06  Score=79.05  Aligned_cols=122  Identities=18%  Similarity=0.194  Sum_probs=75.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc-------------------cccce
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED-------------------HFDLK  249 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~  249 (337)
                      .+++|.+..+..|...+....     -...+.++|+.|+||||+|+.+.+......                   .|...
T Consensus        16 ~diiGq~~~v~~L~~~i~~~r-----l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dl   90 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQK-----VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDL   90 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCce
Confidence            468999999999999886433     245678999999999999999976321100                   11112


Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcE
Q 043252          250 AWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSK  328 (337)
Q Consensus       250 ~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~  328 (337)
                      +++.......+.                   +...+.+.+... ..+++-++|+|++...+...++.|...+......+.
T Consensus        91 ieidaas~~gvd-------------------~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~  151 (546)
T PRK14957         91 IEIDAASRTGVE-------------------ETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVK  151 (546)
T ss_pred             EEeecccccCHH-------------------HHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCce
Confidence            222221111111                   122222222221 235667999999987766778888888876666676


Q ss_pred             EEEEec
Q 043252          329 IIVTTR  334 (337)
Q Consensus       329 iivTTR  334 (337)
                      +|++|-
T Consensus       152 fIL~Tt  157 (546)
T PRK14957        152 FILATT  157 (546)
T ss_pred             EEEEEC
Confidence            665553

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.28  E-value=6.7e-06  Score=82.49  Aligned_cols=123  Identities=15%  Similarity=0.175  Sum_probs=75.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccc------ccc-------------e
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDH------FDL-------------K  249 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~------F~~-------------~  249 (337)
                      ..++|.+.-++.|.+++....     -...+.++|+.|+||||+|+.+.+.-.....      +.|             .
T Consensus        16 ddIIGQe~Iv~~LknaI~~~r-----l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~Dv   90 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQR-----LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDL   90 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-----CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceE
Confidence            568999999999999986543     2356689999999999999999875211111      000             1


Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcE
Q 043252          250 AWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSK  328 (337)
Q Consensus       250 ~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~  328 (337)
                      +++.......                   ..+...+...+... ..+++-++|||++........+.|+..+..-....+
T Consensus        91 iEidAas~~k-------------------VDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vr  151 (944)
T PRK14949         91 IEVDAASRTK-------------------VDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVK  151 (944)
T ss_pred             EEeccccccC-------------------HHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeE
Confidence            1111110011                   11122222222211 236677999999988777788888888866555667


Q ss_pred             EEEEecC
Q 043252          329 IIVTTRN  335 (337)
Q Consensus       329 iivTTR~  335 (337)
                      +|++|.+
T Consensus       152 FILaTTe  158 (944)
T PRK14949        152 FLLATTD  158 (944)
T ss_pred             EEEECCC
Confidence            7766543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.28  E-value=9.6e-07  Score=84.89  Aligned_cols=140  Identities=21%  Similarity=0.202  Sum_probs=75.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+.-.+.|..++....     -...+.++|++|+||||+|+.+.+.......+....|.|.+.. .+.......+
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-----l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~-~i~~~~h~dv   87 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-----LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCL-AVRRGAHPDV   87 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhH-HHhcCCCCce
Confidence            468999999999988886543     2457799999999999999999775322222222223221110 0000000000


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ..+............++...+... ..+++-+||||+++......++.|...+......+.+|++|.
T Consensus        88 ~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~  154 (504)
T PRK14963         88 LEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATT  154 (504)
T ss_pred             EEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcC
Confidence            000000000111112222222211 135666999999987766778888887766555556666553

>PRK04195 replication factor C large subunit; Provisional

Probab=98.27  E-value=6e-06  Score=79.60  Aligned_cols=121  Identities=20%  Similarity=0.182  Sum_probs=72.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|.+..++.|.+|+.....  +...+.+.|+|++|+||||+|+.+++...    |+ .+-++.+...+. ..+..++
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~--g~~~~~lLL~GppG~GKTtla~ala~el~----~~-~ielnasd~r~~-~~i~~~i   85 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLK--GKPKKALLLYGPPGVGKTSLAHALANDYG----WE-VIELNASDQRTA-DVIERVA   85 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhc--CCCCCeEEEECCCCCCHHHHHHHHHHHcC----CC-EEEEcccccccH-HHHHHHH
Confidence            4689999999999999975431  22367899999999999999999988531    22 222344432222 2333333


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCCh----hcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENY----TDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~----~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ........               ....++-+||||++.....    ..+..+...+..  ....||+|+.
T Consensus        86 ~~~~~~~s---------------l~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n  138 (482)
T PRK04195         86 GEAATSGS---------------LFGARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTAN  138 (482)
T ss_pred             HHhhccCc---------------ccCCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEecc
Confidence            32221110               0113677999999976422    235555555543  2345666663

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.26  E-value=9.4e-06  Score=79.11  Aligned_cols=135  Identities=16%  Similarity=0.190  Sum_probs=76.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|.+.....|..++....     -...+.++|+.|+||||+|+.+.+......      |+.. .+++.-...+.+.
T Consensus        15 ddVIGQe~vv~~L~~aI~~gr-----l~HAyLF~GPpGvGKTTlAriLAK~LnC~~------~~~~-~pCg~C~sC~~I~   82 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGR-----LHHAYLFTGTRGVGKTTIARILAKCLNCET------GVTS-TPCEVCATCKAVN   82 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHhCCCc------CCCC-CCCccCHHHHHHh
Confidence            568999999999999997543     246889999999999999998876421111      1100 0001000011110


Q ss_pred             HHhhCC----CCCCCCCHHHHHHHHHH---H-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASD----QNVDNHDLNKLQEELKK---Q-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~----~~~~~~~~~~~~~~l~~---~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..-...    ........+.+.+.+..   . ..+++-++|||++...+....+.|...+.....+.++|++|.+
T Consensus        83 ~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd  157 (702)
T PRK14960         83 EGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTD  157 (702)
T ss_pred             cCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECC
Confidence            000000    00001122222211111   1 1356668999999887667777888777765566778887754

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.26  E-value=1.5e-05  Score=72.60  Aligned_cols=122  Identities=15%  Similarity=0.170  Sum_probs=70.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEe--CCCCCHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV--SDDFDVIRLTKS  266 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v--~~~~~~~~~~~~  266 (337)
                      .+++|+++.++.+..++....      .+.+.|+|++|+||||+|+.+.+... ...+. ..++.+  +...... ...+
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~------~~~~ll~G~~G~GKt~~~~~l~~~l~-~~~~~-~~~i~~~~~~~~~~~-~~~~   87 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKN------MPHLLFAGPPGTGKTTAALALARELY-GEDWR-ENFLELNASDERGID-VIRN   87 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCC------CCeEEEECCCCCCHHHHHHHHHHHHc-CCccc-cceEEeccccccchH-HHHH
Confidence            458899999999999986432      34579999999999999999987521 11121 112222  2222111 1222


Q ss_pred             HHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          267 ILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       267 il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      .+..+....+               .-...+-+|++|++..........+...+......+++|+++.
T Consensus        88 ~i~~~~~~~~---------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~  140 (319)
T PRK00440         88 KIKEFARTAP---------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCN  140 (319)
T ss_pred             HHHHHHhcCC---------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeC
Confidence            2222211110               0012356899999876544455566665554445567777764

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.25  E-value=8e-06  Score=74.40  Aligned_cols=119  Identities=20%  Similarity=0.186  Sum_probs=70.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+...+.+..++....     ...++.++|++|+||||+|+.+++..  ...   ...++.+. .. ...+...+
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~~-----~~~~lll~G~~G~GKT~la~~l~~~~--~~~---~~~i~~~~-~~-~~~i~~~l   88 (316)
T PHA02544         21 DECILPAADKETFKSIVKKGR-----IPNMLLHSPSPGTGKTTVAKALCNEV--GAE---VLFVNGSD-CR-IDFVRNRL   88 (316)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC-----CCeEEEeeCcCCCCHHHHHHHHHHHh--Ccc---ceEeccCc-cc-HHHHHHHH
Confidence            568999999999999986432     34688889999999999999998752  111   22334333 11 11122211


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..+....                .+.+.+-+|||||+... .......+...+.....++++|+||..
T Consensus        89 ~~~~~~~----------------~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~  140 (316)
T PHA02544         89 TRFASTV----------------SLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANN  140 (316)
T ss_pred             HHHHHhh----------------cccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCC
Confidence            1111000                01134557899999655 223333444444444566788888753

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

Probab=98.25  E-value=5.3e-06  Score=75.27  Aligned_cols=90  Identities=29%  Similarity=0.421  Sum_probs=55.0

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHH-HHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEEL-KKQ  292 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l-~~~  292 (337)
                      ..+.-.-+||++|+||||||+.+...  ....|     ..++-..+-.                  .++....+.- ...
T Consensus        46 ~~l~SmIl~GPPG~GKTTlA~liA~~--~~~~f-----~~~sAv~~gv------------------kdlr~i~e~a~~~~  100 (436)
T COG2256          46 GHLHSMILWGPPGTGKTTLARLIAGT--TNAAF-----EALSAVTSGV------------------KDLREIIEEARKNR  100 (436)
T ss_pred             CCCceeEEECCCCCCHHHHHHHHHHh--hCCce-----EEeccccccH------------------HHHHHHHHHHHHHH
Confidence            35677889999999999999999874  33344     2333222211                  2222222222 222


Q ss_pred             cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEE
Q 043252          293 LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIV  331 (337)
Q Consensus       293 L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iiv  331 (337)
                      ..|++.+|.+|.|..-+..+-+.|...   -.+|.-|+|
T Consensus       101 ~~gr~tiLflDEIHRfnK~QQD~lLp~---vE~G~iilI  136 (436)
T COG2256         101 LLGRRTILFLDEIHRFNKAQQDALLPH---VENGTIILI  136 (436)
T ss_pred             hcCCceEEEEehhhhcChhhhhhhhhh---hcCCeEEEE
Confidence            348999999999987654555555443   456766665

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.24  E-value=3.8e-06  Score=76.93  Aligned_cols=51  Identities=25%  Similarity=0.405  Sum_probs=40.2

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+|+|++..++.+..++..... .+.....+.|+|++|+||||||+.+.+.
T Consensus        24 ~~~~vG~~~~~~~l~~~l~~~~~-~~~~~~~~ll~GppG~GKT~la~~ia~~   74 (328)
T PRK00080         24 LDEFIGQEKVKENLKIFIEAAKK-RGEALDHVLLYGPPGLGKTTLANIIANE   74 (328)
T ss_pred             HHHhcCcHHHHHHHHHHHHHHHh-cCCCCCcEEEECCCCccHHHHHHHHHHH
Confidence            35799999999999888864221 1234567889999999999999999885

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.22  E-value=1.4e-05  Score=77.18  Aligned_cols=123  Identities=17%  Similarity=0.158  Sum_probs=75.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccc-------------------ccce
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDH-------------------FDLK  249 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~  249 (337)
                      .+++|-+.-++.|.+++....     -...+.++|+.|+||||+|+.+.+.--....                   |...
T Consensus        16 ~divGq~~v~~~L~~~~~~~~-----l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~   90 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY-----LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDL   90 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-----CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceE
Confidence            568999999999999996543     2347789999999999999988764211111                   1112


Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEE
Q 043252          250 AWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKI  329 (337)
Q Consensus       250 ~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~i  329 (337)
                      +.+..+....++++ ++++..+...                 -..++.-+++||++........+.+...|......+++
T Consensus        91 ~eidaas~~~v~~i-R~l~~~~~~~-----------------p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~f  152 (509)
T PRK14958         91 FEVDAASRTKVEDT-RELLDNIPYA-----------------PTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKF  152 (509)
T ss_pred             EEEcccccCCHHHH-HHHHHHHhhc-----------------cccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEE
Confidence            22222222222221 1222221110                 01355668999999887777888888888766667777


Q ss_pred             EEEec
Q 043252          330 IVTTR  334 (337)
Q Consensus       330 ivTTR  334 (337)
                      |++|-
T Consensus       153 Ilatt  157 (509)
T PRK14958        153 ILATT  157 (509)
T ss_pred             EEEEC
Confidence            77663

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

Probab=98.21  E-value=1.5e-05  Score=70.49  Aligned_cols=108  Identities=17%  Similarity=0.183  Sum_probs=77.3

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc----cccccceEEEEeCCCCCHHHHHHHHHHHh
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV----EDHFDLKAWTCVSDDFDVIRLTKSILLSI  271 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~----~~~F~~~~wv~v~~~~~~~~~~~~il~~~  271 (337)
                      +-++.|.++|..+.   ......+.|||..|.|||++++.++...-.    ...--.++.|.+....+...++..|+.++
T Consensus        44 ~~L~~L~~Ll~~P~---~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~l  120 (302)
T PF05621_consen   44 EALDRLEELLEYPK---RHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEAL  120 (302)
T ss_pred             HHHHHHHHHHhCCc---ccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHh
Confidence            44566777776554   345678999999999999999999864211    11112577888899999999999999999


Q ss_pred             hCCCCCCCCCHHHHHHHHHHHcCC-CeEEEEEeCCCC
Q 043252          272 ASDQNVDNHDLNKLQEELKKQLFG-KKFLLVLDDVWN  307 (337)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~  307 (337)
                      +.... .......+.......|+. +-=+||+|++.+
T Consensus       121 gaP~~-~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~  156 (302)
T PF05621_consen  121 GAPYR-PRDRVAKLEQQVLRLLRRLGVRMLIIDEFHN  156 (302)
T ss_pred             CcccC-CCCCHHHHHHHHHHHHHHcCCcEEEeechHH
Confidence            98765 445555555555555532 233889999966

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

>PLN03025 replication factor C subunit; Provisional

Probab=98.21  E-value=1.6e-05  Score=72.54  Aligned_cols=124  Identities=13%  Similarity=0.137  Sum_probs=69.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccc-eEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDL-KAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~v~~~~~~~~~~~~i  267 (337)
                      .+++|.++.++.|..++...      ..+-+.++|++|+||||+|+.+.+... ...|.. ++=++.+...+. +.++++
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~------~~~~lll~Gp~G~GKTtla~~la~~l~-~~~~~~~~~eln~sd~~~~-~~vr~~   84 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDG------NMPNLILSGPPGTGKTTSILALAHELL-GPNYKEAVLELNASDDRGI-DVVRNK   84 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHHHh-cccCccceeeecccccccH-HHHHHH
Confidence            46889888888888877543      234577999999999999999887421 112211 111222222221 122333


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      +..+..... .             .-.++.-+++||++..-.......+...+..-...+++|+++.
T Consensus        85 i~~~~~~~~-~-------------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n  137 (319)
T PLN03025         85 IKMFAQKKV-T-------------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACN  137 (319)
T ss_pred             HHHHHhccc-c-------------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeC
Confidence            222211100 0             0023466999999987655555566555544345567777664

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.20  E-value=2.2e-05  Score=76.22  Aligned_cols=123  Identities=17%  Similarity=0.201  Sum_probs=73.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc-------------------cccce
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED-------------------HFDLK  249 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~  249 (337)
                      .+++|.+.-++.|..++....     -...+.++|+.|+||||+|+.+...-....                   .|...
T Consensus        16 ~divGq~~v~~~L~~~i~~~~-----~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~   90 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR-----LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDL   90 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCce
Confidence            568999999999999987543     235678999999999999999865321110                   01111


Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEE
Q 043252          250 AWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKI  329 (337)
Q Consensus       250 ~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~i  329 (337)
                      +++..+....+.. +++++..+...                 -..+++-++|+|++........+.|...+......+.+
T Consensus        91 ~ei~~~~~~~vd~-ir~l~~~~~~~-----------------p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~f  152 (527)
T PRK14969         91 IEVDAASNTQVDA-MRELLDNAQYA-----------------PTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKF  152 (527)
T ss_pred             eEeeccccCCHHH-HHHHHHHHhhC-----------------cccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEE
Confidence            2222111111111 11222211100                 01356679999999877666777788777765556667


Q ss_pred             EEEec
Q 043252          330 IVTTR  334 (337)
Q Consensus       330 ivTTR  334 (337)
                      |++|.
T Consensus       153 IL~t~  157 (527)
T PRK14969        153 ILATT  157 (527)
T ss_pred             EEEeC
Confidence            76664

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

Probab=98.20  E-value=5.1e-06  Score=70.35  Aligned_cols=50  Identities=28%  Similarity=0.414  Sum_probs=34.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|+|.+.-++.+.-++..... .++.+.-+.+||++|+||||||..+.+.
T Consensus        24 ~efiGQ~~l~~~l~i~i~aa~~-r~~~l~h~lf~GPPG~GKTTLA~IIA~e   73 (233)
T PF05496_consen   24 DEFIGQEHLKGNLKILIRAAKK-RGEALDHMLFYGPPGLGKTTLARIIANE   73 (233)
T ss_dssp             CCS-S-HHHHHHHHHHHHHHHC-TTS---EEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHccCcHHHHhhhHHHHHHHHh-cCCCcceEEEECCCccchhHHHHHHHhc
Confidence            5799999888887655542211 2345778999999999999999999985

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.

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

Probab=98.20  E-value=1.4e-05  Score=72.00  Aligned_cols=112  Identities=23%  Similarity=0.298  Sum_probs=80.9

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ++.+.+|+.++..+..++...+.   .-++.|-|+|-.|.|||.+.+.+.+....     ..+|+++-+.|+...++..|
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~---~~PS~~~iyG~sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~I   76 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSC---TIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKI   76 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCc---ccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHH
Confidence            46788999999999999975542   23556789999999999999999986422     36899999999999999999


Q ss_pred             HHHhh-CCCCCCC-----CCHHHHHHHHHHH--c--CCCeEEEEEeCCCC
Q 043252          268 LLSIA-SDQNVDN-----HDLNKLQEELKKQ--L--FGKKFLLVLDDVWN  307 (337)
Q Consensus       268 l~~~~-~~~~~~~-----~~~~~~~~~l~~~--L--~~kr~LlVlDdv~~  307 (337)
                      +.... .......     .........+.++  .  .++.++||||++..
T Consensus        77 L~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~  126 (438)
T KOG2543|consen   77 LNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADA  126 (438)
T ss_pred             HHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHh
Confidence            99985 2222111     1122233333331  1  25689999999954

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.19  E-value=1.8e-05  Score=77.77  Aligned_cols=134  Identities=19%  Similarity=0.265  Sum_probs=72.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+..+..|..++....     -...+.++|+.|+||||+|+.+.+.-.......   +    .++..-.....+.
T Consensus        16 ddIIGQe~vv~~L~~ai~~~r-----l~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~---~----~pCg~C~sCr~i~   83 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGR-----LHHAYLLTGTRGVGKTTIARILAKSLNCENAQH---G----EPCGVCQSCTQID   83 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCcHHHHHHHHHHHhcccCCCC---C----CCCcccHHHHHHh
Confidence            578999999999999997543     245789999999999999998876321111000   0    0000000000000


Q ss_pred             HH-----hhCCCCCCCCCHHHHHHHHHH---H-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LS-----IASDQNVDNHDLNKLQEELKK---Q-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~-----~~~~~~~~~~~~~~~~~~l~~---~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..     +..... .....+.+.+.+..   . ..+++-++|||++..........|...+..-...+++|++|.+
T Consensus        84 ~g~~~DvlEidaA-s~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd  158 (709)
T PRK08691         84 AGRYVDLLEIDAA-SNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTD  158 (709)
T ss_pred             ccCccceEEEecc-ccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCC
Confidence            00     000000 11122222222211   1 1256668999999776555666777777554456677777643

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

Probab=98.18  E-value=7.9e-06  Score=81.71  Aligned_cols=110  Identities=23%  Similarity=0.333  Sum_probs=62.8

Q ss_pred             cccccchhHHH---HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKK---EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~---~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      .+|+|.+..+.   .|...+...      ....+.++|++|+||||||+.+++.  ...+|.     .++....      
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~------~~~slLL~GPpGtGKTTLA~aIA~~--~~~~f~-----~lna~~~------   88 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKAD------RVGSLILYGPPGVGKTTLARIIANH--TRAHFS-----SLNAVLA------   88 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHH--hcCcce-----eehhhhh------
Confidence            45889887764   455555432      3456789999999999999999975  333331     1111000      


Q ss_pred             HHHHHhhCCCCCCCCCHHHHHHHHHHHc--CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          266 SILLSIASDQNVDNHDLNKLQEELKKQL--FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       266 ~il~~~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                                  ...+.........+.+  .+++.+|+|||++.-+...++.|...+.   .|+.++++
T Consensus        89 ------------~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE---~g~IiLI~  142 (725)
T PRK13341         89 ------------GVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVE---NGTITLIG  142 (725)
T ss_pred             ------------hhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhc---CceEEEEE
Confidence                        0001111112222222  2467799999998765566666665443   35555553

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.17  E-value=2.5e-06  Score=80.50  Aligned_cols=138  Identities=17%  Similarity=0.196  Sum_probs=75.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+..+..|..++....     -...+.++|+.|+||||+|+.+.+.-........   ..+....+-..+...+.
T Consensus        18 ~dvVGQe~iv~~L~~~i~~~r-----i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~---~pCg~C~sC~~i~~g~~   89 (484)
T PRK14956         18 RDVIHQDLAIGALQNALKSGK-----IGHAYIFFGPRGVGKTTIARILAKRLNCENPIGN---EPCNECTSCLEITKGIS   89 (484)
T ss_pred             HHHhChHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHhcCcccccCc---cccCCCcHHHHHHccCC
Confidence            568999999999999986543     2346899999999999999999764211110000   00001011111111000


Q ss_pred             HH---hhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LS---IASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~---~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ..   +.........+...+.+.+... ..++.-++|||++.......++.|...+........+|++|.
T Consensus        90 ~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTt  159 (484)
T PRK14956         90 SDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATT  159 (484)
T ss_pred             ccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecC
Confidence            00   0000000111222333333222 235566999999988777888888887765444555555553

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.17  E-value=2.4e-05  Score=75.13  Aligned_cols=136  Identities=17%  Similarity=0.181  Sum_probs=74.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccc-eEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDL-KAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~v~~~~~~~~~~~~i  267 (337)
                      .+++|.+.-+..|...+....     -...+.++|+.|+||||+|+.+++.-.....+.. ..+..+...    .....+
T Consensus        21 ~dliGq~~vv~~L~~ai~~~r-----i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C----~~C~~i   91 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILNDR-----LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQC----TNCISF   91 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCC----hHHHHH
Confidence            468999999998888776433     2457889999999999999999764211110000 000000000    000000


Q ss_pred             HHHhhCC----CCCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          268 LLSIASD----QNVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       268 l~~~~~~----~~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      .......    ........+.+.+.+...    +.+++-++|+|+++......|+.|...+......+.+|++|
T Consensus        92 ~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aT  165 (507)
T PRK06645         92 NNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFAT  165 (507)
T ss_pred             hcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEe
Confidence            0000000    000111222222222111    24567799999999877778888888887655666666555

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.16  E-value=4.5e-06  Score=72.15  Aligned_cols=55  Identities=15%  Similarity=0.164  Sum_probs=36.5

Q ss_pred             chhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC
Q 043252          194 RETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD  256 (337)
Q Consensus       194 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~  256 (337)
                      .+..++.+..++...      ....+.|+|+.|+|||+||+.+++...  ......++++++.
T Consensus        22 ~~~~~~~l~~~~~~~------~~~~lll~G~~G~GKT~la~~~~~~~~--~~~~~~~~i~~~~   76 (226)
T TIGR03420        22 NAELLAALRQLAAGK------GDRFLYLWGESGSGKSHLLQAACAAAE--ERGKSAIYLPLAE   76 (226)
T ss_pred             cHHHHHHHHHHHhcC------CCCeEEEECCCCCCHHHHHHHHHHHHH--hcCCcEEEEeHHH
Confidence            345667777775422      345899999999999999999987521  2223345555443

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=98.16  E-value=3.1e-06  Score=73.36  Aligned_cols=37  Identities=22%  Similarity=0.110  Sum_probs=26.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVS  255 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~  255 (337)
                      +.+.|+|++|+|||+|++.+++..  ........|+.+.
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~--~~~~~~~~y~~~~   76 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHY--LLNQRTAIYIPLS   76 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH--HHcCCCeEEeeHH
Confidence            578999999999999999999852  2222334566553

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.15  E-value=1.7e-05  Score=77.95  Aligned_cols=135  Identities=18%  Similarity=0.207  Sum_probs=76.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+.-+..|...+....     -...+.++|+.|+||||+|+.+.+.......+.       ..++..-.....|.
T Consensus        16 ~divGQe~vv~~L~~~l~~~r-----l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~-------~~pCg~C~~C~~i~   83 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGR-----LHHAYLFSGTRGVGKTTIARLLAKGLNCETGIT-------ATPCGECDNCREIE   83 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCC-------CCCCCCCHHHHHHH
Confidence            568999999999998886433     235678999999999999999976421111000       00111111111111


Q ss_pred             HH-------hhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LS-------IASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~-------~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..       +.........+...+.+.+... ..+++-++|||++...+....+.|...+..-....++|++|.+
T Consensus        84 ~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~  158 (647)
T PRK07994         84 QGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTD  158 (647)
T ss_pred             cCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCC
Confidence            10       0000000111122222222211 2456679999999887777888888877765556666666544

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.14  E-value=3.2e-05  Score=75.86  Aligned_cols=137  Identities=15%  Similarity=0.205  Sum_probs=74.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccc--cceEEEEeCCCCCHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF--DLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~v~~~~~~~~~~~~  266 (337)
                      .+++|-+.-+..|.+++....     -...+.++|+.|+||||+|+.+.+.-......  .....    .+++.-.....
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r-----l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~----~pCg~C~~C~~   86 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR-----LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITA----TPCGVCQACRD   86 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCC----CCCCccHHHHH
Confidence            568999998999999987543     24678999999999999999985431110000  00000    00111111111


Q ss_pred             HHHHhhCC----CCCCCCCHHHHHHHHHH---H-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          267 ILLSIASD----QNVDNHDLNKLQEELKK---Q-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       267 il~~~~~~----~~~~~~~~~~~~~~l~~---~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      |...-..+    ........+.+.+.+..   . ..++.-++|||++...+...++.|...+.......++|++|.
T Consensus        87 i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Tt  162 (618)
T PRK14951         87 IDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATT  162 (618)
T ss_pred             HHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEEC
Confidence            10000000    00011122222222211   1 124455899999988877788888888876556667776653

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

Probab=98.12  E-value=1.2e-05  Score=72.01  Aligned_cols=94  Identities=19%  Similarity=0.250  Sum_probs=59.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF  294 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~  294 (337)
                      .+.-+.+||++|+||||||+.+.+..+...    +.+|..|-...-..-.+.|+++...                ...+.
T Consensus       161 ~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq~----------------~~~l~  220 (554)
T KOG2028|consen  161 RIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQN----------------EKSLT  220 (554)
T ss_pred             CCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHHH----------------HHhhh
Confidence            467888999999999999999988643333    4566666544333334444444321                12345


Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEE
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIV  331 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iiv  331 (337)
                      ++|-+|.+|.|..-+..+-+.+   ||.-.+|+-++|
T Consensus       221 krkTilFiDEiHRFNksQQD~f---LP~VE~G~I~lI  254 (554)
T KOG2028|consen  221 KRKTILFIDEIHRFNKSQQDTF---LPHVENGDITLI  254 (554)
T ss_pred             cceeEEEeHHhhhhhhhhhhcc---cceeccCceEEE
Confidence            7899999999976443333333   454556765554

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.12  E-value=2.8e-05  Score=74.28  Aligned_cols=46  Identities=30%  Similarity=0.390  Sum_probs=36.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+.-...|...+....     -.+.+.++|++|+||||+|+.+.+.
T Consensus        14 ~divGq~~i~~~L~~~i~~~~-----l~~~~Lf~GPpGtGKTTlA~~lA~~   59 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKNS-----ISHAYIFAGPRGTGKTTVARILAKS   59 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            568999888888888776433     2356899999999999999999764

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.09  E-value=3.3e-05  Score=72.56  Aligned_cols=139  Identities=14%  Similarity=0.164  Sum_probs=74.7

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEE-eCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC-VSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-v~~~~~~~~~~~~i  267 (337)
                      .+++|.+.-++.|..++.+..     -...+.++|+.|+||||+|+.+.+.-.....+....|.. ...++..-..-..+
T Consensus        16 ~eiiGq~~~~~~L~~~~~~~~-----~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~   90 (397)
T PRK14955         16 ADITAQEHITRTIQNSLRMGR-----VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDF   90 (397)
T ss_pred             hhccChHHHHHHHHHHHHhCC-----cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHH
Confidence            568899999999998886433     235688999999999999998876422111111000110 00111100111111


Q ss_pred             HHHhhCC----CCCCCCCHHHHHHHHHHHc-----CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          268 LLSIASD----QNVDNHDLNKLQEELKKQL-----FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       268 l~~~~~~----~~~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      ......+    ........+.+.+. .+.+     .+++-++|+|++.......++.+...+.+....+.+|++|
T Consensus        91 ~~~~~~n~~~~~~~~~~~id~Ir~l-~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t  164 (397)
T PRK14955         91 DAGTSLNISEFDAASNNSVDDIRLL-RENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFAT  164 (397)
T ss_pred             hcCCCCCeEeecccccCCHHHHHHH-HHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEe
Confidence            1110000    00011112333222 2222     3456688999997766667888888887666677776665

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.07  E-value=4.7e-05  Score=71.05  Aligned_cols=139  Identities=13%  Similarity=0.087  Sum_probs=73.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCC----CCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSR----NDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLT  264 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~----~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~  264 (337)
                      .+++|.+.-++.|..++..+...    ...-...+.++|+.|+|||++|+.+...--....-    +-++...    ..-
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~----~~~Cg~C----~~C   76 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPD----EPGCGEC----RAC   76 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCC----CCCCCCC----HHH
Confidence            46889999999999999764310    01124678899999999999998886531110000    0000000    000


Q ss_pred             HHHHHHhhCC----C-CCCCCCHHH---HHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          265 KSILLSIASD----Q-NVDNHDLNK---LQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       265 ~~il~~~~~~----~-~~~~~~~~~---~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..+...-...    . .......++   +.+.+... ..+++-++++|++...+....+.|...+.....+..+|++|.+
T Consensus        77 ~~~~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~  156 (394)
T PRK07940         77 RTVLAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPS  156 (394)
T ss_pred             HHHhcCCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECC
Confidence            0000000000    0 001111222   22222111 1245568888999877666777777777665566777777654

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

Probab=98.06  E-value=1.1e-05  Score=63.27  Aligned_cols=21  Identities=43%  Similarity=0.464  Sum_probs=19.5

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|++|+||||+|+.+.+.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            579999999999999999986

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 ....

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.04  E-value=4.1e-05  Score=74.40  Aligned_cols=133  Identities=17%  Similarity=0.185  Sum_probs=72.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|.+..++.|..++....     -.+.+.++|+.|+||||+|+.+.+.-.      |.-|.... +++.-...+.+.
T Consensus        16 ~dIIGQe~iv~~L~~aI~~~r-----l~hA~Lf~GP~GvGKTTlA~~lAk~L~------C~~~~~~~-~Cg~C~sCr~i~   83 (605)
T PRK05896         16 KQIIGQELIKKILVNAILNNK-----LTHAYIFSGPRGIGKTSIAKIFAKAIN------CLNPKDGD-CCNSCSVCESIN   83 (605)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHHhc------CCCCCCCC-CCcccHHHHHHH
Confidence            568999999999999986543     235788999999999999999876421      11121110 111111111111


Q ss_pred             HHhhCCC----CCCCCCHH---HHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          269 LSIASDQ----NVDNHDLN---KLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       269 ~~~~~~~----~~~~~~~~---~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      .......    .......+   .+...+... ..+++-++|+|++.......+..|...+......+.+|++|
T Consensus        84 ~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896         84 TNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             cCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEEC
Confidence            1100000    00011122   222222111 12334469999998766677888887776555566666655

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.03  E-value=6.1e-05  Score=71.89  Aligned_cols=123  Identities=17%  Similarity=0.139  Sum_probs=75.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc------ccc-------------ccccce
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK------QVE-------------DHFDLK  249 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~------~~~-------------~~F~~~  249 (337)
                      .+++|.+..++.|.+.+....     -...+.++|+.|+||||+|+.+...-      ...             ..+..+
T Consensus        13 ~dliGQe~vv~~L~~a~~~~r-----i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv   87 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLNK-----IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDV   87 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCE
Confidence            568999999998888886443     23478999999999999998886521      000             011122


Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEE
Q 043252          250 AWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKI  329 (337)
Q Consensus       250 ~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~i  329 (337)
                      +.++.+....+.+ .+++++.+....                 ..+++-++|+|++........+.|...+..-.+.+++
T Consensus        88 ~eidaas~~~vdd-IR~Iie~~~~~P-----------------~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~f  149 (491)
T PRK14964         88 IEIDAASNTSVDD-IKVILENSCYLP-----------------ISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKF  149 (491)
T ss_pred             EEEecccCCCHHH-HHHHHHHHHhcc-----------------ccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEE
Confidence            3333332222222 222222221100                 1245668999999877666788888888766667777


Q ss_pred             EEEec
Q 043252          330 IVTTR  334 (337)
Q Consensus       330 ivTTR  334 (337)
                      |++|.
T Consensus       150 Ilatt  154 (491)
T PRK14964        150 ILATT  154 (491)
T ss_pred             EEEeC
Confidence            77763

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

Probab=98.02  E-value=5.2e-05  Score=65.16  Aligned_cols=122  Identities=24%  Similarity=0.276  Sum_probs=73.2

Q ss_pred             ccccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          186 VEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       186 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      +.-..++|.+.+++.|++-...--  .+....-+.++|..|.|||+|++.+.+...-+.    .--|.+...        
T Consensus        24 ~~l~~L~Gie~Qk~~l~~Nt~~Fl--~G~pannvLL~G~rGtGKSSlVkall~~y~~~G----LRlIev~k~--------   89 (249)
T PF05673_consen   24 IRLDDLIGIERQKEALIENTEQFL--QGLPANNVLLWGARGTGKSSLVKALLNEYADQG----LRLIEVSKE--------   89 (249)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHH--cCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC----ceEEEECHH--------
Confidence            445679999999888765432211  122345678899999999999999987422111    111233221        


Q ss_pred             HHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCC---CCCcEEEEEecC
Q 043252          266 SILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAG---AQGSKIIVTTRN  335 (337)
Q Consensus       266 ~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~---~~gs~iivTTR~  335 (337)
                                  +..++..+.+.++.  ...||+|.+||+..+ ....+..|++.|..+   .+..-+|..|-|
T Consensus        90 ------------~L~~l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSN  149 (249)
T PF05673_consen   90 ------------DLGDLPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSN  149 (249)
T ss_pred             ------------HhccHHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecc
Confidence                        23444555555553  357999999999654 234577777766532   233445555544

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.00  E-value=2.2e-05  Score=72.94  Aligned_cols=53  Identities=25%  Similarity=0.184  Sum_probs=39.7

Q ss_pred             cccccccchhHHHHHHHHHhcCCCC-------CCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSR-------NDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...++.|++..+++|.+.+..+-..       +-...+.+.++|++|+|||+||+.+++.
T Consensus       120 ~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~  179 (364)
T TIGR01242       120 SYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  179 (364)
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            3457899999999998877532110       1123456899999999999999999885

Many proteins may score above the trusted cutoff because an internal

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.00  E-value=5e-05  Score=59.54  Aligned_cols=88  Identities=19%  Similarity=0.057  Sum_probs=46.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      ..+.|+|++|+||||+++.+.....  ......+++..+...........  ........ ...........+.......
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~   77 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELG--PPGGGVIYIDGEDILEEVLDQLL--LIIVGGKK-ASGSGELRLRLALALARKL   77 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccC--CCCCCEEEECCEEccccCHHHHH--hhhhhccC-CCCCHHHHHHHHHHHHHhc
Confidence            4789999999999999999987522  22123455554443322211111  01111111 2222233333444444433


Q ss_pred             -eEEEEEeCCCCCC
Q 043252          297 -KFLLVLDDVWNEN  309 (337)
Q Consensus       297 -r~LlVlDdv~~~~  309 (337)
                       ..+|++|++....
T Consensus        78 ~~~viiiDei~~~~   91 (148)
T smart00382       78 KPDVLILDEITSLL   91 (148)
T ss_pred             CCCEEEEECCcccC
Confidence             3899999998753

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.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.99  E-value=6.7e-05  Score=73.62  Aligned_cols=136  Identities=15%  Similarity=0.177  Sum_probs=74.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccc--eEEEEeCCCCCHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDL--KAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~v~~~~~~~~~~~~  266 (337)
                      .+++|.+..++.|.+++....     -...+.++|+.|+||||+|+.+.+.-........  ..+    ..+..-.-...
T Consensus        24 ~dliGq~~~v~~L~~~~~~gr-----i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~----~~cg~c~~C~~   94 (598)
T PRK09111         24 DDLIGQEAMVRTLTNAFETGR-----IAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTI----DLCGVGEHCQA   94 (598)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCcc----ccCcccHHHHH
Confidence            578999999999999997543     2457889999999999999999764211110000  000    00000011111


Q ss_pred             HHHHhhCCC----CCCCCCHHH---HHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          267 ILLSIASDQ----NVDNHDLNK---LQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       267 il~~~~~~~----~~~~~~~~~---~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      |......+.    .......++   +.+.+... ..+++-++|+|++........+.|...|..-..++++|++|
T Consensus        95 i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111         95 IMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             HhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEe
Confidence            111110000    001112222   22222111 12455689999997766667778887777656677777666

>PRK08116 hypothetical protein; Validated

Probab=97.98  E-value=3.3e-05  Score=68.50  Aligned_cols=103  Identities=26%  Similarity=0.281  Sum_probs=57.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      ..+.++|..|+|||.||..+++..  ...-..+++++      ..+++..+.......   ...+...    +.+.+.+-
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l--~~~~~~v~~~~------~~~ll~~i~~~~~~~---~~~~~~~----~~~~l~~~  179 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANEL--IEKGVPVIFVN------FPQLLNRIKSTYKSS---GKEDENE----IIRSLVNA  179 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHH--HHcCCeEEEEE------HHHHHHHHHHHHhcc---ccccHHH----HHHHhcCC
Confidence            358899999999999999999863  22223345554      344555555444321   1112222    23333332


Q ss_pred             eEEEEEeCCCCCChhcHHH--hhccCCC-CCCCcEEEEEecC
Q 043252          297 KFLLVLDDVWNENYTDWVH--LSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~--l~~~l~~-~~~gs~iivTTR~  335 (337)
                      . ||||||+......+|..  +...+.. -.+|..+|+||..
T Consensus       180 d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~  220 (268)
T PRK08116        180 D-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNL  220 (268)
T ss_pred             C-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            3 89999996543344533  3332221 1345678998863

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.97  E-value=7.8e-05  Score=75.66  Aligned_cols=131  Identities=14%  Similarity=0.087  Sum_probs=74.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+..++.|..++....     -.+.+.++|+.|+||||+|+.+.+.......+...       .+..-.-...|.
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-----i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~-------pCg~C~sC~~~~   82 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-----INHAYLFSGPRGCGKTSSARILARSLNCVEGPTST-------PCGECDSCVALA   82 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-----CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCC-------CCcccHHHHHHH
Confidence            568999999999999997543     23578899999999999999987642211111000       000000000000


Q ss_pred             HH---------hhCCCCCCCCCHHHH---HHHHHH-HcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LS---------IASDQNVDNHDLNKL---QEELKK-QLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~---------~~~~~~~~~~~~~~~---~~~l~~-~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ..         +...   .....+++   .+.+.. -..+++-++|||++.......++.|+..|..-...+.+|++|.
T Consensus        83 ~g~~~~~dv~eidaa---s~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt  158 (824)
T PRK07764         83 PGGPGSLDVTEIDAA---SHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATT  158 (824)
T ss_pred             cCCCCCCcEEEeccc---ccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeC
Confidence            00         0000   11112222   221111 1235555889999988777888888888877666777776663

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.97  E-value=0.00013  Score=67.45  Aligned_cols=46  Identities=20%  Similarity=0.242  Sum_probs=37.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+..++.|.+++....     -...+.++|++|+||||+|+.+...
T Consensus        14 ~~iig~~~~~~~l~~~~~~~~-----~~~~~Ll~G~~G~GKt~~a~~la~~   59 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNGR-----IAHAYLFSGPRGTGKTSIARIFAKA   59 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999986433     2457889999999999999888654

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.94  E-value=0.00018  Score=60.38  Aligned_cols=41  Identities=12%  Similarity=0.126  Sum_probs=30.5

Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +.+-++|+|++.......++.|...+......+.+|++|.+
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~  135 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPS  135 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECC
Confidence            45668999999776666778888888765666777777754

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.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=4.3e-05  Score=75.35  Aligned_cols=135  Identities=13%  Similarity=0.172  Sum_probs=74.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+.-++.|..++....     -...+.++|+.|+||||+|+.+.+.-.....+.      ...+++.-.....|.
T Consensus        16 ~eiiGq~~~~~~L~~~i~~~~-----i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~------~~~~c~~c~~c~~i~   84 (585)
T PRK14950         16 AELVGQEHVVQTLRNAIAEGR-----VAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP------KGRPCGTCEMCRAIA   84 (585)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-----CceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCCCCccCHHHHHHh
Confidence            578999999999998886433     235678999999999999999976421110000      001111112222222


Q ss_pred             HHhhCCC----CCCCCCHHHH---HHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LSIASDQ----NVDNHDLNKL---QEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~~~~~~----~~~~~~~~~~---~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      .......    .......+.+   .+.+... ..+++-+||||++........+.|...+......+.+|++|.
T Consensus        85 ~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~  158 (585)
T PRK14950         85 EGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATT  158 (585)
T ss_pred             cCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeC
Confidence            2111100    0011122222   2222111 124567899999976655667777777765555666666653

>PRK10536 hypothetical protein; Provisional

Probab=97.89  E-value=0.00017  Score=62.67  Aligned_cols=131  Identities=13%  Similarity=0.164  Sum_probs=71.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEE----eCC-----CCC
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC----VSD-----DFD  259 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~----v~~-----~~~  259 (337)
                      ..+.++......+..+|.+.        .++.+.|+.|.|||+||..+..+.-..+.|+..+-..    +.+     +-+
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~--------~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~ge~LGfLPG~  126 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESK--------QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGD  126 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcC--------CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCchhhhCcCCCC
Confidence            34667888888888888532        3999999999999999988876422223344332221    111     001


Q ss_pred             HHHH----HHHHHHHhhCCCCCCCCCHHHHHH--------HHHHHcCCCeE---EEEEeCCCCCChhcHHHhhccCCCCC
Q 043252          260 VIRL----TKSILLSIASDQNVDNHDLNKLQE--------ELKKQLFGKKF---LLVLDDVWNENYTDWVHLSLPFQAGA  324 (337)
Q Consensus       260 ~~~~----~~~il~~~~~~~~~~~~~~~~~~~--------~l~~~L~~kr~---LlVlDdv~~~~~~~~~~l~~~l~~~~  324 (337)
                      ..+-    +.-+...+..-.  .....+.+..        .=..+++|+.+   +||+|+..+.+......+...+   +
T Consensus       127 ~~eK~~p~~~pi~D~L~~~~--~~~~~~~~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~~k~~ltR~---g  201 (262)
T PRK10536        127 IAEKFAPYFRPVYDVLVRRL--GASFMQYCLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQMKMFLTRL---G  201 (262)
T ss_pred             HHHHHHHHHHHHHHHHHHHh--ChHHHHHHHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHHHHHHHhhc---C
Confidence            1111    111111111100  0001111100        00235567655   9999999887665555555443   5


Q ss_pred             CCcEEEEE
Q 043252          325 QGSKIIVT  332 (337)
Q Consensus       325 ~gs~iivT  332 (337)
                      .+|+||+|
T Consensus       202 ~~sk~v~~  209 (262)
T PRK10536        202 ENVTVIVN  209 (262)
T ss_pred             CCCEEEEe
Confidence            78999986

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.88  E-value=0.00021  Score=69.92  Aligned_cols=133  Identities=14%  Similarity=0.089  Sum_probs=74.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+.-++.|..++....     -...+.++|+.|+||||+|+.+.+.-.......   +    .+++.-.....|.
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r-----~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~---~----~pCg~C~~C~~i~   80 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGR-----INHAYLFSGPRGCGKTSSARILARSLNCAQGPT---A----TPCGVCESCVALA   80 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHhccccCCC---C----CcccccHHHHHhh
Confidence            568999999999999997543     245678999999999999998876421111000   0    0000000001110


Q ss_pred             HH---------hhCCCCCCCCCHHHHHHHHHHHc-CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          269 LS---------IASDQNVDNHDLNKLQEELKKQL-FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       269 ~~---------~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      ..         +.........+..++.+.+...- .+++-++|||++........+.|...+..-.....+|++|
T Consensus        81 ~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952         81 PNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             cccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEe
Confidence            00         00000001111222222222211 3455689999998877778888888887666666666655

>PRK08118 topology modulation protein; Reviewed

Probab=97.87  E-value=8e-06  Score=67.16  Aligned_cols=34  Identities=38%  Similarity=0.638  Sum_probs=27.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhccccc-ccccceEE
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVE-DHFDLKAW  251 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~w  251 (337)
                      -|.|+|++|+||||||+.+++..... -+|+..+|
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            58999999999999999999875443 45777774

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.85  E-value=0.00026  Score=65.98  Aligned_cols=46  Identities=20%  Similarity=0.308  Sum_probs=38.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+...+.+.+.+....     -.+.+.++|+.|+||||+|+.+.+.
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~-----~~~~~L~~G~~G~GKt~~a~~la~~   62 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNH-----LAQALLFCGPRGVGKTTCARILARK   62 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999996433     2458899999999999999988764

>PRK08727 hypothetical protein; Validated

Probab=97.84  E-value=8.7e-05  Score=64.51  Aligned_cols=36  Identities=25%  Similarity=0.229  Sum_probs=26.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEe
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV  254 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  254 (337)
                      ..+.|+|..|+|||+|++.+++..  ........|+++
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~--~~~~~~~~y~~~   77 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAA--EQAGRSSAYLPL   77 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEEeH
Confidence            459999999999999999998752  222224456653

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.84  E-value=0.00014  Score=64.37  Aligned_cols=50  Identities=22%  Similarity=0.240  Sum_probs=33.3

Q ss_pred             ccccchhHHHHHHH---HHhc------CCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVE---LLLK------DDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~---~L~~------~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|.+..+++|.+   ++.-      ......+...-+.++|++|+||||+|+.+++.
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~   65 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKL   65 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHH
Confidence            47888777765543   3311      11112334567889999999999999999764

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.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=0.00019  Score=70.64  Aligned_cols=141  Identities=14%  Similarity=0.152  Sum_probs=74.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEE-eCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC-VSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-v~~~~~~~~~~~~i  267 (337)
                      ..++|.+.-+..|..++....     -...+.++|+.|+||||+|+.+.+.-.....++.-.|.. +..++..-.....+
T Consensus        16 ~eivGQe~i~~~L~~~i~~~r-----i~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~   90 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDR-----VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDF   90 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHH
Confidence            568999999999999886433     235688999999999999988875421111110000110 00011100111111


Q ss_pred             HHHhhCC----CCCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          268 LLSIASD----QNVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       268 l~~~~~~----~~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ...-..+    ........+++...+...    ..+++-++|+|++........+.|...+..-...+.+|++|.
T Consensus        91 ~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~  165 (620)
T PRK14954         91 DAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATT  165 (620)
T ss_pred             hccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeC
Confidence            1100000    000111223332222111    234555889999977666677788888876555666666553

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=0.0002  Score=70.37  Aligned_cols=134  Identities=17%  Similarity=0.221  Sum_probs=73.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+.-...|..++....     -.+.+.++|+.|+||||+|+.+.+.--.......       .+++.-.....|.
T Consensus        16 ~~iiGq~~v~~~L~~~i~~~~-----~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~-------~~c~~c~~c~~i~   83 (576)
T PRK14965         16 SDLTGQEHVSRTLQNAIDTGR-----VAHAFLFTGARGVGKTSTARILAKALNCEQGLTA-------EPCNVCPPCVEIT   83 (576)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC-------CCCCccHHHHHHh
Confidence            578999999999999986543     2456789999999999999988764211110000       0000000001110


Q ss_pred             HH-------hhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LS-------IASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~-------~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ..       +.........+..++.+.+... ..+++-++|+|++...+....+.|...|..-...+.+|++|.
T Consensus        84 ~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~  157 (576)
T PRK14965         84 EGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATT  157 (576)
T ss_pred             cCCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeC
Confidence            00       0000000111222222222211 124555899999987766777888887766555666666553

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.83  E-value=0.00019  Score=70.26  Aligned_cols=134  Identities=16%  Similarity=0.222  Sum_probs=72.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+..+..|...+....     -...+.++|+.|+||||+|+.+.+..-.......       .+++.-.....|.
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~r-----i~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~-------~pCg~C~sC~~i~   83 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENR-----VAPAYLFSGTRGVGKTTIARIFAKALNCETAPTG-------EPCNTCEQCRKVT   83 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHhccccCCCCC-------CCCcccHHHHHHh
Confidence            468899888888888886432     2457889999999999999988764211110000       0111111111111


Q ss_pred             HHhhCCC----CCCCCCHHH---HHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LSIASDQ----NVDNHDLNK---LQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~~~~~~----~~~~~~~~~---~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      .......    .......+.   +.+.+... ..+++-+||||++.......++.|...+..-.....+|++|.
T Consensus        84 ~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt  157 (624)
T PRK14959         84 QGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATT  157 (624)
T ss_pred             cCCCCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecC
Confidence            1100000    000111222   22222111 135667999999987766777888877765444556666554

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.82  E-value=0.00037  Score=56.94  Aligned_cols=121  Identities=15%  Similarity=0.107  Sum_probs=73.1

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccc------------------ccccceEEEEe
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVE------------------DHFDLKAWTCV  254 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~------------------~~F~~~~wv~v  254 (337)
                      |-++..+.|...+.+..     -...+.++|+.|+||+++|..+.+.---.                  .......|+.-
T Consensus         1 gq~~~~~~L~~~~~~~~-----l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~   75 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR-----LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKP   75 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC-------SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEET
T ss_pred             CcHHHHHHHHHHHHcCC-----cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEec
Confidence            55667777777776543     24578999999999999998876531111                  11222333332


Q ss_pred             CCC---CCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEE
Q 043252          255 SDD---FDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIV  331 (337)
Q Consensus       255 ~~~---~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iiv  331 (337)
                      ...   ...+++. ++...+.....                 .+++=++|||++.....+.+..|+..+..-...+.+|+
T Consensus        76 ~~~~~~i~i~~ir-~i~~~~~~~~~-----------------~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL  137 (162)
T PF13177_consen   76 DKKKKSIKIDQIR-EIIEFLSLSPS-----------------EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFIL  137 (162)
T ss_dssp             TTSSSSBSHHHHH-HHHHHCTSS-T-----------------TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEE
T ss_pred             ccccchhhHHHHH-HHHHHHHHHHh-----------------cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEE
Confidence            221   2222222 33333322111                 23456899999988888899999998887778899999


Q ss_pred             EecCC
Q 043252          332 TTRNQ  336 (337)
Q Consensus       332 TTR~~  336 (337)
                      +|.+.
T Consensus       138 ~t~~~  142 (162)
T PF13177_consen  138 ITNNP  142 (162)
T ss_dssp             EES-G
T ss_pred             EECCh
Confidence            98764

...

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.81  E-value=0.00032  Score=67.43  Aligned_cols=46  Identities=22%  Similarity=0.226  Sum_probs=37.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+.-...|.+++....     -...+.++|+.|+||||+|+.+...
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~-----i~hayLf~Gp~G~GKTtlAr~lAk~   61 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR-----VSHAYIFAGPRGTGKTTIARILAKV   61 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999996543     2356778999999999999988653

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.80  E-value=7.6e-05  Score=69.93  Aligned_cols=52  Identities=23%  Similarity=0.164  Sum_probs=39.0

Q ss_pred             ccccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++.|++..+++|.+.+..+-.       -+-...+-|.++|++|+|||++|+.+++.
T Consensus       130 ~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~  188 (389)
T PRK03992        130 YEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  188 (389)
T ss_pred             HHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHH
Confidence            45789999999999887643110       01133567899999999999999999874

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

Probab=97.80  E-value=4.6e-05  Score=65.78  Aligned_cols=36  Identities=31%  Similarity=0.316  Sum_probs=28.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEe
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV  254 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  254 (337)
                      -.++|+|..|+|||||...+..+  ....|..+++++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~--~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYY--LRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHh--hcccCCEEEEEec
Confidence            36889999999999999998865  6667876666643

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

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.79  E-value=0.00033  Score=69.19  Aligned_cols=122  Identities=14%  Similarity=0.185  Sum_probs=73.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc---------------------ccccc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV---------------------EDHFD  247 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~---------------------~~~F~  247 (337)
                      ..++|.+...+.|..++....     -...+.++|+.|+||||+|+.+......                     ..+|+
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~-----l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n   91 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNK-----LAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYN   91 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCc
Confidence            568999999999999996543     2457889999999999999887653210                     11222


Q ss_pred             ceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCc
Q 043252          248 LKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGS  327 (337)
Q Consensus       248 ~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs  327 (337)
                      . ..+.........+ +++++.++....                 ..+++=++|+|++.......++.|...+..-...+
T Consensus        92 ~-~~ld~~~~~~vd~-Ir~li~~~~~~P-----------------~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~t  152 (614)
T PRK14971         92 I-HELDAASNNSVDD-IRNLIEQVRIPP-----------------QIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYA  152 (614)
T ss_pred             e-EEecccccCCHHH-HHHHHHHHhhCc-----------------ccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCe
Confidence            1 1122211111111 112222211100                 12445588999998776678888888887656667


Q ss_pred             EEEEEec
Q 043252          328 KIIVTTR  334 (337)
Q Consensus       328 ~iivTTR  334 (337)
                      .+|++|.
T Consensus       153 ifIL~tt  159 (614)
T PRK14971        153 IFILATT  159 (614)
T ss_pred             EEEEEeC
Confidence            7666553

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.79  E-value=0.00039  Score=64.40  Aligned_cols=140  Identities=13%  Similarity=0.093  Sum_probs=78.0

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceE------EEEeCCCCCHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKA------WTCVSDDFDVI  261 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~------wv~v~~~~~~~  261 (337)
                      -.+++|.+.....|.+.+....     -...+.++|+.|+||+|+|..+...---........      -..+....   
T Consensus        18 ~~~iiGq~~~~~~L~~~~~~~r-----l~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c---   89 (365)
T PRK07471         18 TTALFGHAAAEAALLDAYRSGR-----LHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDH---   89 (365)
T ss_pred             hhhccChHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCC---
Confidence            3578999999999999987543     245799999999999999977754311111000000      00000000   


Q ss_pred             HHHHHHHHHhhCC---------CC----CCCCCHHHHHHHHHHHc-----CCCeEEEEEeCCCCCChhcHHHhhccCCCC
Q 043252          262 RLTKSILLSIASD---------QN----VDNHDLNKLQEELKKQL-----FGKKFLLVLDDVWNENYTDWVHLSLPFQAG  323 (337)
Q Consensus       262 ~~~~~il~~~~~~---------~~----~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~  323 (337)
                      ...+.+...-..+         ..    ......++ ...+.+.+     .+.+-++|||++...+....+.|...+..-
T Consensus        90 ~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~Vdq-iR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEep  168 (365)
T PRK07471         90 PVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDE-VRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEP  168 (365)
T ss_pred             hHHHHHHccCCCCeEEEecccccccccccccccHHH-HHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcC
Confidence            0111111100000         00    01112333 22333333     255669999999888778888888888765


Q ss_pred             CCCcEEEEEecCC
Q 043252          324 AQGSKIIVTTRNQ  336 (337)
Q Consensus       324 ~~gs~iivTTR~~  336 (337)
                      ..++.+|++|.+.
T Consensus       169 p~~~~~IL~t~~~  181 (365)
T PRK07471        169 PARSLFLLVSHAP  181 (365)
T ss_pred             CCCeEEEEEECCc
Confidence            5667778777653

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.78  E-value=8.9e-05  Score=64.45  Aligned_cols=91  Identities=24%  Similarity=0.215  Sum_probs=55.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhccccccc----ccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCC-
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDH----FDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHD-  281 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~-  281 (337)
                      .-.++.|+|++|+|||+|+.+++-.......    ...++|++....++..++.. +++.......        ....+ 
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~-~~~~~~~~~~~~~~~i~~~~~~~~   96 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQ-IAERFGLDPEEVLDNIYVARAYNS   96 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHH-HHHHhccChHhHhcCEEEEecCCH
Confidence            4579999999999999999988643222221    35789999888877655443 3333221110        01122 


Q ss_pred             --HHHHHHHHHHHcC-C-CeEEEEEeCCC
Q 043252          282 --LNKLQEELKKQLF-G-KKFLLVLDDVW  306 (337)
Q Consensus       282 --~~~~~~~l~~~L~-~-kr~LlVlDdv~  306 (337)
                        ...+...+...+. . +--|||+|.+.
T Consensus        97 ~~l~~~l~~l~~~l~~~~~~~liVIDSis  125 (235)
T cd01123          97 DHQLQLLEELEAILIESSRIKLVIVDSVT  125 (235)
T ss_pred             HHHHHHHHHHHHHHhhcCCeeEEEEeCcH
Confidence              2333445555553 3 56699999994

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 .

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.77  E-value=0.00044  Score=66.77  Aligned_cols=120  Identities=14%  Similarity=0.161  Sum_probs=73.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc---cc---cccc-------------e
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV---ED---HFDL-------------K  249 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~---~F~~-------------~  249 (337)
                      .+++|-+.-.+.|...+....     -.....++|+.|+||||+|+.+.+.---   .+   +..|             .
T Consensus        14 deiiGqe~v~~~L~~~I~~gr-----l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv   88 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR-----LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDI   88 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeE
Confidence            568999999999999986433     3457789999999999999977653110   00   0000             1


Q ss_pred             EEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCC
Q 043252          250 AWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQ  325 (337)
Q Consensus       250 ~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~  325 (337)
                      +.+..+..                      ...+.+.+.+...    ..+++-++|+|++.....+..+.|...+.....
T Consensus        89 ~eldaas~----------------------~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~  146 (535)
T PRK08451         89 IEMDAASN----------------------RGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPS  146 (535)
T ss_pred             EEeccccc----------------------cCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCC
Confidence            11111111                      1122322222210    114556899999988777778888888766566


Q ss_pred             CcEEEEEecC
Q 043252          326 GSKIIVTTRN  335 (337)
Q Consensus       326 gs~iivTTR~  335 (337)
                      .+++|++|.+
T Consensus       147 ~t~FIL~ttd  156 (535)
T PRK08451        147 YVKFILATTD  156 (535)
T ss_pred             ceEEEEEECC
Confidence            6777777643

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.74  E-value=0.00018  Score=64.93  Aligned_cols=121  Identities=16%  Similarity=0.211  Sum_probs=68.6

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhh
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIA  272 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~  272 (337)
                      ++........+++..-..  .....-+.|+|..|+|||.||..+++... ...+. +.+++++      .++.++-....
T Consensus       135 ~~~~~~~~~~~fi~~~~~--~~~~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~~-v~~~~~~------~l~~~lk~~~~  204 (306)
T PRK08939        135 DRLDALMAALDFLEAYPP--GEKVKGLYLYGDFGVGKSYLLAAIANELA-KKGVS-STLLHFP------EFIRELKNSIS  204 (306)
T ss_pred             HHHHHHHHHHHHHHHhhc--cCCCCeEEEECCCCCCHHHHHHHHHHHHH-HcCCC-EEEEEHH------HHHHHHHHHHh
Confidence            454455555666653221  12346799999999999999999998632 22232 4455443      45555544442


Q ss_pred             CCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHH--hhccC-CCC-CCCcEEEEEec
Q 043252          273 SDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVH--LSLPF-QAG-AQGSKIIVTTR  334 (337)
Q Consensus       273 ~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~--l~~~l-~~~-~~gs~iivTTR  334 (337)
                      .      .+...   .+.. + .+-=||||||+..+....|..  +...+ ... ..+-.+|+||-
T Consensus       205 ~------~~~~~---~l~~-l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSN  259 (306)
T PRK08939        205 D------GSVKE---KIDA-V-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSN  259 (306)
T ss_pred             c------CcHHH---HHHH-h-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECC
Confidence            1      12222   2222 2 244599999998766667753  44433 211 23445777774

>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=97.73  E-value=0.00015  Score=62.40  Aligned_cols=125  Identities=19%  Similarity=0.245  Sum_probs=66.0

Q ss_pred             cccchh-HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          191 VYGRET-EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       191 ~vGr~~-~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      ++|-.. ..-.....+....   +.....+.|+|..|+|||.|.+.+++.......=..++|++      ..++...+..
T Consensus        11 v~g~~N~~a~~~~~~ia~~~---~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~------~~~f~~~~~~   81 (219)
T PF00308_consen   11 VVGESNELAYAAAKAIAENP---GERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS------AEEFIREFAD   81 (219)
T ss_dssp             --TTTTHHHHHHHHHHHHST---TTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE------HHHHHHHHHH
T ss_pred             CcCCcHHHHHHHHHHHHhcC---CCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec------HHHHHHHHHH
Confidence            456532 2334444444432   12345689999999999999999998532111111244543      4566666666


Q ss_pred             HhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCC-hhcHHH-hhccCCC-CCCCcEEEEEecC
Q 043252          270 SIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNEN-YTDWVH-LSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~-~~~~~~-l~~~l~~-~~~gs~iivTTR~  335 (337)
                      .+..      ....    .+++.+. .-=+|+|||+..-. ...|.. +...+.. ...|-+||+|+..
T Consensus        82 ~~~~------~~~~----~~~~~~~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~  139 (219)
T PF00308_consen   82 ALRD------GEIE----EFKDRLR-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDR  139 (219)
T ss_dssp             HHHT------TSHH----HHHHHHC-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS
T ss_pred             HHHc------ccch----hhhhhhh-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCC
Confidence            6643      1222    2333443 23388999996532 122332 2222211 1346689999854

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.

>CHL00181 cbbX CbbX; Provisional

Probab=97.73  E-value=0.00055  Score=61.35  Aligned_cols=23  Identities=30%  Similarity=0.309  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.++|++|+||||+|+.++..
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~   82 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADI   82 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            45888999999999999999764

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=97.71  E-value=0.0018  Score=63.18  Aligned_cols=105  Identities=24%  Similarity=0.326  Sum_probs=66.8

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      +.+-+|.++-++.|.+++.-..-+++-+-++++.+|++|+|||.+|+.+..-  ....|   +-+++.+-.|..++    
T Consensus       410 deDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~A--LnRkF---fRfSvGG~tDvAeI----  480 (906)
T KOG2004|consen  410 DEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARA--LNRKF---FRFSVGGMTDVAEI----  480 (906)
T ss_pred             cccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHH--hCCce---EEEeccccccHHhh----
Confidence            3456799999999999987544334556789999999999999999999874  33333   22455555554432    


Q ss_pred             HHHhhCCCC--CCCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          268 LLSIASDQN--VDNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       268 l~~~~~~~~--~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                          .++..  ..++ ...+.+.|++. +..+=|+.||.|..
T Consensus       481 ----kGHRRTYVGAM-PGkiIq~LK~v-~t~NPliLiDEvDK  516 (906)
T KOG2004|consen  481 ----KGHRRTYVGAM-PGKIIQCLKKV-KTENPLILIDEVDK  516 (906)
T ss_pred             ----cccceeeeccC-ChHHHHHHHhh-CCCCceEEeehhhh
Confidence                22221  1222 23334444333 44567889999853

>PRK08181 transposase; Validated

Probab=97.70  E-value=0.0001  Score=65.25  Aligned_cols=98  Identities=20%  Similarity=0.136  Sum_probs=52.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCe
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKK  297 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr  297 (337)
                      -+.++|++|+|||.||..+.+..  ......+.|+.      ..+++..+....      ...........+     .+-
T Consensus       108 nlll~Gp~GtGKTHLa~Aia~~a--~~~g~~v~f~~------~~~L~~~l~~a~------~~~~~~~~l~~l-----~~~  168 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGLAL--IENGWRVLFTR------TTDLVQKLQVAR------RELQLESAIAKL-----DKF  168 (269)
T ss_pred             eEEEEecCCCcHHHHHHHHHHHH--HHcCCceeeee------HHHHHHHHHHHH------hCCcHHHHHHHH-----hcC
Confidence            58999999999999999998642  11222334443      344555553322      112222222222     133


Q ss_pred             EEEEEeCCCCCChhcHH--HhhccCCCC-CCCcEEEEEecC
Q 043252          298 FLLVLDDVWNENYTDWV--HLSLPFQAG-AQGSKIIVTTRN  335 (337)
Q Consensus       298 ~LlVlDdv~~~~~~~~~--~l~~~l~~~-~~gs~iivTTR~  335 (337)
                      =||||||+.......|.  .+...+... ..+ .+||||..
T Consensus       169 dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~-s~IiTSN~  208 (269)
T PRK08181        169 DLLILDDLAYVTKDQAETSVLFELISARYERR-SILITANQ  208 (269)
T ss_pred             CEEEEeccccccCCHHHHHHHHHHHHHHHhCC-CEEEEcCC
Confidence            49999999654332332  233333211 234 48888764

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.70  E-value=0.00013  Score=74.77  Aligned_cols=136  Identities=15%  Similarity=0.163  Sum_probs=76.4

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+.+.+.....   ..+....++.++|+.|+|||.||+.+...  +-......+-++++.-.+     .
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~--l~~~~~~~~~~dmse~~~-----~  638 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAEL--LYGGEQNLITINMSEFQE-----A  638 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHH--HhCCCcceEEEeHHHhhh-----h
Confidence            4689999999999888864211   11334568999999999999999888653  111111122222222111     0


Q ss_pred             HHHHHhhCCCCC--CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC-----------CCcEEEEE
Q 043252          266 SILLSIASDQNV--DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA-----------QGSKIIVT  332 (337)
Q Consensus       266 ~il~~~~~~~~~--~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~-----------~gs~iivT  332 (337)
                      .-...+.+..+.  .......+...+++   ...-+|+||++...++..++.|...+..+.           ..+-||+|
T Consensus       639 ~~~~~l~g~~~gyvg~~~~g~L~~~v~~---~p~svvllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~T  715 (852)
T TIGR03345       639 HTVSRLKGSPPGYVGYGEGGVLTEAVRR---KPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLT  715 (852)
T ss_pred             hhhccccCCCCCcccccccchHHHHHHh---CCCcEEEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEe
Confidence            111122222110  11122233444433   345699999998777777777776665442           34556667


Q ss_pred             ec
Q 043252          333 TR  334 (337)
Q Consensus       333 TR  334 (337)
                      |.
T Consensus       716 SN  717 (852)
T TIGR03345       716 SN  717 (852)
T ss_pred             CC
Confidence            64

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.70  E-value=0.0003  Score=72.51  Aligned_cols=125  Identities=15%  Similarity=0.205  Sum_probs=72.3

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+...+.....   ..+....++.++|+.|+|||++|+.+....  ...-...+.++++.-.+...   
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l--~~~~~~~i~~d~s~~~~~~~---  639 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFL--FDDEDAMVRIDMSEYMEKHS---  639 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHh--cCCCCcEEEEechhhcccch---
Confidence            4689999999999998875321   012235678899999999999999998641  11112233344443222111   


Q ss_pred             HHHHHhhCCCC--CCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCC
Q 043252          266 SILLSIASDQN--VDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAG  323 (337)
Q Consensus       266 ~il~~~~~~~~--~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~  323 (337)
                        ...+.+..+  ........+...++.   ....+|+||++...++..+..|...|..+
T Consensus       640 --~~~l~g~~~g~~g~~~~g~l~~~v~~---~p~~vlllDeieka~~~v~~~Ll~~l~~g  694 (852)
T TIGR03346       640 --VARLIGAPPGYVGYEEGGQLTEAVRR---KPYSVVLFDEVEKAHPDVFNVLLQVLDDG  694 (852)
T ss_pred             --HHHhcCCCCCccCcccccHHHHHHHc---CCCcEEEEeccccCCHHHHHHHHHHHhcC
Confidence              112212111  011122233333332   22349999999888888888887777543

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.

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

Probab=97.70  E-value=0.00029  Score=71.39  Aligned_cols=121  Identities=17%  Similarity=0.175  Sum_probs=70.8

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.|...+.....   ..+....++.++|+.|+|||+||+.+....     +...+.++++.-.+..    
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l-----~~~~~~~d~se~~~~~----  524 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL-----GVHLERFDMSEYMEKH----  524 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHh-----cCCeEEEeCchhhhcc----
Confidence            4578888888888888764211   012235578999999999999999998742     2233455554422111    


Q ss_pred             HHHHHhhCCCC--CCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCC
Q 043252          266 SILLSIASDQN--VDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQA  322 (337)
Q Consensus       266 ~il~~~~~~~~--~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~  322 (337)
                       ....+.+...  ........+...++.   ...-+|+||++...+.+.++.|...|..
T Consensus       525 -~~~~lig~~~gyvg~~~~~~l~~~~~~---~p~~VvllDEieka~~~~~~~Ll~~ld~  579 (731)
T TIGR02639       525 -TVSRLIGAPPGYVGFEQGGLLTEAVRK---HPHCVLLLDEIEKAHPDIYNILLQVMDY  579 (731)
T ss_pred             -cHHHHhcCCCCCcccchhhHHHHHHHh---CCCeEEEEechhhcCHHHHHHHHHhhcc
Confidence             1111111111  012222233333332   2345999999988887888887776654

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.69  E-value=0.00072  Score=62.27  Aligned_cols=139  Identities=13%  Similarity=0.129  Sum_probs=78.4

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc--cccceEEEEeCCCCCHHHHH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED--HFDLKAWTCVSDDFDVIRLT  264 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~F~~~~wv~v~~~~~~~~~~  264 (337)
                      .-..++|-+.....|...+.+..     -...+.|+|+.|+||||+|+.+.+.--...  .+...   ....++......
T Consensus        21 ~~~~l~Gh~~a~~~L~~a~~~gr-----l~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~---~~~~~~~~c~~c   92 (351)
T PRK09112         21 ENTRLFGHEEAEAFLAQAYREGK-----LHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPE---TLADPDPASPVW   92 (351)
T ss_pred             chhhccCcHHHHHHHHHHHHcCC-----CCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcc---ccCCCCCCCHHH
Confidence            34578999999999999996543     345799999999999999988876421100  01111   001111111122


Q ss_pred             HHHHHHhh-------CCC-C-----CCCCCHHHHHHHHHHHc-----CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCC
Q 043252          265 KSILLSIA-------SDQ-N-----VDNHDLNKLQEELKKQL-----FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQG  326 (337)
Q Consensus       265 ~~il~~~~-------~~~-~-----~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~g  326 (337)
                      ..+...-.       ... .     ......+++ ..+.+.+     .+++-++|+|++...+....+.|...+......
T Consensus        93 ~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~i-R~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~  171 (351)
T PRK09112         93 RQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEI-RRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPAR  171 (351)
T ss_pred             HHHHcCCCCCEEEeecccccccccccccCCHHHH-HHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCC
Confidence            22222110       000 0     011223332 2344443     356679999999887777778887777654445


Q ss_pred             cEEEEEec
Q 043252          327 SKIIVTTR  334 (337)
Q Consensus       327 s~iivTTR  334 (337)
                      ..+|++|.
T Consensus       172 ~~fiLit~  179 (351)
T PRK09112        172 ALFILISH  179 (351)
T ss_pred             ceEEEEEC
Confidence            55555554

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.69  E-value=0.00017  Score=73.87  Aligned_cols=45  Identities=24%  Similarity=0.435  Sum_probs=37.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+.++.+++..|....      ..-+.++|++|+||||||+.+...
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~------~~n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRR------QNNPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCC------cCceeEECCCCCCHHHHHHHHHHH
Confidence            468999999999999997543      234569999999999999998864

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.66  E-value=0.00021  Score=62.15  Aligned_cols=23  Identities=17%  Similarity=0.289  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.|+|+.|+|||+|++.+++.
T Consensus        46 ~~l~l~Gp~G~GKThLl~a~~~~   68 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLHAACAE   68 (235)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999875

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.66  E-value=0.00058  Score=67.90  Aligned_cols=132  Identities=16%  Similarity=0.245  Sum_probs=72.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccc---c-cceEEE-EeCCCCCHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDH---F-DLKAWT-CVSDDFDVIRL  263 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---F-~~~~wv-~v~~~~~~~~~  263 (337)
                      ..++|.+..+..|..++....     -.+.+.++|+.|+||||+|+.+...--....   + .|.... +....++..  
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r-----l~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvi--   90 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK-----ISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDII--   90 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEE--
Confidence            568999999999999997543     2457789999999999999988653111000   0 000000 000000000  


Q ss_pred             HHHHHHHhhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          264 TKSILLSIASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       264 ~~~il~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                            .+.........+...+.+.+... ..+++-++|+|++.......+..|...|......+.+|++|
T Consensus        91 ------eidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133         91 ------EMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             ------EEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEc
Confidence                  00000000011122333333222 13566699999998776677888887776545556655555

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.65  E-value=0.00034  Score=67.87  Aligned_cols=143  Identities=20%  Similarity=0.102  Sum_probs=88.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc------ccccccceEEEEeCCCCCHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ------VEDHFDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~------~~~~F~~~~wv~v~~~~~~~~  262 (337)
                      ..+-+|+.+..+|-.++...=. .....+++.|.|.+|.|||..+..|.+...      --..|. ++.|+.-.-..+.+
T Consensus       396 ~sLpcRe~E~~~I~~f~~~~i~-~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~l~~~~~  473 (767)
T KOG1514|consen  396 ESLPCRENEFSEIEDFLRSFIS-DQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLRLASPRE  473 (767)
T ss_pred             ccccchhHHHHHHHHHHHhhcC-CCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEcceeecCHHH
Confidence            3467899999999888864332 113345999999999999999999987432      122343 44555555567899


Q ss_pred             HHHHHHHHhhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCC-CCCCCcEEEEEe
Q 043252          263 LTKSILLSIASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQ-AGAQGSKIIVTT  333 (337)
Q Consensus       263 ~~~~il~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~-~~~~gs~iivTT  333 (337)
                      ++..|...+.+........++.+...+..- -..+.++|++|++...-...-+.+...|. ...++||++|.+
T Consensus       474 ~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~  546 (767)
T KOG1514|consen  474 IYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIA  546 (767)
T ss_pred             HHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEE
Confidence            999999999876543333344443333300 12457788888873320011122333333 235678887764

>PRK05642 DNA replication initiation factor; Validated

Probab=97.65  E-value=0.00024  Score=61.78  Aligned_cols=37  Identities=19%  Similarity=0.210  Sum_probs=26.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEe
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV  254 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  254 (337)
                      ...+.|+|..|+|||.|++.+++...  ..-..++|++.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~--~~~~~v~y~~~   81 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFE--QRGEPAVYLPL   81 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH--hCCCcEEEeeH
Confidence            35789999999999999999987421  11123556654

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.65  E-value=0.00057  Score=65.17  Aligned_cols=46  Identities=22%  Similarity=0.318  Sum_probs=37.7

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+..+..|..++....     -...+.++|+.|+||||+|+.+.+.
T Consensus        17 ~diiGq~~~v~~L~~~i~~~~-----i~ha~Lf~Gp~G~GKtt~A~~lAk~   62 (451)
T PRK06305         17 SEILGQDAVVAVLKNALRFNR-----AAHAYLFSGIRGTGKTTLARIFAKA   62 (451)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-----CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            578999999999999996433     2357889999999999999888653

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.64  E-value=0.001  Score=65.27  Aligned_cols=133  Identities=17%  Similarity=0.177  Sum_probs=72.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|.+...+.|.+++....     -.+.+.++|+.|+||||+|+.+...--....-+       ..+++.-.....|.
T Consensus        16 ~~viGq~~v~~~L~~~i~~~~-----~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~-------~~pC~~C~~C~~i~   83 (559)
T PRK05563         16 EDVVGQEHITKTLKNAIKQGK-----ISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPD-------GEPCNECEICKAIT   83 (559)
T ss_pred             HhccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCccHHHHHHh
Confidence            578999999999999997543     245778899999999999998865311110000       00111111111111


Q ss_pred             HHhhCCC----CCCCCCHH---HHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          269 LSIASDQ----NVDNHDLN---KLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       269 ~~~~~~~----~~~~~~~~---~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      .....+.    .......+   .+.+.+... ..+++-++|+|++.......+..|...+........+|++|
T Consensus        84 ~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlat  156 (559)
T PRK05563         84 NGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILAT  156 (559)
T ss_pred             cCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEe
Confidence            1000000    00011222   222222211 13556688999998766677888887776544455555544

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.63  E-value=0.00033  Score=72.00  Aligned_cols=124  Identities=15%  Similarity=0.156  Sum_probs=69.5

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+...+.....   ..+....++.++|+.|+|||+||+.+.+..  -..-...+.+.++.-.. .    
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l--~~~~~~~i~id~se~~~-~----  640 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM--FDSDDAMVRIDMSEFME-K----  640 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHh--hcCCCcEEEEEhHHhhh-h----
Confidence            4688999999888888764210   012234578899999999999999998642  11112233444433211 1    


Q ss_pred             HHHHHhhCCCCC--CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCC
Q 043252          266 SILLSIASDQNV--DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQA  322 (337)
Q Consensus       266 ~il~~~~~~~~~--~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~  322 (337)
                      .....+.+..+.  .......+...++.   ...-+|+||++...+...+..|...|..
T Consensus       641 ~~~~~LiG~~pgy~g~~~~g~l~~~v~~---~p~~vLllDEieka~~~v~~~Ll~ile~  696 (857)
T PRK10865        641 HSVSRLVGAPPGYVGYEEGGYLTEAVRR---RPYSVILLDEVEKAHPDVFNILLQVLDD  696 (857)
T ss_pred             hhHHHHhCCCCcccccchhHHHHHHHHh---CCCCeEEEeehhhCCHHHHHHHHHHHhh
Confidence            112222222110  11111223333221   2235999999987777888877776643

>PRK09087 hypothetical protein; Validated

Probab=97.63  E-value=0.00016  Score=62.51  Aligned_cols=24  Identities=33%  Similarity=0.391  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.+.|+|+.|+|||+|++.++..
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            357899999999999999998864

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.63  E-value=0.00089  Score=65.49  Aligned_cols=130  Identities=15%  Similarity=0.111  Sum_probs=73.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc---cccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED---HFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      .+++|-+.-+..|..++....     -.+.+.++|+.|+||||+|+.+.+.--...   .+.|.      ...+-    .
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~-----i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~------~C~~C----~   80 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK-----IANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCG------ECSSC----K   80 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCc------cchHH----H
Confidence            568999999999999997543     345788999999999999999876421111   01110      00000    0


Q ss_pred             HHHHHhhCC----CCCCCCCHHHHH---HHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          266 SILLSIASD----QNVDNHDLNKLQ---EELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       266 ~il~~~~~~----~~~~~~~~~~~~---~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                      .|...-..+    ........+.+.   +.+... ..+++-++|+|++.......++.|...+......+.+|++|
T Consensus        81 ~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~t  156 (563)
T PRK06647         81 SIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFAT  156 (563)
T ss_pred             HHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEec
Confidence            110000000    000011222222   221111 13556689999998776677888888887655666666655

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

Probab=97.62  E-value=0.00025  Score=70.57  Aligned_cols=120  Identities=15%  Similarity=0.242  Sum_probs=77.1

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccc---cceEEEEeCCCCCHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF---DLKAWTCVSDDFDVIR  262 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~v~~~~~~~~  262 (337)
                      ..++|.++.++.+.+.+.....   ..+..+.+...+|+.|||||.||+.+...     -|   +..+-+      |+.+
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~-----Lfg~e~aliR~------DMSE  559 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEA-----LFGDEQALIRI------DMSE  559 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHH-----hcCCCccceee------chHH
Confidence            4689999999999888864321   12345678888999999999999988753     23   222333      3333


Q ss_pred             HH-HHHHHHhhCCCCC--CCCCHHHHHHHHHHHcCCCeE-EEEEeCCCCCChhcHHHhhccCCCC
Q 043252          263 LT-KSILLSIASDQNV--DNHDLNKLQEELKKQLFGKKF-LLVLDDVWNENYTDWVHLSLPFQAG  323 (337)
Q Consensus       263 ~~-~~il~~~~~~~~~--~~~~~~~~~~~l~~~L~~kr~-LlVlDdv~~~~~~~~~~l~~~l~~~  323 (337)
                      .. ..-++.+-+..+.  ....-.    .|.+..+.+.| +|.||+|...+++..+.|...|.++
T Consensus       560 y~EkHsVSrLIGaPPGYVGyeeGG----~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         560 YMEKHSVSRLIGAPPGYVGYEEGG----QLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             HHHHHHHHHHhCCCCCCceecccc----chhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCC
Confidence            22 2223444443331  222223    34555566767 8889999988888888888777654

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.62  E-value=6.7e-05  Score=68.41  Aligned_cols=52  Identities=15%  Similarity=0.246  Sum_probs=42.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      ..++|.++.++++++++.......+...+++.++|++|+||||||+.+.+..
T Consensus        51 ~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l  102 (361)
T smart00763       51 HDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL  102 (361)
T ss_pred             hhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3799999999999999976443123456899999999999999999997753

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK12377 putative replication protein; Provisional

Probab=97.62  E-value=0.00022  Score=62.29  Aligned_cols=100  Identities=21%  Similarity=0.105  Sum_probs=54.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      ..+.|+|..|+|||+||..+.+..  ......++++++.      +++..+-.....     ......    +.+.+ .+
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l--~~~g~~v~~i~~~------~l~~~l~~~~~~-----~~~~~~----~l~~l-~~  163 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRL--LAKGRSVIVVTVP------DVMSRLHESYDN-----GQSGEK----FLQEL-CK  163 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH--HHcCCCeEEEEHH------HHHHHHHHHHhc-----cchHHH----HHHHh-cC
Confidence            578999999999999999999863  2233334565543      444444433321     111222    22222 34


Q ss_pred             eEEEEEeCCCCCChhcHH--HhhccCCCC-CCCcEEEEEec
Q 043252          297 KFLLVLDDVWNENYTDWV--HLSLPFQAG-AQGSKIIVTTR  334 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~--~l~~~l~~~-~~gs~iivTTR  334 (337)
                      -=||||||+.......|.  .|...+... .+.--+||||-
T Consensus       164 ~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSN  204 (248)
T PRK12377        164 VDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTN  204 (248)
T ss_pred             CCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcC
Confidence            559999999554333443  233333211 12223677764

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

Probab=97.61  E-value=9.8e-05  Score=61.32  Aligned_cols=98  Identities=21%  Similarity=0.314  Sum_probs=49.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      .-+.|+|..|+|||.||..+.+.. +...+ .+.|+.+      .+++..    +....  ...........+   .  +
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~-~~~g~-~v~f~~~------~~L~~~----l~~~~--~~~~~~~~~~~l---~--~  108 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEA-IRKGY-SVLFITA------SDLLDE----LKQSR--SDGSYEELLKRL---K--R  108 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHH-HHTT---EEEEEH------HHHHHH----HHCCH--CCTTHCHHHHHH---H--T
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHh-ccCCc-ceeEeec------Cceecc----ccccc--cccchhhhcCcc---c--c
Confidence            469999999999999999987742 22222 2455543      333333    33221  122222332222   2  2


Q ss_pred             eEEEEEeCCCCCChhcHHH--hhccCCC-CCCCcEEEEEec
Q 043252          297 KFLLVLDDVWNENYTDWVH--LSLPFQA-GAQGSKIIVTTR  334 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~--l~~~l~~-~~~gs~iivTTR  334 (337)
                      -=||||||+.......|..  +...+.. -.++ .+||||.
T Consensus       109 ~dlLilDDlG~~~~~~~~~~~l~~ii~~R~~~~-~tIiTSN  148 (178)
T PF01695_consen  109 VDLLILDDLGYEPLSEWEAELLFEIIDERYERK-PTIITSN  148 (178)
T ss_dssp             SSCEEEETCTSS---HHHHHCTHHHHHHHHHT--EEEEEES
T ss_pred             ccEecccccceeeecccccccchhhhhHhhccc-CeEeeCC
Confidence            3488899997764444432  2222211 1234 4777875

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.

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.60  E-value=0.002  Score=54.95  Aligned_cols=122  Identities=22%  Similarity=0.259  Sum_probs=72.6

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~  266 (337)
                      +-..++|.+..++.|++--..--  .+..---|.+||..|.||++|++.+.+.  +....-.  -|.|...         
T Consensus        58 ~L~~l~Gvd~qk~~L~~NT~~F~--~G~pANnVLLwGaRGtGKSSLVKA~~~e--~~~~glr--LVEV~k~---------  122 (287)
T COG2607          58 DLADLVGVDRQKEALVRNTEQFA--EGLPANNVLLWGARGTGKSSLVKALLNE--YADEGLR--LVEVDKE---------  122 (287)
T ss_pred             CHHHHhCchHHHHHHHHHHHHHH--cCCcccceEEecCCCCChHHHHHHHHHH--HHhcCCe--EEEEcHH---------
Confidence            44568999888888765433211  1222346889999999999999999875  2222211  2333221         


Q ss_pred             HHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCC---CCCcEEEEEecCC
Q 043252          267 ILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAG---AQGSKIIVTTRNQ  336 (337)
Q Consensus       267 il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~---~~gs~iivTTR~~  336 (337)
                                 +..++..+.+.|+.  ...||.|..||+..+ ....+..+...|..+   .+..-++..|.++
T Consensus       123 -----------dl~~Lp~l~~~Lr~--~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNR  183 (287)
T COG2607         123 -----------DLATLPDLVELLRA--RPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNR  183 (287)
T ss_pred             -----------HHhhHHHHHHHHhc--CCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCC
Confidence                       12233333333333  267999999999654 345778888887643   3334455555543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.60  E-value=0.00079  Score=60.31  Aligned_cols=22  Identities=32%  Similarity=0.318  Sum_probs=18.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -+.++|++|.||||+|+.+...
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~   81 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQI   81 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH
Confidence            5889999999999999777653

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.56  E-value=0.001  Score=65.81  Aligned_cols=136  Identities=14%  Similarity=0.180  Sum_probs=74.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|.+.-...|..++....     -...+.++|+.|+||||+|+.+.+.--....+..     ...++..-...+.+.
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r-----l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~-----~~~~Cg~C~~C~~i~   85 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR-----IAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKP-----TPEPCGKCELCRAIA   85 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC-----CCceEEEECCCCCChHHHHHHHHHHhcCCCcCCC-----CCCCCcccHHHHHHh
Confidence            468899999999999987543     2347889999999999999999764211110000     001111111222222


Q ss_pred             HHhhCCC----CCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          269 LSIASDQ----NVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       269 ~~~~~~~----~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      .......    .......+.+.+.+...    ..+++-++|||++.......++.|...+..-...+.+|++|.
T Consensus        86 ~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~  159 (620)
T PRK14948         86 AGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATT  159 (620)
T ss_pred             cCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeC
Confidence            1111100    00112222222222111    124556899999987666778888887776545555565553

>PRK06526 transposase; Provisional

Probab=97.56  E-value=0.00019  Score=63.04  Aligned_cols=99  Identities=21%  Similarity=0.186  Sum_probs=51.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      .-+.|+|++|+|||+||..+..... ...+. +.|+      +..+++..+.....      ...   +...+...  .+
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~-~~g~~-v~f~------t~~~l~~~l~~~~~------~~~---~~~~l~~l--~~  159 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRAC-QAGHR-VLFA------TAAQWVARLAAAHH------AGR---LQAELVKL--GR  159 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHH-HCCCc-hhhh------hHHHHHHHHHHHHh------cCc---HHHHHHHh--cc
Confidence            3689999999999999999876421 12222 2222      33444444433211      111   12223332  23


Q ss_pred             eEEEEEeCCCCCChhcHH--HhhccCCC-CCCCcEEEEEecC
Q 043252          297 KFLLVLDDVWNENYTDWV--HLSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~--~l~~~l~~-~~~gs~iivTTR~  335 (337)
                      .-||||||+.......+.  .+...+.. -.++| +|+||..
T Consensus       160 ~dlLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s-~IitSn~  200 (254)
T PRK06526        160 YPLLIVDEVGYIPFEPEAANLFFQLVSSRYERAS-LIVTSNK  200 (254)
T ss_pred             CCEEEEcccccCCCCHHHHHHHHHHHHHHHhcCC-EEEEcCC
Confidence            458999999654322222  23333221 12355 8888764

>PRK06921 hypothetical protein; Provisional

Probab=97.56  E-value=0.00045  Score=61.19  Aligned_cols=37  Identities=22%  Similarity=0.170  Sum_probs=26.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhccccccc-ccceEEEEe
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDH-FDLKAWTCV  254 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~v  254 (337)
                      ...+.++|..|+|||+||..+.+.  +... -..++++..
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~--l~~~~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANE--LMRKKGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HhhhcCceEEEEEH
Confidence            457899999999999999999885  2222 233456553

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.56  E-value=0.00028  Score=72.46  Aligned_cols=45  Identities=29%  Similarity=0.444  Sum_probs=37.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+++++++++.|.....      .-+.++|++|+|||++|+.+...
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~------~n~lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTK------NNPILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             CCCCCcHHHHHHHHHHHccccc------CCeEEECCCCCCHHHHHHHHHHH
Confidence            3589999999999999975432      24569999999999999988764

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.56  E-value=0.00081  Score=59.53  Aligned_cols=56  Identities=20%  Similarity=0.163  Sum_probs=35.7

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHH
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLT  264 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~  264 (337)
                      .-++.+..++...        .-|.+.|++|+|||+||+.+...  ...   ....+++....+..+++
T Consensus         9 ~l~~~~l~~l~~g--------~~vLL~G~~GtGKT~lA~~la~~--lg~---~~~~i~~~~~~~~~dll   64 (262)
T TIGR02640         9 RVTSRALRYLKSG--------YPVHLRGPAGTGKTTLAMHVARK--RDR---PVMLINGDAELTTSDLV   64 (262)
T ss_pred             HHHHHHHHHHhcC--------CeEEEEcCCCCCHHHHHHHHHHH--hCC---CEEEEeCCccCCHHHHh
Confidence            3445566666432        25678999999999999999862  221   23456666655555544

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).

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.55  E-value=0.00027  Score=69.66  Aligned_cols=51  Identities=16%  Similarity=0.241  Sum_probs=40.3

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|-++.++++..||..... ......++.|+|++|+||||+++.+...
T Consensus        83 ldel~~~~~ki~~l~~~l~~~~~-~~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        83 QHELAVHKKKIEEVETWLKAQVL-ENAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             HHHhcCcHHHHHHHHHHHHhccc-ccCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999875432 1223458999999999999999999874

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

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.55  E-value=0.0003  Score=72.30  Aligned_cols=45  Identities=24%  Similarity=0.397  Sum_probs=37.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+.+++++++.|....      ..-+.++|++|+|||+||+.+...
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~------~~n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRT------KNNPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCC------cCceEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999997543      235669999999999999988764

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

Probab=97.55  E-value=0.00033  Score=71.05  Aligned_cols=45  Identities=24%  Similarity=0.365  Sum_probs=37.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||++++++++..|....      ..-+.++|++|+|||++|+.+...
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~------~~n~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRK------KNNPLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCC------CCceEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999986543      234579999999999999999874

>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=97.54  E-value=6.1e-05  Score=59.81  Aligned_cols=88  Identities=23%  Similarity=0.088  Sum_probs=47.4

Q ss_pred             EEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeE
Q 043252          219 IPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKF  298 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~  298 (337)
                      |.++|++|+|||+||+.++...  ..   ...-+.++...+..+++...--.    ..........+...+     .+..
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~--~~---~~~~i~~~~~~~~~dl~g~~~~~----~~~~~~~~~~l~~a~-----~~~~   67 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL--GR---PVIRINCSSDTTEEDLIGSYDPS----NGQFEFKDGPLVRAM-----RKGG   67 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH--TC---EEEEEE-TTTSTHHHHHCEEET-----TTTTCEEE-CCCTTH-----HEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHh--hc---ceEEEEeccccccccceeeeeec----ccccccccccccccc-----ccee
Confidence            6799999999999999998742  11   12336777777776655322211    000000000000001     1788


Q ss_pred             EEEEeCCCCCChhcHHHhhccC
Q 043252          299 LLVLDDVWNENYTDWVHLSLPF  320 (337)
Q Consensus       299 LlVlDdv~~~~~~~~~~l~~~l  320 (337)
                      ++|||++.......+..+...+
T Consensus        68 il~lDEin~a~~~v~~~L~~ll   89 (139)
T PF07728_consen   68 ILVLDEINRAPPEVLESLLSLL   89 (139)
T ss_dssp             EEEESSCGG--HHHHHTTHHHH
T ss_pred             EEEECCcccCCHHHHHHHHHHH
Confidence            9999999765555555554443

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.53  E-value=0.00033  Score=60.51  Aligned_cols=88  Identities=16%  Similarity=0.114  Sum_probs=52.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHH----hhCCC-CCCCCCHHH---HH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLS----IASDQ-NVDNHDLNK---LQ  286 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~----~~~~~-~~~~~~~~~---~~  286 (337)
                      .-.++.|+|.+|+|||+|+.++....  ...-..++|++.. .++...+. ++...    +.... .....+..+   ..
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~~--~~~~~~v~yi~~e-~~~~~r~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i   97 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVEA--AKNGKKVIYIDTE-GLSPERFK-QIAGEDFEELLSNIIIFEPSSFEEQSEAI   97 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH--HHCCCeEEEEECC-CCCHHHHH-HHHhhChHhHhhCeEEEeCCCHHHHHHHH
Confidence            45799999999999999998887642  1223567899887 56655533 23222    10000 001223322   33


Q ss_pred             HHHHHHcCCCeEEEEEeCCC
Q 043252          287 EELKKQLFGKKFLLVLDDVW  306 (337)
Q Consensus       287 ~~l~~~L~~kr~LlVlDdv~  306 (337)
                      ..+...+..+--+||+|.+-
T Consensus        98 ~~~~~~~~~~~~lvVIDsi~  117 (225)
T PRK09361         98 RKAEKLAKENVGLIVLDSAT  117 (225)
T ss_pred             HHHHHHHHhcccEEEEeCcH
Confidence            44444444566699999983

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.52  E-value=0.00073  Score=69.42  Aligned_cols=125  Identities=14%  Similarity=0.159  Sum_probs=70.1

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+...+.....   ..+.....+.++|+.|+|||+||+.+.+..  -..-...+-+.++.-.+...+ .
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l--~~~~~~~~~~d~s~~~~~~~~-~  585 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYF--FGSEDAMIRLDMSEYMEKHTV-S  585 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHh--cCCccceEEEEchhccccccH-H
Confidence            5688999999999888763221   112334567889999999999999887531  000112233344332211111 1


Q ss_pred             HHHHHhhCCC-CCCCCCHHHHHHHHHHHcCCCe-EEEEEeCCCCCChhcHHHhhccCCCC
Q 043252          266 SILLSIASDQ-NVDNHDLNKLQEELKKQLFGKK-FLLVLDDVWNENYTDWVHLSLPFQAG  323 (337)
Q Consensus       266 ~il~~~~~~~-~~~~~~~~~~~~~l~~~L~~kr-~LlVlDdv~~~~~~~~~~l~~~l~~~  323 (337)
                      .+   ++.+. .........+    .+.++.+. -+|+||++...+++.++.|...|..+
T Consensus       586 ~l---~g~~~gyvg~~~~~~l----~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g  638 (821)
T CHL00095        586 KL---IGSPPGYVGYNEGGQL----TEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDG  638 (821)
T ss_pred             Hh---cCCCCcccCcCccchH----HHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccC
Confidence            11   11111 1011222233    33343344 48999999888888888887777543

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.49  E-value=0.00072  Score=62.05  Aligned_cols=102  Identities=20%  Similarity=0.178  Sum_probs=63.2

Q ss_pred             HHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccc-eEEEEeCCC-CCHHHHHHHHHHHhhCCC
Q 043252          198 KKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDL-KAWTCVSDD-FDVIRLTKSILLSIASDQ  275 (337)
Q Consensus       198 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~v~~~-~~~~~~~~~il~~~~~~~  275 (337)
                      ..++++.+..-.     .-.-+.|+|..|+|||||++.+.+... .++-+. ++|+.+.+. .++.+++..+...+....
T Consensus       120 ~~RvID~l~PiG-----kGQR~LIvG~pGtGKTTLl~~la~~i~-~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast  193 (380)
T PRK12608        120 SMRVVDLVAPIG-----KGQRGLIVAPPRAGKTVLLQQIAAAVA-ANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYAST  193 (380)
T ss_pred             hHhhhhheeecC-----CCceEEEECCCCCCHHHHHHHHHHHHH-hcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeec
Confidence            345777776432     223669999999999999999887421 122234 467777654 467788888877665443


Q ss_pred             CCCCCCHH-----HHHHHHHHHc--CCCeEEEEEeCCC
Q 043252          276 NVDNHDLN-----KLQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       276 ~~~~~~~~-----~~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      . +.....     .....+.+++  ++++.+||+|++.
T Consensus       194 ~-de~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        194 F-DRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             C-CCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcH
Confidence            2 111111     1122222333  5899999999994

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.49  E-value=0.00044  Score=59.83  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+.|+|..|+|||+||+.+++.
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            457889999999999999999875

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

Probab=97.48  E-value=0.0013  Score=60.01  Aligned_cols=125  Identities=14%  Similarity=0.094  Sum_probs=73.8

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc-------------------cccceE
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED-------------------HFDLKA  250 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~~  250 (337)
                      .++|-+.....+..+......    ....+.++|+.|+||||+|..+.+.---..                   ......
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~----~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~l   77 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGR----LPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFL   77 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCC----CCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceE
Confidence            356777888888888874431    233699999999999999988876421111                   011223


Q ss_pred             EEEeCCCCC---HHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCc
Q 043252          251 WTCVSDDFD---VIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGS  327 (337)
Q Consensus       251 wv~v~~~~~---~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs  327 (337)
                      .+.-+....   ..+..+++.+.......                 .++.-+++||++.....+.-..+...+..-...+
T Consensus        78 el~~s~~~~~~i~~~~vr~~~~~~~~~~~-----------------~~~~kviiidead~mt~~A~nallk~lEep~~~~  140 (325)
T COG0470          78 ELNPSDLRKIDIIVEQVRELAEFLSESPL-----------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNT  140 (325)
T ss_pred             EecccccCCCcchHHHHHHHHHHhccCCC-----------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCe
Confidence            333333222   12222222222211110                 2567789999997766666677777666656677


Q ss_pred             EEEEEecC
Q 043252          328 KIIVTTRN  335 (337)
Q Consensus       328 ~iivTTR~  335 (337)
                      .+|++|..
T Consensus       141 ~~il~~n~  148 (325)
T COG0470         141 RFILITND  148 (325)
T ss_pred             EEEEEcCC
Confidence            88887753

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.48  E-value=0.00077  Score=56.94  Aligned_cols=127  Identities=22%  Similarity=0.240  Sum_probs=61.7

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC------CCHHHH---
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD------FDVIRL---  263 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~------~~~~~~---  263 (337)
                      .+..+-...++.|..        ..++.+.|++|.|||.||-...-+.-....|+..+++.-.-+      |-+.++   
T Consensus         4 p~~~~Q~~~~~al~~--------~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK   75 (205)
T PF02562_consen    4 PKNEEQKFALDALLN--------NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEK   75 (205)
T ss_dssp             --SHHHHHHHHHHHH---------SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS-------
T ss_pred             CCCHHHHHHHHHHHh--------CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHH
Confidence            445556666777762        239999999999999999777655434467777766542111      000110   


Q ss_pred             ----HHHHHHHhhCCCCCCCCCHHHHHHH------HHHHcCCC---eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEE
Q 043252          264 ----TKSILLSIASDQNVDNHDLNKLQEE------LKKQLFGK---KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKII  330 (337)
Q Consensus       264 ----~~~il~~~~~~~~~~~~~~~~~~~~------l~~~L~~k---r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~ii  330 (337)
                          +.-+...+..-.  .....+.+...      -..+++|+   ..+|++|+..+.....+..+...+   +.|||||
T Consensus        76 ~~p~~~p~~d~l~~~~--~~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR~---g~~skii  150 (205)
T PF02562_consen   76 MEPYLRPIYDALEELF--GKEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILTRI---GEGSKII  150 (205)
T ss_dssp             --TTTHHHHHHHTTTS---TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB----TT-EEE
T ss_pred             HHHHHHHHHHHHHHHh--ChHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHccc---CCCcEEE
Confidence                111111111100  11222222211      01234555   459999999887777777765543   5789999


Q ss_pred             EE
Q 043252          331 VT  332 (337)
Q Consensus       331 vT  332 (337)
                      ++
T Consensus       151 ~~  152 (205)
T PF02562_consen  151 IT  152 (205)
T ss_dssp             EE
T ss_pred             Ee
Confidence            87

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

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.48  E-value=0.0009  Score=58.34  Aligned_cols=101  Identities=15%  Similarity=0.160  Sum_probs=55.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFG  295 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~  295 (337)
                      ...+.++|.+|+|||+||..+.+....  .-..+++++      ..+++..+-.....    ...+...+    .+.+. 
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~--~g~~v~~it------~~~l~~~l~~~~~~----~~~~~~~~----l~~l~-  161 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLL--RGKSVLIIT------VADIMSAMKDTFSN----SETSEEQL----LNDLS-  161 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEE------HHHHHHHHHHHHhh----ccccHHHH----HHHhc-
Confidence            347899999999999999999885322  222344443      34444444433321    11222222    23343 


Q ss_pred             CeEEEEEeCCCCCChhcHHH--hhccCC--CCCCCcEEEEEec
Q 043252          296 KKFLLVLDDVWNENYTDWVH--LSLPFQ--AGAQGSKIIVTTR  334 (337)
Q Consensus       296 kr~LlVlDdv~~~~~~~~~~--l~~~l~--~~~~gs~iivTTR  334 (337)
                      +.=||||||+......+|..  +...+.  ..... .+||||-
T Consensus       162 ~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~-~tiitSN  203 (244)
T PRK07952        162 NVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKR-PTGMLTN  203 (244)
T ss_pred             cCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCC-CEEEeCC
Confidence            33489999997765556653  222222  11233 4677764

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.47  E-value=0.00041  Score=59.13  Aligned_cols=88  Identities=15%  Similarity=0.097  Sum_probs=53.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHh-h---CCC-CCCCCC---HHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSI-A---SDQ-NVDNHD---LNKLQ  286 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~-~---~~~-~~~~~~---~~~~~  286 (337)
                      .-.++.|+|++|+|||+++..+....  ...-..++|++... ++...+.+. .+.. .   ..- .....+   .....
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~--~~~g~~v~yi~~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~~~~~~~~~   86 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNA--ARQGKKVVYIDTEG-LSPERFKQI-AEDRPERALSNFIVFEVFDFDEQGVAI   86 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH--HhCCCeEEEEECCC-CCHHHHHHH-HHhChHHHhcCEEEEECCCHHHHHHHH
Confidence            45799999999999999998876542  22345688999876 666655443 2221 0   000 001122   22335


Q ss_pred             HHHHHHcCC-CeEEEEEeCCC
Q 043252          287 EELKKQLFG-KKFLLVLDDVW  306 (337)
Q Consensus       287 ~~l~~~L~~-kr~LlVlDdv~  306 (337)
                      ..+.+.+.. +--+||+|.+-
T Consensus        87 ~~l~~~~~~~~~~lvVIDSis  107 (209)
T TIGR02237        87 QKTSKFIDRDSASLVVVDSFT  107 (209)
T ss_pred             HHHHHHHhhcCccEEEEeCcH
Confidence            555555543 45599999984

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

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.46  E-value=0.00072  Score=64.48  Aligned_cols=104  Identities=16%  Similarity=0.182  Sum_probs=57.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFG  295 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~  295 (337)
                      ...+.|+|..|+|||+|++.+.+.......-..++++      +..+++..+...+....        .....+.+.+. 
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv------~~~~f~~~~~~~l~~~~--------~~~~~~~~~~~-  205 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYM------SGDEFARKAVDILQKTH--------KEIEQFKNEIC-  205 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEE------EHHHHHHHHHHHHHHhh--------hHHHHHHHHhc-
Confidence            4568999999999999999998742111111122333      34566777776664311        11223444443 


Q ss_pred             CeEEEEEeCCCCCCh-hcH-HHhhccCCC-CCCCcEEEEEec
Q 043252          296 KKFLLVLDDVWNENY-TDW-VHLSLPFQA-GAQGSKIIVTTR  334 (337)
Q Consensus       296 kr~LlVlDdv~~~~~-~~~-~~l~~~l~~-~~~gs~iivTTR  334 (337)
                      +.-+|||||+..... ..+ +.+...|.. ...|..||+|+.
T Consensus       206 ~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd  247 (450)
T PRK14087        206 QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSD  247 (450)
T ss_pred             cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECC
Confidence            344899999965421 122 233333321 134556888865

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.45  E-value=0.00026  Score=64.47  Aligned_cols=101  Identities=19%  Similarity=0.260  Sum_probs=52.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      ..+.++|..|+|||+||..+.+.. ....+ .++++++.      +++..+...-. .   ...+....   +.. +. +
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l-~~~g~-~V~y~t~~------~l~~~l~~~~~-~---~~~~~~~~---~~~-l~-~  246 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKEL-LDRGK-SVIYRTAD------ELIEILREIRF-N---NDKELEEV---YDL-LI-N  246 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHH-HHCCC-eEEEEEHH------HHHHHHHHHHh-c---cchhHHHH---HHH-hc-c
Confidence            569999999999999999998853 22222 34555433      33333322111 1   11111111   222 21 2


Q ss_pred             eEEEEEeCCCCCChhcHH--HhhccCCCC-CCCcEEEEEec
Q 043252          297 KFLLVLDDVWNENYTDWV--HLSLPFQAG-AQGSKIIVTTR  334 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~--~l~~~l~~~-~~gs~iivTTR  334 (337)
                      -=||||||+.......|.  .+...+... ..+-.+||||.
T Consensus       247 ~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSN  287 (329)
T PRK06835        247 CDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTN  287 (329)
T ss_pred             CCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECC
Confidence            238999999665333332  233333211 23445888875

>PRK06620 hypothetical protein; Validated

Probab=97.44  E-value=0.00033  Score=60.02  Aligned_cols=23  Identities=30%  Similarity=0.252  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.|+|++|+|||+|++.+++.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhc
Confidence            57899999999999999998775

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.44  E-value=0.00065  Score=70.03  Aligned_cols=45  Identities=24%  Similarity=0.393  Sum_probs=36.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+.++.+++..|....      ..-+.++|++|+|||++|..+...
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~------~~n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRT------KNNPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCC------CCceEEEcCCCCCHHHHHHHHHHH
Confidence            358999999999999996543      234558999999999999988764

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.

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

Probab=97.44  E-value=0.0011  Score=62.36  Aligned_cols=92  Identities=20%  Similarity=0.191  Sum_probs=57.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCe
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKK  297 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr  297 (337)
                      ++.|.|+.++|||||++.+...  ..+.   .+++...+......-+.+.+.                  .+.+.-..++
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~--~~~~---~iy~~~~d~~~~~~~l~d~~~------------------~~~~~~~~~~   95 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKG--LLEE---IIYINFDDLRLDRIELLDLLR------------------AYIELKEREK   95 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhh--CCcc---eEEEEecchhcchhhHHHHHH------------------HHHHhhccCC
Confidence            9999999999999999766553  1111   455543332211111111111                  1111111278


Q ss_pred             EEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          298 FLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       298 ~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      .+|+||.|...  ..|......+.+..+. +|++|+-+
T Consensus        96 ~yifLDEIq~v--~~W~~~lk~l~d~~~~-~v~itgss  130 (398)
T COG1373          96 SYIFLDEIQNV--PDWERALKYLYDRGNL-DVLITGSS  130 (398)
T ss_pred             ceEEEecccCc--hhHHHHHHHHHccccc-eEEEECCc
Confidence            89999999765  7899888888776665 88888755

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

Probab=97.43  E-value=0.00037  Score=61.37  Aligned_cols=90  Identities=28%  Similarity=0.320  Sum_probs=55.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhccccccc----ccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDH----FDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDL  282 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~  282 (337)
                      .-.+.=|+|++|+|||.|+..++-...+...    =..++|++....|+..++. +|++.......        ....+.
T Consensus        37 ~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~  115 (256)
T PF08423_consen   37 TGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDL  115 (256)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSH
T ss_pred             CCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCH
Confidence            3459999999999999999877644322221    2358999999999988865 46655432110        012233


Q ss_pred             HHH---HHHHHHHcC-CCeEEEEEeCC
Q 043252          283 NKL---QEELKKQLF-GKKFLLVLDDV  305 (337)
Q Consensus       283 ~~~---~~~l~~~L~-~kr~LlVlDdv  305 (337)
                      +++   ...+...+. .+=-|||+|.+
T Consensus       116 ~~l~~~L~~l~~~l~~~~ikLIVIDSI  142 (256)
T PF08423_consen  116 EELLELLEQLPKLLSESKIKLIVIDSI  142 (256)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETS
T ss_pred             HHHHHHHHHHHhhccccceEEEEecch
Confidence            333   333444443 34449999999

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 ....

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.43  E-value=0.0017  Score=59.48  Aligned_cols=134  Identities=12%  Similarity=0.049  Sum_probs=71.0

Q ss_pred             cccc-chhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          190 KVYG-RETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       190 ~~vG-r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .++| -+.-++.|...+....     -.....++|+.|+||||+|+.+...---.......       +++.-..-..+.
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~-----l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~-------~cg~C~~c~~~~   73 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNR-----LSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVE-------PCGTCTNCKRID   73 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCC-----CCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCC-------CCCcCHHHHHHh
Confidence            4566 6667777777775433     34678999999999999998885431111100000       000000000000


Q ss_pred             HHhhCC----C-CCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASD----Q-NVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~----~-~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..-..+    . .......+++.+.+...    ..+.+=++|+|++...+....+.|...+..-+.++.+|++|.+
T Consensus        74 ~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~  149 (329)
T PRK08058         74 SGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTEN  149 (329)
T ss_pred             cCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCC
Confidence            000000    0 00111222222222111    2345557999999777667778888888776677888888765

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.41  E-value=0.00053  Score=64.72  Aligned_cols=100  Identities=19%  Similarity=0.274  Sum_probs=54.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccc--cceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF--DLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL  293 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L  293 (337)
                      ...+.|+|+.|+|||+|++.+++..  ....  ..+++++      ..++...+...+...      ......    +.+
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l--~~~~~~~~v~yi~------~~~~~~~~~~~~~~~------~~~~~~----~~~  197 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEI--LENNPNAKVVYVS------SEKFTNDFVNALRNN------KMEEFK----EKY  197 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHH--HHhCCCCcEEEEE------HHHHHHHHHHHHHcC------CHHHHH----HHH
Confidence            4568999999999999999999853  2222  1344553      334455555555321      223332    333


Q ss_pred             CCCeEEEEEeCCCCCChh-cH-HHhhccCCC-CCCCcEEEEEec
Q 043252          294 FGKKFLLVLDDVWNENYT-DW-VHLSLPFQA-GAQGSKIIVTTR  334 (337)
Q Consensus       294 ~~kr~LlVlDdv~~~~~~-~~-~~l~~~l~~-~~~gs~iivTTR  334 (337)
                      .+ .-+|+|||+...... .+ ..+...|.. ...|..+|+||.
T Consensus       198 ~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~  240 (405)
T TIGR00362       198 RS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSD  240 (405)
T ss_pred             Hh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecC
Confidence            22 238999999653211 11 223222211 123456777775

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).

>TIGR00763 lon ATP-dependent protease La

Probab=97.41  E-value=0.0019  Score=65.94  Aligned_cols=51  Identities=25%  Similarity=0.391  Sum_probs=38.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+.-++.|.+++............++.++|++|+|||++|+.+.+.
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~  370 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKA  370 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            458899999999988775322111223458999999999999999999875

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.

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

Probab=97.40  E-value=0.0001  Score=74.21  Aligned_cols=44  Identities=25%  Similarity=0.405  Sum_probs=36.6

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++||+.+++++++.|.....      .-+.++|++|+|||+||+.++..
T Consensus       187 ~liGR~~ei~~~i~iL~r~~~------~n~LLvGppGvGKT~lae~la~~  230 (758)
T PRK11034        187 PLIGREKELERAIQVLCRRRK------NNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_pred             cCcCCCHHHHHHHHHHhccCC------CCeEEECCCCCCHHHHHHHHHHH
Confidence            589999999999999976431      23468999999999999998864

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.38  E-value=0.00057  Score=65.04  Aligned_cols=75  Identities=25%  Similarity=0.295  Sum_probs=46.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF  294 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~  294 (337)
                      ..-+.|+|+.|+|||+|++.+++... +.+.. .++|++.      .+++.++...+...      ....    +.+.+.
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~-~~~~~~~v~yi~~------~~f~~~~~~~~~~~------~~~~----f~~~~~  192 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVV-QNEPDLRVMYITS------EKFLNDLVDSMKEG------KLNE----FREKYR  192 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHH-HhCCCCeEEEEEH------HHHHHHHHHHHhcc------cHHH----HHHHHH
Confidence            34599999999999999999998521 22222 3455543      45666666655321      2222    233333


Q ss_pred             CCeEEEEEeCCCC
Q 043252          295 GKKFLLVLDDVWN  307 (337)
Q Consensus       295 ~kr~LlVlDdv~~  307 (337)
                      .+.-+|+|||+..
T Consensus       193 ~~~dvLlIDDi~~  205 (440)
T PRK14088        193 KKVDVLLIDDVQF  205 (440)
T ss_pred             hcCCEEEEechhh
Confidence            3455899999964

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

Probab=97.38  E-value=0.00069  Score=59.71  Aligned_cols=127  Identities=18%  Similarity=0.205  Sum_probs=78.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEE-EEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAW-TCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~w-v~v~~~~~~~~~~~~i  267 (337)
                      .+++|.+..+.-|.+.+..      ........+|++|.|||+-|..+...---.+.|.+++. .++|..-... +.+. 
T Consensus        36 de~~gQe~vV~~L~~a~~~------~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGis-vvr~-  107 (346)
T KOG0989|consen   36 DELAGQEHVVQVLKNALLR------RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGIS-VVRE-  107 (346)
T ss_pred             HhhcchHHHHHHHHHHHhh------cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhccccccccc-chhh-
Confidence            4688999999999998875      24678999999999999999888764333455666543 3334322211 1100 


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHc--CCCeE-EEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEe
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQL--FGKKF-LLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT  333 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L--~~kr~-LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTT  333 (337)
                                ...+...+........  ..+.| .||||+......+.|..++..+.+....++.|+.+
T Consensus       108 ----------Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIc  166 (346)
T KOG0989|consen  108 ----------KIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILIC  166 (346)
T ss_pred             ----------hhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEc
Confidence                      1111111111111111  12343 78899999888899999998887756666655544

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.36  E-value=0.00016  Score=55.78  Aligned_cols=22  Identities=45%  Similarity=0.504  Sum_probs=20.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|.|++|+||||+|+.+.+.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999874

...

>PRK13531 regulatory ATPase RavA; Provisional

Probab=97.36  E-value=0.00066  Score=64.32  Aligned_cols=43  Identities=16%  Similarity=0.255  Sum_probs=37.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||++.++.+...+....        -|.|.|++|+|||+||+.+...
T Consensus        20 ~~i~gre~vI~lll~aalag~--------hVLL~GpPGTGKT~LAraLa~~   62 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGE--------SVFLLGPPGIAKSLIARRLKFA   62 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCC--------CEEEECCCChhHHHHHHHHHHH
Confidence            358899999999999887654        6889999999999999999874

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=97.36  E-value=0.0056  Score=62.33  Aligned_cols=52  Identities=29%  Similarity=0.406  Sum_probs=40.3

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.+.+|.++-++.|+++|............++.++|++|+||||+|+.+...
T Consensus       321 ~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~  372 (784)
T PRK10787        321 DTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKA  372 (784)
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999887422112224458999999999999999999864

>PRK07261 topology modulation protein; Provisional

Probab=97.36  E-value=0.00049  Score=56.76  Aligned_cols=54  Identities=26%  Similarity=0.245  Sum_probs=32.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhccccc-ccccceEEEEeCCCCCHHHHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVE-DHFDLKAWTCVSDDFDVIRLTKSILLSI  271 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~v~~~~~~~~~~~~il~~~  271 (337)
                      .|.|+|++|+||||||+.+.....+. -+.+...|-......+..++...+...+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~~~~~~~~~~~~~~~~~~   56 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPNWQERDDDDMIADISNFL   56 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccccccCCHHHHHHHHHHHH
Confidence            48999999999999999987643221 1345555643333334444444443333

>PRK04296 thymidine kinase; Provisional

Probab=97.35  E-value=0.00053  Score=57.63  Aligned_cols=113  Identities=12%  Similarity=-0.028  Sum_probs=59.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC-CCCCHHHHHHHHHHHcCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV-DNHDLNKLQEELKKQLFG  295 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~-~~~~~~~~~~~l~~~L~~  295 (337)
                      .++.|+|+.|.||||++..+.....  .+-..++.+.  ..++.......++.+++..... .......+...+.+ ..+
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~--~~g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~   77 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYE--ERGMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGE   77 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHH--HcCCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCC
Confidence            4788999999999999977765421  1222222231  2222222233344444322110 12334455555555 333


Q ss_pred             CeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          296 KKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       296 kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      +.-+||+|.+..-+.++...+...+.  ..|..||+|.++.
T Consensus        78 ~~dvviIDEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~~  116 (190)
T PRK04296         78 KIDCVLIDEAQFLDKEQVVQLAEVLD--DLGIPVICYGLDT  116 (190)
T ss_pred             CCCEEEEEccccCCHHHHHHHHHHHH--HcCCeEEEEecCc
Confidence            44489999995543232333333322  3577899998763

>PRK09183 transposase/IS protein; Provisional

Probab=97.34  E-value=0.00066  Score=59.91  Aligned_cols=23  Identities=35%  Similarity=0.482  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.|+|++|+|||+||..+...
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHH
Confidence            36789999999999999999764

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=97.34  E-value=0.00059  Score=56.07  Aligned_cols=131  Identities=18%  Similarity=0.147  Sum_probs=64.7

Q ss_pred             cccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc-ccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          191 VYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       191 ~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      ++|....+.++++.+..-..    ...-|.|+|..|.||+.+|+.+++... ....|   +-|+++. ++.+.+-.++.-
T Consensus         1 liG~s~~m~~~~~~~~~~a~----~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pf---i~vnc~~-~~~~~~e~~LFG   72 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS----SDLPVLITGETGTGKELLARAIHNNSPRKNGPF---ISVNCAA-LPEELLESELFG   72 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT----STS-EEEECSTTSSHHHHHHHHHHCSTTTTS-E---EEEETTT-S-HHHHHHHHHE
T ss_pred             CEeCCHHHHHHHHHHHHHhC----CCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCe---EEEehhh-hhcchhhhhhhc
Confidence            46777777777777654332    124667999999999999999998421 22223   3344443 333333333322


Q ss_pred             HhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCC------C-----CCcEEEEEecC
Q 043252          270 SIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAG------A-----QGSKIIVTTRN  335 (337)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~------~-----~gs~iivTTR~  335 (337)
                      ..............   ..+...   ..=-|+||+|.......-..|...+..+      .     ...|||.||..
T Consensus        73 ~~~~~~~~~~~~~~---G~l~~A---~~GtL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~  143 (168)
T PF00158_consen   73 HEKGAFTGARSDKK---GLLEQA---NGGTLFLDEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSK  143 (168)
T ss_dssp             BCSSSSTTTSSEBE---HHHHHT---TTSEEEEETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS
T ss_pred             cccccccccccccC---Cceeec---cceEEeecchhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCc
Confidence            21111110001000   112122   2226789999776554444555444321      1     14588888864

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.30  E-value=0.0012  Score=53.24  Aligned_cols=40  Identities=23%  Similarity=0.293  Sum_probs=28.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCC
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFD  259 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~  259 (337)
                      ++.|+|++|+||||++..+....  ...-..++|+.....+.
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~--~~~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNI--ATKGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHH--HhcCCEEEEEECCcchH
Confidence            36899999999999999997642  22234567777765543

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.

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

Probab=97.30  E-value=0.00023  Score=61.98  Aligned_cols=50  Identities=26%  Similarity=0.458  Sum_probs=42.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|+|.++-+++|.=++..... .++.+--+.++|++|.||||||.-+.+.
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~-r~e~lDHvLl~GPPGlGKTTLA~IIA~E   75 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKK-RGEALDHVLLFGPPGLGKTTLAHIIANE   75 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHh-cCCCcCeEEeeCCCCCcHHHHHHHHHHH
Confidence            5799999999988777765443 4567889999999999999999999885

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

Probab=97.29  E-value=0.0017  Score=56.03  Aligned_cols=92  Identities=20%  Similarity=0.153  Sum_probs=55.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccc----cccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVED----HFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDL  282 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~  282 (337)
                      .-.++.|+|++|+|||+|+..+........    .=..++|+.....++...+. .+.........        ....+.
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~   96 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVARPYNG   96 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEeCCCH
Confidence            456999999999999999988865321111    01457899988877765543 33333221100        022445


Q ss_pred             HHHHHHHHHHcC----CCeEEEEEeCCCC
Q 043252          283 NKLQEELKKQLF----GKKFLLVLDDVWN  307 (337)
Q Consensus       283 ~~~~~~l~~~L~----~kr~LlVlDdv~~  307 (337)
                      +++...+...+.    .+--|||+|.+..
T Consensus        97 ~~~~~~l~~~~~~~~~~~~~lvVIDsis~  125 (226)
T cd01393          97 EQQLEIVEELERIMSSGRVDLVVVDSVAA  125 (226)
T ss_pred             HHHHHHHHHHHHHhhcCCeeEEEEcCcch
Confidence            555555555542    3445999999853

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.

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

Probab=97.29  E-value=0.00068  Score=61.39  Aligned_cols=85  Identities=21%  Similarity=0.138  Sum_probs=54.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCC----CCCCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQ----NVDNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~----~~~~~~~~~~~~~l~  290 (337)
                      .-+++-|+|++|+||||||.+++-..  ...-...+||+..+.++..     .++.++...    .....+.++....+.
T Consensus        54 ~G~iteI~Gp~GsGKTtLal~~~~~~--~~~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~  126 (325)
T cd00983          54 KGRIIEIYGPESSGKTTLALHAIAEA--QKLGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIAD  126 (325)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHH
Confidence            45799999999999999998876542  2233467899887777653     233332211    012334566666665


Q ss_pred             HHcC-CCeEEEEEeCCC
Q 043252          291 KQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       291 ~~L~-~kr~LlVlDdv~  306 (337)
                      ..++ +.--|||+|.|-
T Consensus       127 ~li~s~~~~lIVIDSva  143 (325)
T cd00983         127 SLVRSGAVDLIVVDSVA  143 (325)
T ss_pred             HHHhccCCCEEEEcchH
Confidence            5554 345599999984

RecA couples ATP hydrolysis to DNA strand exchange.

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

Probab=97.28  E-value=0.0013  Score=66.54  Aligned_cols=119  Identities=13%  Similarity=0.105  Sum_probs=68.6

Q ss_pred             ccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~  266 (337)
                      .++|.++.++.|...+.....   ..+.....+.++|+.|+|||+||+.+....  ..   ..+.++++.-.....    
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l--~~---~~i~id~se~~~~~~----  529 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL--GI---ELLRFDMSEYMERHT----  529 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh--CC---CcEEeechhhccccc----
Confidence            478999999988888763210   012335678999999999999999997642  22   233444443221111    


Q ss_pred             HHHHhhCCCCC--CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCC
Q 043252          267 ILLSIASDQNV--DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQ  321 (337)
Q Consensus       267 il~~~~~~~~~--~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~  321 (337)
                       ...+.+..+.  .......+.+.+++   ....+|+||++...+.+.+..|...|.
T Consensus       530 -~~~LiG~~~gyvg~~~~g~L~~~v~~---~p~sVlllDEieka~~~v~~~LLq~ld  582 (758)
T PRK11034        530 -VSRLIGAPPGYVGFDQGGLLTDAVIK---HPHAVLLLDEIEKAHPDVFNLLLQVMD  582 (758)
T ss_pred             -HHHHcCCCCCcccccccchHHHHHHh---CCCcEEEeccHhhhhHHHHHHHHHHHh
Confidence             1222221110  11111222233322   234699999998887777777776654

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.28  E-value=0.00081  Score=64.63  Aligned_cols=51  Identities=22%  Similarity=0.169  Sum_probs=37.6

Q ss_pred             cccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.|.+..+++|.+.+..+-.       .+-...+-+.++|++|+|||++|+.+++.
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh
Confidence            4578899999888887642110       01123456899999999999999999985

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.28  E-value=0.004  Score=57.62  Aligned_cols=24  Identities=33%  Similarity=0.389  Sum_probs=21.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++|+++|++|+||||++..+..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~  263 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAW  263 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHH
Confidence            357999999999999999988865

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.26  E-value=0.0007  Score=61.33  Aligned_cols=91  Identities=18%  Similarity=0.176  Sum_probs=56.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhccccc----ccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVE----DHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDL  282 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~  282 (337)
                      .-+++-|+|++|+|||+|+..++-.....    ..=..++||+..+.|+++++.+ +++.++....        ....+.
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~-~a~~~g~d~~~~l~~i~~~~~~~~  173 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA-IAERFGVDPDAVLDNILYARAYTS  173 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH-HHHHcCCChHHhcCcEEEecCCCH
Confidence            45799999999999999997765332221    1113688999999999888654 5555543211        012233


Q ss_pred             HHHH---HHHHHHcC-CCeEEEEEeCCC
Q 043252          283 NKLQ---EELKKQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       283 ~~~~---~~l~~~L~-~kr~LlVlDdv~  306 (337)
                      ++..   ..+...+. ++-=|||+|.+-
T Consensus       174 e~~~~~l~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       174 EHQMELLDYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEEcch
Confidence            4333   33333443 334489999984

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=97.26  E-value=0.0008  Score=60.88  Aligned_cols=86  Identities=20%  Similarity=0.155  Sum_probs=54.5

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEEL  289 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l  289 (337)
                      +.-+++-|+|++|+||||||.++....  ...-..++||...+.++..     .+++++....    ......++....+
T Consensus        53 p~G~iteI~G~~GsGKTtLaL~~~~~~--~~~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~  125 (321)
T TIGR02012        53 PRGRIIEIYGPESSGKTTLALHAIAEA--QKAGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIA  125 (321)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            345799999999999999998876542  2223457788877766653     2333332110    1234456666666


Q ss_pred             HHHcC-CCeEEEEEeCCC
Q 043252          290 KKQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       290 ~~~L~-~kr~LlVlDdv~  306 (337)
                      ...++ +.--+||+|.+-
T Consensus       126 ~~li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       126 ETLVRSGAVDIIVVDSVA  143 (321)
T ss_pred             HHHhhccCCcEEEEcchh
Confidence            55553 445699999984

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.26  E-value=0.0011  Score=60.49  Aligned_cols=91  Identities=15%  Similarity=0.185  Sum_probs=56.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccc----cceEEEEeCCCCCHHHHHHHHHHHhhCCCCC--------CCCC-
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF----DLKAWTCVSDDFDVIRLTKSILLSIASDQNV--------DNHD-  281 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~--------~~~~-  281 (337)
                      ...++-|+|++|+|||+|+..++-.......+    ...+||+..+.|++..+.+ +++.++.....        ...+ 
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g~~~~~~l~~i~~~~~~~~  179 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALGLDPDEVLDNIHVARAYNS  179 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcCCChHhhhccEEEEeCCCH
Confidence            45799999999999999998886542221111    3689999999888877654 33443321100        1111 


Q ss_pred             --HHHHHHHHHHHcCC-Ce-EEEEEeCCC
Q 043252          282 --LNKLQEELKKQLFG-KK-FLLVLDDVW  306 (337)
Q Consensus       282 --~~~~~~~l~~~L~~-kr-~LlVlDdv~  306 (337)
                        ...+...+...+.. .+ -|||+|.+-
T Consensus       180 ~~~~~~~~~l~~~i~~~~~~~lvVIDSis  208 (317)
T PRK04301        180 DHQMLLAEKAEELIKEGENIKLVIVDSLT  208 (317)
T ss_pred             HHHHHHHHHHHHHHhccCceeEEEEECch
Confidence              12334555555543 33 499999984

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

Probab=97.26  E-value=0.0012  Score=58.00  Aligned_cols=81  Identities=23%  Similarity=0.309  Sum_probs=47.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFG  295 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~  295 (337)
                      ..-+.++|.+|+|||.||..+.+..- +..+. +.+++      ..+++.++......         ......|.+.+ .
T Consensus       105 ~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~s-v~f~~------~~el~~~Lk~~~~~---------~~~~~~l~~~l-~  166 (254)
T COG1484         105 GENLVLLGPPGVGKTHLAIAIGNELL-KAGIS-VLFIT------APDLLSKLKAAFDE---------GRLEEKLLREL-K  166 (254)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHH-HcCCe-EEEEE------HHHHHHHHHHHHhc---------CchHHHHHHHh-h
Confidence            34789999999999999999988633 32232 34443      34455555554432         11222233322 1


Q ss_pred             CeEEEEEeCCCCCChhcHH
Q 043252          296 KKFLLVLDDVWNENYTDWV  314 (337)
Q Consensus       296 kr~LlVlDdv~~~~~~~~~  314 (337)
                      +-=||||||+-......|.
T Consensus       167 ~~dlLIiDDlG~~~~~~~~  185 (254)
T COG1484         167 KVDLLIIDDIGYEPFSQEE  185 (254)
T ss_pred             cCCEEEEecccCccCCHHH
Confidence            2239999999765444443

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=97.24  E-value=0.00087  Score=55.62  Aligned_cols=23  Identities=43%  Similarity=0.674  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.|+.|.|||||++.+...
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          29 EKIALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            48999999999999999999764

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.22  E-value=0.0011  Score=63.57  Aligned_cols=73  Identities=19%  Similarity=0.285  Sum_probs=43.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhccccccccc--ceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD--LKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL  293 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L  293 (337)
                      ...+.|+|+.|+|||+|++.+.+.  +...+.  .+++++.      .++...+...+..      .....    +.+.+
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~v~yi~~------~~~~~~~~~~~~~------~~~~~----~~~~~  209 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNY--ILEKNPNAKVVYVTS------EKFTNDFVNALRN------NTMEE----FKEKY  209 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEEEH------HHHHHHHHHHHHc------CcHHH----HHHHH
Confidence            456899999999999999999985  323321  2345443      3344445544422      12222    33333


Q ss_pred             CCCeEEEEEeCCCC
Q 043252          294 FGKKFLLVLDDVWN  307 (337)
Q Consensus       294 ~~kr~LlVlDdv~~  307 (337)
                      + +.-+|+|||+..
T Consensus       210 ~-~~dlLiiDDi~~  222 (450)
T PRK00149        210 R-SVDVLLIDDIQF  222 (450)
T ss_pred             h-cCCEEEEehhhh
Confidence            3 234899999965

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=97.21  E-value=0.0018  Score=53.78  Aligned_cols=115  Identities=14%  Similarity=0.149  Sum_probs=61.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEE---eCCCCCHHHH------HHHHHHHhhCCC-----CCCCCCH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC---VSDDFDVIRL------TKSILLSIASDQ-----NVDNHDL  282 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---v~~~~~~~~~------~~~il~~~~~~~-----~~~~~~~  282 (337)
                      .+++|+|+.|.|||||.+.++...   ......+++.   +. ..+....      ..++++.++...     ......-
T Consensus        26 ~~~~l~G~nGsGKStLl~~i~G~~---~~~~G~v~~~g~~~~-~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G  101 (180)
T cd03214          26 EIVGILGPNGAGKSTLLKTLAGLL---KPSSGEILLDGKDLA-SLSPKELARKIAYVPQALELLGLAHLADRPFNELSGG  101 (180)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---CCCCcEEEECCEECC-cCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHH
Confidence            499999999999999999998642   2233334332   21 1122221      112344433221     1011222


Q ss_pred             HHHHHHHHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCC-CC-CcEEEEEecC
Q 043252          283 NKLQEELKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAG-AQ-GSKIIVTTRN  335 (337)
Q Consensus       283 ~~~~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~-~~-gs~iivTTR~  335 (337)
                      +...-.+...|-...-+++||+.-.. +......+...+..- .. |..||++|.+
T Consensus       102 ~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~  157 (180)
T cd03214         102 ERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHD  157 (180)
T ss_pred             HHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            22333455566667788999998643 333444444444322 22 5678888865

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.

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.21  E-value=0.00095  Score=56.30  Aligned_cols=23  Identities=35%  Similarity=0.502  Sum_probs=19.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|.++|+.|+||||.+-++...
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~   24 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAAR   24 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCchHhHHHHHHHH
Confidence            69999999999999998777553

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 ....

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=97.21  E-value=0.00093  Score=61.13  Aligned_cols=91  Identities=19%  Similarity=0.128  Sum_probs=56.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhccccc----ccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVE----DHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDL  282 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~  282 (337)
                      .-++.-|+|.+|+|||+|+..++-.....    ..-...+||+....|++.++.+ +++.++....        ....+.
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~~~~~~~  203 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIYARAYTY  203 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEEecCCCH
Confidence            45789999999999999998776332221    1124679999999999888654 5555543211        022344


Q ss_pred             HHHH---HHHHHHcC-CCeEEEEEeCCC
Q 043252          283 NKLQ---EELKKQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       283 ~~~~---~~l~~~L~-~kr~LlVlDdv~  306 (337)
                      +++.   ..+...+. .+--|||+|.+-
T Consensus       204 e~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        204 EHQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence            4433   33333343 334489999984

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.20  E-value=0.001  Score=65.00  Aligned_cols=100  Identities=16%  Similarity=0.216  Sum_probs=54.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccc--cceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHF--DLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF  294 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~  294 (337)
                      ..+.|+|..|+|||.|++.+++..  ...+  ..+++++      ..+++.++...+...      ..+.    +++.+.
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a--~~~~~g~~V~Yit------aeef~~el~~al~~~------~~~~----f~~~y~  376 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYA--RRLYPGTRVRYVS------SEEFTNEFINSIRDG------KGDS----FRRRYR  376 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHH--HHhCCCCeEEEee------HHHHHHHHHHHHHhc------cHHH----HHHHhh
Confidence            358999999999999999999852  2211  1234443      344555555544321      1222    333332


Q ss_pred             CCeEEEEEeCCCCCCh-hcHH-HhhccCCC-CCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNENY-TDWV-HLSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~-~~~~-~l~~~l~~-~~~gs~iivTTR~  335 (337)
                      . -=||+|||+..... +.|. .|...|.. ...|..|||||..
T Consensus       377 ~-~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~  419 (617)
T PRK14086        377 E-MDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDR  419 (617)
T ss_pred             c-CCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCC
Confidence            2 24889999965421 2222 22222211 1234568888864

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.20  E-value=0.002  Score=61.39  Aligned_cols=102  Identities=17%  Similarity=0.199  Sum_probs=54.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF  294 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~  294 (337)
                      ....+.|+|+.|+|||+|++.+.+...  .....+++++      ...+...+...+...      ..    ..++..+.
T Consensus       140 ~~npl~L~G~~G~GKTHLl~Ai~~~l~--~~~~~v~yi~------~~~f~~~~~~~l~~~------~~----~~f~~~~~  201 (445)
T PRK12422        140 PFNPIYLFGPEGSGKTHLMQAAVHALR--ESGGKILYVR------SELFTEHLVSAIRSG------EM----QRFRQFYR  201 (445)
T ss_pred             CCceEEEEcCCCCCHHHHHHHHHHHHH--HcCCCEEEee------HHHHHHHHHHHHhcc------hH----HHHHHHcc
Confidence            345789999999999999999998532  1112234443      334445555554321      11    22334333


Q ss_pred             CCeEEEEEeCCCCCChhc--HHHhhccCCC-CCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNENYTD--WVHLSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~--~~~l~~~l~~-~~~gs~iivTTR~  335 (337)
                       +.-+|+|||+.......  .+.+...+.. ...|..||+||..
T Consensus       202 -~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~  244 (445)
T PRK12422        202 -NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTC  244 (445)
T ss_pred             -cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCC
Confidence             34488899996532111  1222222210 0134568888743

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=97.20  E-value=0.0013  Score=59.80  Aligned_cols=91  Identities=16%  Similarity=0.085  Sum_probs=54.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccc----cccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVED----HFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDL  282 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~  282 (337)
                      ...++.|+|.+|+|||||+..++.......    .-..++|++..+.|+..++ .++.+.+.....        ....+.
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~~~~~~l~~i~~~~~~~~  173 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGLNPEDVLDNVAYARAYNT  173 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCCChHHhhccEEEEecCCh
Confidence            467999999999999999988865322211    1135689999888888764 334444432211        012233


Q ss_pred             HHH---HHHHHHHcCC-CeEEEEEeCCC
Q 043252          283 NKL---QEELKKQLFG-KKFLLVLDDVW  306 (337)
Q Consensus       283 ~~~---~~~l~~~L~~-kr~LlVlDdv~  306 (337)
                      +++   ...+...+.. +--|||+|.+-
T Consensus       174 ~~~~~~l~~~~~~~~~~~~~LvVIDSI~  201 (316)
T TIGR02239       174 DHQLQLLQQAAAMMSESRFALLIVDSAT  201 (316)
T ss_pred             HHHHHHHHHHHHhhccCCccEEEEECcH
Confidence            333   3333333433 44599999984

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).

>PRK09354 recA recombinase A; Provisional

Probab=97.20  E-value=0.0011  Score=60.46  Aligned_cols=86  Identities=20%  Similarity=0.154  Sum_probs=55.9

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEEL  289 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l  289 (337)
                      +.-+++-|+|++|+|||||+.+++...  ...-...+||...+.++..     .+++++.+..    ....+.++....+
T Consensus        58 p~G~IteI~G~~GsGKTtLal~~~~~~--~~~G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~  130 (349)
T PRK09354         58 PRGRIVEIYGPESSGKTTLALHAIAEA--QKAGGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIA  130 (349)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            346799999999999999998876542  2233567899888877753     2333332210    1233456666666


Q ss_pred             HHHcC-CCeEEEEEeCCC
Q 043252          290 KKQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       290 ~~~L~-~kr~LlVlDdv~  306 (337)
                      ...++ +.--|||+|.|-
T Consensus       131 ~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        131 DTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             HHHhhcCCCCEEEEeChh
Confidence            65554 345599999985

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

Probab=97.17  E-value=0.0059  Score=56.84  Aligned_cols=101  Identities=21%  Similarity=0.264  Sum_probs=58.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF  294 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~  294 (337)
                      ....+.|+|..|.|||.|++.+.+.  ...+......+++    +.+....+++..+...          -.+.+++.. 
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~--~~~~~~~a~v~y~----~se~f~~~~v~a~~~~----------~~~~Fk~~y-  174 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNE--ALANGPNARVVYL----TSEDFTNDFVKALRDN----------EMEKFKEKY-  174 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHH--HHhhCCCceEEec----cHHHHHHHHHHHHHhh----------hHHHHHHhh-
Confidence            4679999999999999999999985  3334432223333    2345555555555321          123344444 


Q ss_pred             CCeEEEEEeCCCCCC-----hhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNEN-----YTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~-----~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                       .-=++++||++.-.     ++....+...+..  .|-.||+|++.
T Consensus       175 -~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~--~~kqIvltsdr  217 (408)
T COG0593         175 -SLDLLLIDDIQFLAGKERTQEEFFHTFNALLE--NGKQIVLTSDR  217 (408)
T ss_pred             -ccCeeeechHhHhcCChhHHHHHHHHHHHHHh--cCCEEEEEcCC
Confidence             33388899996521     1222223333333  23378888753

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.17  E-value=0.0059  Score=55.43  Aligned_cols=140  Identities=14%  Similarity=0.118  Sum_probs=76.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc-------------cccccceEEEEeC
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV-------------EDHFDLKAWTCVS  255 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-------------~~~F~~~~wv~v~  255 (337)
                      ..++|.+..++.+...+....     -.....++|+.|+||+++|..+...---             ...+....|+.-.
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r-----l~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~   78 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR-----IAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPT   78 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC-----CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEecc
Confidence            468899999999999996543     2469999999999999999777543100             1111223344211


Q ss_pred             CCCCHHHHHHHHHHHhhCCC-CCCCCCHHHHHHHHHHHc-----CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEE
Q 043252          256 DDFDVIRLTKSILLSIASDQ-NVDNHDLNKLQEELKKQL-----FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKI  329 (337)
Q Consensus       256 ~~~~~~~~~~~il~~~~~~~-~~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~i  329 (337)
                      -..+-..+-...+...+... .......++. +.+.+.+     .+++-++|+|++...+....+.|...|..-+ .+.+
T Consensus        79 ~~~~g~~~~~~~~~~~~~~~~~~~~I~id~i-r~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~f  156 (314)
T PRK07399         79 YQHQGKLITASEAEEAGLKRKAPPQIRLEQI-REIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPG-NGTL  156 (314)
T ss_pred             ccccccccchhhhhhccccccccccCcHHHH-HHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeE
Confidence            00000000001111111000 0011222222 2233333     3567799999998777777888888886544 4466


Q ss_pred             EEEecC
Q 043252          330 IVTTRN  335 (337)
Q Consensus       330 ivTTR~  335 (337)
                      |++|.+
T Consensus       157 ILi~~~  162 (314)
T PRK07399        157 ILIAPS  162 (314)
T ss_pred             EEEECC
Confidence            666643

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.17  E-value=0.00077  Score=55.82  Aligned_cols=36  Identities=31%  Similarity=0.432  Sum_probs=26.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEE
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWT  252 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  252 (337)
                      ...+|.+.|+.|+||||+|+.++..  ....+...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~--l~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYER--LKLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH--HHHcCCcEEEE
Confidence            3469999999999999999999874  33344444444

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.16  E-value=0.00035  Score=67.22  Aligned_cols=50  Identities=22%  Similarity=0.311  Sum_probs=39.9

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +++|.++.+++|++.|......-...-+++.++|++|+||||||+.+.+-
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~  126 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSL  126 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHH
Confidence            58999999999999994322112234579999999999999999999874

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

Probab=97.13  E-value=0.0029  Score=60.77  Aligned_cols=98  Identities=17%  Similarity=0.229  Sum_probs=64.0

Q ss_pred             ccccccchhHHHHHHHHHhcCCCC------CCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSR------NDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVI  261 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~------~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~  261 (337)
                      -..+=|.+..+.+|.+++..-..+      +-...+-|.++|++|+|||.||+.+.+..  .=.|     +.++.     
T Consensus       189 f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel--~vPf-----~~isA-----  256 (802)
T KOG0733|consen  189 FSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL--GVPF-----LSISA-----  256 (802)
T ss_pred             hhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhc--CCce-----Eeecc-----
Confidence            346778998888888877652221      22345678999999999999999999853  2223     23322     


Q ss_pred             HHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCC
Q 043252          262 RLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVW  306 (337)
Q Consensus       262 ~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~  306 (337)
                         .+|+..+      ...+.+.+.+-+.+.-..-.|+++||++.
T Consensus       257 ---peivSGv------SGESEkkiRelF~~A~~~aPcivFiDeID  292 (802)
T KOG0733|consen  257 ---PEIVSGV------SGESEKKIRELFDQAKSNAPCIVFIDEID  292 (802)
T ss_pred             ---hhhhccc------CcccHHHHHHHHHHHhccCCeEEEeeccc
Confidence               1233333      23344555555666667789999999994

>CHL00176 ftsH cell division protein; Validated

Probab=97.13  E-value=0.0024  Score=63.34  Aligned_cols=98  Identities=19%  Similarity=0.247  Sum_probs=54.5

Q ss_pred             cccccchhHHHHH---HHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHH
Q 043252          189 AKVYGRETEKKEI---VELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       189 ~~~vGr~~~~~~l---~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~  262 (337)
                      .++.|.++.++++   +++|..+..   -+....+-+.++|++|+|||+||+.++...  ...     ++.++.    .+
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~--~~p-----~i~is~----s~  251 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA--EVP-----FFSISG----SE  251 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh--CCC-----eeeccH----HH
Confidence            4578887666554   444433221   012234568999999999999999998742  112     233321    11


Q ss_pred             HHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          263 LTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       263 ~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                      +.    ....      ......+...+........++|+|||+..
T Consensus       252 f~----~~~~------g~~~~~vr~lF~~A~~~~P~ILfIDEID~  286 (638)
T CHL00176        252 FV----EMFV------GVGAARVRDLFKKAKENSPCIVFIDEIDA  286 (638)
T ss_pred             HH----HHhh------hhhHHHHHHHHHHHhcCCCcEEEEecchh
Confidence            11    1110      01122333444555567789999999953

>PRK06696 uridine kinase; Validated

Probab=97.11  E-value=0.0008  Score=58.07  Aligned_cols=44  Identities=27%  Similarity=0.262  Sum_probs=34.8

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|..-+++|.+.+....   .....+|+|.|.+|+||||||+.+...
T Consensus         2 ~~~~~~~~la~~~~~~~---~~~~~iI~I~G~sgsGKSTlA~~L~~~   45 (223)
T PRK06696          2 SRKQLIKELAEHILTLN---LTRPLRVAIDGITASGKTTFADELAEE   45 (223)
T ss_pred             cHHHHHHHHHHHHHHhC---CCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            35667788888886532   235789999999999999999999864

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=97.11  E-value=0.00075  Score=53.53  Aligned_cols=107  Identities=16%  Similarity=0.130  Sum_probs=59.7

Q ss_pred             ccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc-cccccceEEEEeCCCCCHHHHHHHHHHH
Q 043252          192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV-EDHFDLKAWTCVSDDFDVIRLTKSILLS  270 (337)
Q Consensus       192 vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F~~~~wv~v~~~~~~~~~~~~il~~  270 (337)
                      ||....+.++.+.+..-..    .-..|.|.|..|+||+++|+.++..... ...|...   .+.. ..     .+++. 
T Consensus         1 vG~S~~~~~l~~~l~~~a~----~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~---~~~~-~~-----~~~l~-   66 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAK----SSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVI---DCAS-LP-----AELLE-   66 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHC----SSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCC---CHHC-TC-----HHHHH-
T ss_pred             CCCCHHHHHHHHHHHHHhC----CCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEe---chhh-Cc-----HHHHH-
Confidence            4666666666666543221    2246799999999999999999875322 2223211   0111 00     11111 


Q ss_pred             hhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCC-CCCcEEEEEecC
Q 043252          271 IASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAG-AQGSKIIVTTRN  335 (337)
Q Consensus       271 ~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~-~~gs~iivTTR~  335 (337)
                                          . .  +.--|+|+|+..-+......+...+... ....|+|.||..
T Consensus        67 --------------------~-a--~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~  109 (138)
T PF14532_consen   67 --------------------Q-A--KGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQ  109 (138)
T ss_dssp             --------------------H-C--TTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC
T ss_pred             --------------------H-c--CCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCC
Confidence                                1 1  3445778999777666666666666532 456799998864

>PRK08233 hypothetical protein; Provisional

Probab=97.11  E-value=0.0024  Score=52.97  Aligned_cols=24  Identities=33%  Similarity=0.466  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|+|.|.+|+||||||+.+...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            469999999999999999999864

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.08  E-value=0.0007  Score=57.19  Aligned_cols=103  Identities=17%  Similarity=0.181  Sum_probs=50.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc---
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL---  293 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L---  293 (337)
                      ++..|.|++|.||||+++.+.......+   ..+.+......-...+.    .....    ...+...+.......-   
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g---~~v~~~apT~~Aa~~L~----~~~~~----~a~Ti~~~l~~~~~~~~~~   87 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAG---KRVIGLAPTNKAAKELR----EKTGI----EAQTIHSFLYRIPNGDDEG   87 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT-----EEEEESSHHHHHHHH----HHHTS-----EEEHHHHTTEECCEECCS
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCC---CeEEEECCcHHHHHHHH----HhhCc----chhhHHHHHhcCCcccccc
Confidence            4888999999999999998876422221   23333333322222222    22211    1111111100000000   


Q ss_pred             ---CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          294 ---FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       294 ---~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                         ..++-+||+|+....+...+..+....+.  .|+|||+.
T Consensus        88 ~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilv  127 (196)
T PF13604_consen   88 RPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILV  127 (196)
T ss_dssp             SCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEE
T ss_pred             cccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEE
Confidence               12345899999977666667666665543  46777764

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

Probab=97.06  E-value=0.0031  Score=59.09  Aligned_cols=52  Identities=25%  Similarity=0.194  Sum_probs=37.9

Q ss_pred             ccccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.++.|.+..+++|.+.+..+-.       .+-...+-+.++|++|+|||+||+.+.+.
T Consensus       144 ~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        144 YSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            45688999888888776532100       01134567899999999999999999885

>cd01394 radB RadB

Probab=97.05  E-value=0.0023  Score=54.92  Aligned_cols=88  Identities=20%  Similarity=0.091  Sum_probs=50.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHh----hCCCC-CCCCCHHH---HH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSI----ASDQN-VDNHDLNK---LQ  286 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~----~~~~~-~~~~~~~~---~~  286 (337)
                      .-.++.|.|.+|+|||||+.++....  ...=..++|++....+.  +-+.+++...    ..... ....+..+   ..
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~--~~~g~~v~yi~~e~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVET--AGQGKKVAYIDTEGLSS--ERFRQIAGDRPERAASSIIVFEPMDFNEQGRAI   93 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH--HhcCCeEEEEECCCCCH--HHHHHHHhHChHhhhcCEEEEeCCCHHHHHHHH
Confidence            45799999999999999998887542  12223467887665554  3333443321    10000 01222222   23


Q ss_pred             HHHHHHcCCCeEEEEEeCCC
Q 043252          287 EELKKQLFGKKFLLVLDDVW  306 (337)
Q Consensus       287 ~~l~~~L~~kr~LlVlDdv~  306 (337)
                      ..+...+..+--+||+|.+-
T Consensus        94 ~~~~~~~~~~~~lvvIDsi~  113 (218)
T cd01394          94 QETETFADEKVDLVVVDSAT  113 (218)
T ss_pred             HHHHHHHhcCCcEEEEechH
Confidence            34445554445699999984

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

>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=97.05  E-value=0.0038  Score=51.65  Aligned_cols=111  Identities=17%  Similarity=0.225  Sum_probs=57.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcc-cc--cc---ccc--ceEEEEeCCCCCHHHHHHHHHHHhhCCCC-----CCCCCH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDK-QV--ED---HFD--LKAWTCVSDDFDVIRLTKSILLSIASDQN-----VDNHDL  282 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~-~~--~~---~F~--~~~wv~v~~~~~~~~~~~~il~~~~~~~~-----~~~~~~  282 (337)
                      -.+++|+|+.|+|||||.+.+..+. ++  ..   .|.  ...|+  .+        .+.+..+.....     ...-+.
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~--~q--------~~~l~~~~L~~~~~~~~~~~LSg   90 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFI--DQ--------LQFLIDVGLGYLTLGQKLSTLSG   90 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEE--hH--------HHHHHHcCCCccccCCCcCcCCH
Confidence            3589999999999999999886321 11  11   111  12222  22        345555543211     011121


Q ss_pred             -HHHHHHHHHHcCCC--eEEEEEeCCCCC-ChhcHHHhhccCCCC-CCCcEEEEEecCC
Q 043252          283 -NKLQEELKKQLFGK--KFLLVLDDVWNE-NYTDWVHLSLPFQAG-AQGSKIIVTTRNQ  336 (337)
Q Consensus       283 -~~~~~~l~~~L~~k--r~LlVlDdv~~~-~~~~~~~l~~~l~~~-~~gs~iivTTR~~  336 (337)
                       +...-.+...|-.+  .=+++||+.-.. +......+...+... ..|..||++|.+.
T Consensus        91 Gq~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~  149 (176)
T cd03238          91 GELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNL  149 (176)
T ss_pred             HHHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence             22233344455455  668888988553 333334444444321 2466788888753

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.

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

Probab=97.04  E-value=0.0031  Score=55.67  Aligned_cols=88  Identities=17%  Similarity=0.238  Sum_probs=52.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCHH-----
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDLN-----  283 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~~-----  283 (337)
                      .-++|+|..|+|||||++.+++.  +..+|. .++++-+.+.. .+.++..++...-......      +.....     
T Consensus        70 Qr~~If~~~G~GKTtLa~~i~~~--i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~  147 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELINN--IAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVA  147 (274)
T ss_pred             CEEEEecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            47899999999999999999986  333443 45566665543 3455555555431111100      111111     


Q ss_pred             HHHHHHHHHc--C-CCeEEEEEeCCC
Q 043252          284 KLQEELKKQL--F-GKKFLLVLDDVW  306 (337)
Q Consensus       284 ~~~~~l~~~L--~-~kr~LlVlDdv~  306 (337)
                      ...-.+.+++  + ++..||++||+.
T Consensus       148 ~~a~~~AEyfr~~~g~~Vl~~~Dslt  173 (274)
T cd01133         148 LTGLTMAEYFRDEEGQDVLLFIDNIF  173 (274)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEeChh
Confidence            1223345555  3 899999999993

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.03  E-value=0.0037  Score=55.90  Aligned_cols=86  Identities=20%  Similarity=0.217  Sum_probs=45.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhccccc-ccccceEEEEeCCCCC--HHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVE-DHFDLKAWTCVSDDFD--VIRLTKSILLSIASDQNVDNHDLNKLQEELKK  291 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~v~~~~~--~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~  291 (337)
                      ...++.|+|+.|+||||++..+......+ ..+ .+..|+.. ++.  ..+.+......++.... ...+...+...+..
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~-~V~li~~D-~~r~~a~eql~~~~~~~~~p~~-~~~~~~~l~~~l~~  269 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNK-KVALITTD-TYRIGAVEQLKTYAKILGVPVK-VARDPKELRKALDR  269 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCC-eEEEEECC-ccchhHHHHHHHHHHHhCCcee-ccCCHHHHHHHHHH
Confidence            45799999999999999998887643222 112 23444433 222  12222222232222221 23344555555544


Q ss_pred             HcCCCeEEEEEeCC
Q 043252          292 QLFGKKFLLVLDDV  305 (337)
Q Consensus       292 ~L~~kr~LlVlDdv  305 (337)
                      . .+ .=+|++|..
T Consensus       270 ~-~~-~d~vliDt~  281 (282)
T TIGR03499       270 L-RD-KDLILIDTA  281 (282)
T ss_pred             c-cC-CCEEEEeCC
Confidence            3 33 347777753

>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=97.03  E-value=0.0046  Score=49.39  Aligned_cols=23  Identities=35%  Similarity=0.632  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|..|.|||||++.+...
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~   49 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGE   49 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCC
Confidence            48999999999999999999864

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.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=97.03  E-value=0.0006  Score=66.54  Aligned_cols=105  Identities=21%  Similarity=0.286  Sum_probs=64.2

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      +.+-+|.++-+++|+++|.-......-+-+++++||++|+|||+|++.+..-  ....|-   -+++.+-.|..+     
T Consensus       322 d~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~a--l~Rkfv---R~sLGGvrDEAE-----  391 (782)
T COG0466         322 DKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKA--LGRKFV---RISLGGVRDEAE-----  391 (782)
T ss_pred             cccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHH--hCCCEE---EEecCccccHHH-----
Confidence            3456799999999999986433222334579999999999999999999874  444452   234444333322     


Q ss_pred             HHHhhCCCC--CCCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          268 LLSIASDQN--VDNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       268 l~~~~~~~~--~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                         +.++..  ..+.. ..+...+++. +.+.=|++||.+..
T Consensus       392 ---IRGHRRTYIGamP-GrIiQ~mkka-~~~NPv~LLDEIDK  428 (782)
T COG0466         392 ---IRGHRRTYIGAMP-GKIIQGMKKA-GVKNPVFLLDEIDK  428 (782)
T ss_pred             ---hccccccccccCC-hHHHHHHHHh-CCcCCeEEeechhh
Confidence               222211  12222 2233333333 45677899999954

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.01  E-value=0.0026  Score=51.99  Aligned_cols=111  Identities=18%  Similarity=0.106  Sum_probs=57.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC--CCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD--DFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF  294 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~--~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~  294 (337)
                      .+++|+|+.|.|||||.+.++...   ......+++.-..  ..+..+...   ..+..- . +...-+...-.+.+.+-
T Consensus        27 e~~~l~G~nGsGKSTLl~~i~G~~---~~~~G~v~~~g~~~~~~~~~~~~~---~~i~~~-~-qLS~G~~qrl~laral~   98 (163)
T cd03216          27 EVHALLGENGAGKSTLMKILSGLY---KPDSGEILVDGKEVSFASPRDARR---AGIAMV-Y-QLSVGERQMVEIARALA   98 (163)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCEECCcCCHHHHHh---cCeEEE-E-ecCHHHHHHHHHHHHHh
Confidence            489999999999999999998632   2233344432111  111111111   011100 0 12222223334555555


Q ss_pred             CCeEEEEEeCCCCC-ChhcHHHhhccCCCC-CCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNE-NYTDWVHLSLPFQAG-AQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~-~~gs~iivTTR~  335 (337)
                      .+.-+++||+.-.. +......+...+..- ..|..||++|.+
T Consensus        99 ~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~  141 (163)
T cd03216          99 RNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHR  141 (163)
T ss_pred             cCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence            66778889998653 333344444444321 235668888765

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.

>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=97.01  E-value=0.004  Score=51.59  Aligned_cols=23  Identities=39%  Similarity=0.608  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|.|||||.+.+..-
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~Gl   48 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAGQ   48 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHcC
Confidence            49999999999999999999763

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.

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

Probab=97.00  E-value=0.0016  Score=62.32  Aligned_cols=135  Identities=19%  Similarity=0.202  Sum_probs=77.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ++++|.+.-...|...|....     -..--...|+.|+||||+|+.+...--...      | ....+++.-..-+.|-
T Consensus        16 ~evvGQe~v~~~L~nal~~~r-----i~hAYlfsG~RGvGKTt~Ari~AkalNC~~------~-~~~ePC~~C~~Ck~I~   83 (515)
T COG2812          16 DDVVGQEHVVKTLSNALENGR-----IAHAYLFSGPRGVGKTTIARILAKALNCEN------G-PTAEPCGKCISCKEIN   83 (515)
T ss_pred             HHhcccHHHHHHHHHHHHhCc-----chhhhhhcCCCCcCchhHHHHHHHHhcCCC------C-CCCCcchhhhhhHhhh
Confidence            457999999999999997654     244667789999999999998865321111      0 0111111111112222


Q ss_pred             HH-------hhCCCCCCCCCHHHHHHHHHHHc-CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LS-------IASDQNVDNHDLNKLQEELKKQL-FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~-------~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..       +........++...+.+.+.-.- .++-=+.++|+|.-.....|+.|...|..-...-..|+.|.+
T Consensus        84 ~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe  158 (515)
T COG2812          84 EGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTE  158 (515)
T ss_pred             cCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCC
Confidence            11       00001112223333333333332 244448999999887778999999888765555555555543

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=97.00  E-value=0.003  Score=57.38  Aligned_cols=92  Identities=15%  Similarity=0.148  Sum_probs=55.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccc----cccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVED----HFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDL  282 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~  282 (337)
                      ...++-|+|++|+|||+|+..++-......    .=..++||+....|+..++. ++++.++....        ....+.
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl~~~~~~~~i~i~~~~~~  172 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGLDPDEVLKNIYVARAYNS  172 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCCCHHHHhhceEEEecCCH
Confidence            457999999999999999988865422211    01268999999988887754 34444332110        011111


Q ss_pred             ---HHHHHHHHHHcCCC---eEEEEEeCCCC
Q 043252          283 ---NKLQEELKKQLFGK---KFLLVLDDVWN  307 (337)
Q Consensus       283 ---~~~~~~l~~~L~~k---r~LlVlDdv~~  307 (337)
                         ..+.+.+.+.+...   --|||+|.+-.
T Consensus       173 ~~~~~lld~l~~~i~~~~~~~~lVVIDSisa  203 (310)
T TIGR02236       173 NHQMLLVEKAEDLIKELNNPVKLLIVDSLTS  203 (310)
T ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEecchH
Confidence               12334455555332   34999999853

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.

>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=97.00  E-value=0.0063  Score=49.88  Aligned_cols=111  Identities=13%  Similarity=0.075  Sum_probs=56.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccc-ccc--ccc---eEEEEeCCCCCH--HHHHHHHHHHhhCCCCCCCCCHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQV-EDH--FDL---KAWTCVSDDFDV--IRLTKSILLSIASDQNVDNHDLNKLQEE  288 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~--F~~---~~wv~v~~~~~~--~~~~~~il~~~~~~~~~~~~~~~~~~~~  288 (337)
                      .+++|+|+.|.|||||++.+...... ...  |+.   ..+  +.+....  ..+...+.    .........-+...-.
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~--~~q~~~~~~~tv~~nl~----~~~~~~LS~G~~~rv~  101 (166)
T cd03223          28 DRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLF--LPQRPYLPLGTLREQLI----YPWDDVLSGGEQQRLA  101 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEE--ECCCCccccccHHHHhh----ccCCCCCCHHHHHHHH
Confidence            48999999999999999999864211 111  111   112  2232211  12222221    1011122223333344


Q ss_pred             HHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          289 LKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       289 l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +.+.|-.+.=+++||+.-.. +......+...+...  +..||++|.+
T Consensus       102 laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~  147 (166)
T cd03223         102 FARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHR  147 (166)
T ss_pred             HHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCC
Confidence            55555566678899988553 233333344444322  3568888765

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

>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots

Probab=96.99  E-value=0.02  Score=45.74  Aligned_cols=83  Identities=14%  Similarity=0.174  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHccc-cCChHHHHHHHHHHHHHHhhhhhh
Q 043252            5 GEAILTASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKK-TTDDSVKLWLGELQNLAYDVEDLL   83 (337)
Q Consensus         5 ~~~~~~~~~~~l~~kl~s~~~~~~~~~~~v~~~~~~L~~~L~~i~~~L~~ae~~~-~~~~~~~~Wl~~lr~~ayd~eD~l   83 (337)
                      |+.+.+|+++.+++.|...+..........+.-+++|...++.|..++++.+.-. ..+..-+.-++++.+...++++++
T Consensus         3 ~eL~~gaalG~~~~eLlk~v~~~~~k~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~~ee~e~L~~~L~~g~~LV   82 (147)
T PF05659_consen    3 AELVGGAALGAVFGELLKAVIDASKKSLSFKSILKRLESTLESIIPIIKEIDKLNVELDRPRQEEIERLKELLEKGKELV   82 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCchhHHHHHHHHHHHHHHHHH
Confidence            4444444444444444454455555566678889999999999999999988754 334444677888899999999999


Q ss_pred             HHHH
Q 043252           84 DEFQ   87 (337)
Q Consensus        84 D~~~   87 (337)
                      ..|.
T Consensus        83 ~k~s   86 (147)
T PF05659_consen   83 EKCS   86 (147)
T ss_pred             HHhc
Confidence            9873

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.95  E-value=0.0024  Score=54.08  Aligned_cols=26  Identities=35%  Similarity=0.418  Sum_probs=23.1

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....+|+|.|.+|+||||+|+.++..
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~   31 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQ   31 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHH
Confidence            35689999999999999999999874

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.94  E-value=0.0048  Score=54.63  Aligned_cols=91  Identities=22%  Similarity=0.165  Sum_probs=59.1

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHH-hhC---CCCCCCCCHHHHHHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLS-IAS---DQNVDNHDLNKLQEEL  289 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~-~~~---~~~~~~~~~~~~~~~l  289 (337)
                      +.-+++=|+|+.|.||||||-+++-.  .+..-...+|++.-+.+++..+. ++... +..   ..+........+.+.+
T Consensus        58 ~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~-~l~~~~~d~l~v~~~~~~e~q~~i~~~~  134 (279)
T COG0468          58 PRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAK-QLGVDLLDNLLVSQPDTGEQQLEIAEKL  134 (279)
T ss_pred             ccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHH-HHHHhhhcceeEecCCCHHHHHHHHHHH
Confidence            45679999999999999999887654  33334478999999999988744 34333 221   1121222233344555


Q ss_pred             HHHcCCCeEEEEEeCCCC
Q 043252          290 KKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       290 ~~~L~~kr~LlVlDdv~~  307 (337)
                      .+....+--|||+|.+-.
T Consensus       135 ~~~~~~~i~LvVVDSvaa  152 (279)
T COG0468         135 ARSGAEKIDLLVVDSVAA  152 (279)
T ss_pred             HHhccCCCCEEEEecCcc
Confidence            555444456999999844

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.93  E-value=0.0013  Score=55.61  Aligned_cols=107  Identities=14%  Similarity=0.179  Sum_probs=53.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      .+|.|+|+.|+||||++..+...  ........++. +.++..  ...... ..+..... ...+.....+.++..|...
T Consensus         2 GlilI~GptGSGKTTll~~ll~~--~~~~~~~~i~t-~e~~~E--~~~~~~-~~~i~q~~-vg~~~~~~~~~i~~aLr~~   74 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY--INKNKTHHILT-IEDPIE--FVHESK-RSLINQRE-VGLDTLSFENALKAALRQD   74 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--hhhcCCcEEEE-EcCCcc--ccccCc-cceeeecc-cCCCccCHHHHHHHHhcCC
Confidence            37899999999999999987653  22222333332 222111  000000 00000000 1112233455677777656


Q ss_pred             eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          297 KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      .=+|++|++.+.  +.+..+...   ...|-.++.|+..
T Consensus        75 pd~ii~gEird~--e~~~~~l~~---a~~G~~v~~t~Ha  108 (198)
T cd01131          75 PDVILVGEMRDL--ETIRLALTA---AETGHLVMSTLHT  108 (198)
T ss_pred             cCEEEEcCCCCH--HHHHHHHHH---HHcCCEEEEEecC
Confidence            669999999653  333332222   1235456666643

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.

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

Probab=96.92  E-value=0.0011  Score=62.75  Aligned_cols=51  Identities=29%  Similarity=0.221  Sum_probs=37.2

Q ss_pred             cccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|.+..+++|.+.+.-+-.       -+-.....+.++|++|+|||+||+.+++.
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~e  240 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANE  240 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHh
Confidence            4578999999888877642110       01123456889999999999999999985

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.92  E-value=0.0059  Score=53.03  Aligned_cols=87  Identities=20%  Similarity=0.138  Sum_probs=53.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC------------------
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN------------------  276 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~------------------  276 (337)
                      .-+++.|+|.+|+|||+|+.++.... .+ .=..++|++..++  ...++..+- +++-...                  
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~-~~-~g~~~~y~~~e~~--~~~~~~~~~-~~g~~~~~~~~~g~l~i~~~~~~~~   98 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGA-LK-QGKKVYVITTENT--SKSYLKQME-SVKIDISDFFLWGYLRIFPLNTEGF   98 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHH-Hh-CCCEEEEEEcCCC--HHHHHHHHH-HCCCChhHHHhCCCceEEecccccc
Confidence            45799999999999999998885431 12 1235778887654  345544432 2211000                  


Q ss_pred             -CCCCCHHHHHHHHHHHcCC-CeEEEEEeCCC
Q 043252          277 -VDNHDLNKLQEELKKQLFG-KKFLLVLDDVW  306 (337)
Q Consensus       277 -~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~  306 (337)
                       ....+.+.+...+.+.+.. +.-++|+|.+-
T Consensus        99 ~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         99 EWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             ccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence             0123345666777777653 44589999985

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.92  E-value=0.0089  Score=54.63  Aligned_cols=42  Identities=7%  Similarity=0.128  Sum_probs=31.6

Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      +++-++|||++...+....+.|...+..-..++.+|+||.+.
T Consensus       105 ~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~  146 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQP  146 (328)
T ss_pred             CCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECCh
Confidence            344456789998887788888888887656677888888653

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.91  E-value=0.012  Score=55.67  Aligned_cols=23  Identities=30%  Similarity=0.417  Sum_probs=19.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++.++|++|+||||++..+..
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~  243 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAA  243 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999877754

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.91  E-value=0.0021  Score=53.25  Aligned_cols=22  Identities=41%  Similarity=0.531  Sum_probs=20.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999875

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.90  E-value=0.0031  Score=51.94  Aligned_cols=23  Identities=35%  Similarity=0.556  Sum_probs=21.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|.|||||.+.++.-
T Consensus        29 ~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          29 EKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            48999999999999999999864

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PTZ00035 Rad51 protein; Provisional

Probab=96.89  E-value=0.0046  Score=56.72  Aligned_cols=93  Identities=16%  Similarity=0.108  Sum_probs=55.4

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhccccc----ccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCC
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVE----DHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHD  281 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~  281 (337)
                      +.-.++.|+|.+|+|||||+..++-.....    ..=..++|++....|+..++ .++.+.+.....        ....+
T Consensus       116 ~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g~~~~~~l~nI~~~~~~~  194 (337)
T PTZ00035        116 ETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFGLDPEDVLDNIAYARAYN  194 (337)
T ss_pred             CCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhCCChHhHhhceEEEccCC
Confidence            346799999999999999998886432211    01134679998888887774 344444432210        01233


Q ss_pred             HHHHHHHH---HHHcC-CCeEEEEEeCCCC
Q 043252          282 LNKLQEEL---KKQLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       282 ~~~~~~~l---~~~L~-~kr~LlVlDdv~~  307 (337)
                      .+++...+   ...+. ++--|||+|.+..
T Consensus       195 ~e~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        195 HEHQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             HHHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence            33433333   33333 3445999999953

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

Probab=96.89  E-value=0.0042  Score=60.89  Aligned_cols=87  Identities=18%  Similarity=0.188  Sum_probs=57.1

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHH
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQ  292 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~  292 (337)
                      .+.-+++.++|++|+||||||.-+.+..    -|. ++=|+.|+.-+...+-..|...+.-+...++             
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkqa----GYs-VvEINASDeRt~~~v~~kI~~avq~~s~l~a-------------  384 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQA----GYS-VVEINASDERTAPMVKEKIENAVQNHSVLDA-------------  384 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHhc----Cce-EEEecccccccHHHHHHHHHHHHhhcccccc-------------
Confidence            3456899999999999999999987642    232 4557788877777776666665543322111             


Q ss_pred             cCCCeEEEEEeCCCCCChhcHHHhhc
Q 043252          293 LFGKKFLLVLDDVWNENYTDWVHLSL  318 (337)
Q Consensus       293 L~~kr~LlVlDdv~~~~~~~~~~l~~  318 (337)
                       .++...||+|.+.-......+.+..
T Consensus       385 -dsrP~CLViDEIDGa~~~~Vdvils  409 (877)
T KOG1969|consen  385 -DSRPVCLVIDEIDGAPRAAVDVILS  409 (877)
T ss_pred             -CCCcceEEEecccCCcHHHHHHHHH
Confidence             1466778999997654333333433

>PHA02244 ATPase-like protein

Probab=96.88  E-value=0.012  Score=54.11  Aligned_cols=22  Identities=23%  Similarity=0.351  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|+.|+|||+||+.+...
T Consensus       121 PVLL~GppGtGKTtLA~aLA~~  142 (383)
T PHA02244        121 PVFLKGGAGSGKNHIAEQIAEA  142 (383)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999999999874

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.88  E-value=0.006  Score=59.20  Aligned_cols=52  Identities=25%  Similarity=0.292  Sum_probs=34.7

Q ss_pred             ccccccchhHHHHHHHHH---hcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELL---LKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L---~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|.+..++++.+++   ..+..   .+....+-+.++|++|+|||+||+.+.+.
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~  111 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE  111 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            356889877766555443   22110   01223456889999999999999999875

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.

>PRK13695 putative NTPase; Provisional

Probab=96.87  E-value=0.00056  Score=56.56  Aligned_cols=22  Identities=41%  Similarity=0.427  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|.|.+|+|||||++.++..
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~   23 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAEL   23 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998765

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.85  E-value=0.0075  Score=55.28  Aligned_cols=91  Identities=18%  Similarity=0.094  Sum_probs=56.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccc----cccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC--------CCCCH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVED----HFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV--------DNHDL  282 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~--------~~~~~  282 (337)
                      ...++-|+|.+|+|||+|+..++-......    .-..++||+....|+++++. +|++.+......        ...+.
T Consensus       122 ~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~-qia~~~~~~~~~~l~~i~~~~~~~~  200 (342)
T PLN03186        122 TGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLI-QIAERFGLNGADVLENVAYARAYNT  200 (342)
T ss_pred             CceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHH-HHHHHcCCChhhhccceEEEecCCH
Confidence            467899999999999999987764322211    11268999999999988754 555555432210        12334


Q ss_pred             HHHHHHH---HHHcC-CCeEEEEEeCCC
Q 043252          283 NKLQEEL---KKQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       283 ~~~~~~l---~~~L~-~kr~LlVlDdv~  306 (337)
                      +++...+   ...+. .+--|||+|.+-
T Consensus       201 e~~~~ll~~~~~~~~~~~~~LIVIDSI~  228 (342)
T PLN03186        201 DHQSELLLEAASMMAETRFALMIVDSAT  228 (342)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEeCcH
Confidence            4433333   23333 345599999984

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.83  E-value=0.016  Score=54.86  Aligned_cols=25  Identities=32%  Similarity=0.353  Sum_probs=22.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.++|.+|+||||++..+...
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~  118 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARY  118 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4679999999999999999888764

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

Probab=96.82  E-value=0.0063  Score=51.77  Aligned_cols=44  Identities=23%  Similarity=0.297  Sum_probs=35.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++||-++-++.|.-.-.+      ++.+-+.|.||+|+||||-+..+.+
T Consensus        27 ~dIVGNe~tv~rl~via~~------gnmP~liisGpPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKE------GNMPNLIISGPPGTGKTTSILCLAR   70 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHc------CCCCceEeeCCCCCchhhHHHHHHH
Confidence            5789999988888766643      3567889999999999998877765

>TIGR00959 ffh signal recognition particle protein

Probab=96.81  E-value=0.0098  Score=56.18  Aligned_cols=24  Identities=33%  Similarity=0.401  Sum_probs=20.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...++.++|.+|+||||++..+..
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~  121 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAY  121 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH
Confidence            467999999999999999866654

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.80  E-value=0.006  Score=56.43  Aligned_cols=24  Identities=29%  Similarity=0.383  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.++.++|+.|+||||++.++...
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~  160 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAAR  160 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            359999999999999999888764

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.79  E-value=0.007  Score=52.06  Aligned_cols=22  Identities=32%  Similarity=0.409  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|+|.|..|+||||||+.+...
T Consensus         1 IigI~G~sGSGKTTla~~L~~~   22 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQAL   22 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHH
Confidence            5899999999999999998764

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.79  E-value=0.013  Score=53.23  Aligned_cols=129  Identities=22%  Similarity=0.296  Sum_probs=68.3

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc-cccccccceEE----EEeCCCC-----CH-H
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK-QVEDHFDLKAW----TCVSDDF-----DV-I  261 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~-~~~~~F~~~~w----v~v~~~~-----~~-~  261 (337)
                      +|..+..--.++|+.++      +..|++.|.+|.|||-||-...-.. ..++.|..++-    +.+.+..     .. +
T Consensus       228 prn~eQ~~ALdlLld~d------I~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG~eEe  301 (436)
T COG1875         228 PRNAEQRVALDLLLDDD------IDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPGTEEE  301 (436)
T ss_pred             cccHHHHHHHHHhcCCC------CCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCCchhh
Confidence            35666666677787554      7799999999999999995543211 12333432221    2222211     00 0


Q ss_pred             H------HHHHHHHHhhCCCCCCCCCHHHHHHHH---------HHHcCCC---eEEEEEeCCCCCChhcHHHhhccCCCC
Q 043252          262 R------LTKSILLSIASDQNVDNHDLNKLQEEL---------KKQLFGK---KFLLVLDDVWNENYTDWVHLSLPFQAG  323 (337)
Q Consensus       262 ~------~~~~il~~~~~~~~~~~~~~~~~~~~l---------~~~L~~k---r~LlVlDdv~~~~~~~~~~l~~~l~~~  323 (337)
                      +      -..+-++.+.....   .....+...+         ..+.+|+   .-+|++|...+..+.....+   +...
T Consensus       302 Km~PWmq~i~DnLE~L~~~~~---~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTpheikTi---ltR~  375 (436)
T COG1875         302 KMGPWMQAIFDNLEVLFSPNE---PGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTPHELKTI---LTRA  375 (436)
T ss_pred             hccchHHHHHhHHHHHhcccc---cchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccCHHHHHHH---HHhc
Confidence            0      11122233332221   1122222221         1233455   44899999988755555444   4455


Q ss_pred             CCCcEEEEEe
Q 043252          324 AQGSKIIVTT  333 (337)
Q Consensus       324 ~~gs~iivTT  333 (337)
                      +.||||++|-
T Consensus       376 G~GsKIVl~g  385 (436)
T COG1875         376 GEGSKIVLTG  385 (436)
T ss_pred             cCCCEEEEcC
Confidence            7899999873

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.79  E-value=0.0082  Score=56.12  Aligned_cols=23  Identities=30%  Similarity=0.294  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++.++|++|+||||++..+..
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~  245 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAA  245 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999988865

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.77  E-value=0.0042  Score=51.25  Aligned_cols=23  Identities=43%  Similarity=0.647  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|.|||||.+.+...
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~   51 (173)
T cd03246          29 ESLAIIGPSGSGKSTLARLILGL   51 (173)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            48999999999999999999863

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

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.76  E-value=0.0013  Score=56.26  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=20.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            36899999999999999998864

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

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.76  E-value=0.0062  Score=57.71  Aligned_cols=52  Identities=31%  Similarity=0.336  Sum_probs=38.9

Q ss_pred             cccccch---hHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          189 AKVYGRE---TEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       189 ~~~vGr~---~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      .++-|-+   .|+++|+++|.++..   -++.-.+-|.++|++|.|||-||+.|.-..
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA  361 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc
Confidence            3455664   567888999987642   123446789999999999999999998753

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.75  E-value=0.0012  Score=51.19  Aligned_cols=21  Identities=43%  Similarity=0.564  Sum_probs=19.2

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|.|..|+||||+|+.+...
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            689999999999999999874

...

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=96.74  E-value=0.0083  Score=53.78  Aligned_cols=114  Identities=23%  Similarity=0.293  Sum_probs=65.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc-ccccccccceEEEEeCCCCCH-HHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND-KQVEDHFDLKAWTCVSDDFDV-IRLTKS  266 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~-~~~~~~F~~~~wv~v~~~~~~-~~~~~~  266 (337)
                      ..++|-.++..++-.||.+.-.  -+...-+.|+|+.|.|||+|......+ .+..++|   +-|...+.... .-.+..
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~--~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~---l~v~Lng~~~~dk~al~~   98 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTIL--HGESNSVIIIGPRGSGKTILIDTRLSDIQENGENF---LLVRLNGELQTDKIALKG   98 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHH--hcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeE---EEEEECccchhhHHHHHH
Confidence            4578998898888888865321  112236789999999999999888776 1233333   33455544333 224555


Q ss_pred             HHHHhhCCCCC---CCCCHHHHHHHHHHHcC------CCeEEEEEeCCCC
Q 043252          267 ILLSIASDQNV---DNHDLNKLQEELKKQLF------GKKFLLVLDDVWN  307 (337)
Q Consensus       267 il~~~~~~~~~---~~~~~~~~~~~l~~~L~------~kr~LlVlDdv~~  307 (337)
                      |..++......   ...+..+....+...|+      +-+.++|+|.++-
T Consensus        99 I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDl  148 (408)
T KOG2228|consen   99 ITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDL  148 (408)
T ss_pred             HHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhc
Confidence            55554332111   22333333444444442      2367888887754

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.73  E-value=0.0015  Score=55.65  Aligned_cols=25  Identities=40%  Similarity=0.566  Sum_probs=22.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|+|.|.+|+|||||++.++..
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999999874

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.72  E-value=0.012  Score=52.61  Aligned_cols=25  Identities=28%  Similarity=0.303  Sum_probs=21.4

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....+|+|.|..|+||||+|+.+..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~   84 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQA   84 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999987643

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PRK10867 signal recognition particle protein; Provisional

Probab=96.71  E-value=0.013  Score=55.43  Aligned_cols=25  Identities=36%  Similarity=0.436  Sum_probs=20.2

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....+|.++|++|+||||++..+..
T Consensus        98 ~~p~vI~~vG~~GsGKTTtaakLA~  122 (433)
T PRK10867         98 KPPTVIMMVGLQGAGKTTTAGKLAK  122 (433)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHH
Confidence            3468999999999999997765543

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=96.71  E-value=0.0013  Score=55.34  Aligned_cols=81  Identities=23%  Similarity=0.205  Sum_probs=42.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhccccccccc---ceEEEEeCCCCCHHHHHHHHHHHhhCC---CCCCCCCHHHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFD---LKAWTCVSDDFDVIRLTKSILLSIASD---QNVDNHDLNKLQEELKK  291 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~---~~~wv~v~~~~~~~~~~~~il~~~~~~---~~~~~~~~~~~~~~l~~  291 (337)
                      ||+|.|++|+||||||+.+...... ..+.   ....++... +....-....-......   ..+...+.+.+.+.|..
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~-~~~~~~~~~~~~~~d~-~~~~~~~~~~~~~~~~~~~~~~p~a~d~~~l~~~l~~   78 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNK-RGIPAMEMDIILSLDD-FYDDYHLRDRKGRGENRYNFDHPDAFDFDLLKEDLKA   78 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT-CTTTCCCSEEEEEGGG-GBHHHHHHHHHHHCTTTSSTTSGGGBSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCc-cCcCccceeEEEeecc-cccccchhhHhhccccccCCCCccccCHHHHHHHHHH
Confidence            6999999999999999999764211 1111   122222222 22211111111111111   11245677888888877


Q ss_pred             HcCCCeEEE
Q 043252          292 QLFGKKFLL  300 (337)
Q Consensus       292 ~L~~kr~Ll  300 (337)
                      ..+++..-+
T Consensus        79 L~~g~~i~~   87 (194)
T PF00485_consen   79 LKNGGSIEI   87 (194)
T ss_dssp             HHTTSCEEE
T ss_pred             HhCCCcccc
Confidence            766665433

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=96.71  E-value=0.0035  Score=53.40  Aligned_cols=23  Identities=35%  Similarity=0.541  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|+|.|.+|+||||||+.+.+
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHH
Confidence            46999999999999999988764

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=96.70  E-value=0.0056  Score=55.34  Aligned_cols=86  Identities=20%  Similarity=0.129  Sum_probs=52.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~  290 (337)
                      .-+++-|+|+.|+||||||..+...  .+..-..++||...+.++...     ++.++.+...    .+...++....+.
T Consensus        52 ~G~ivEi~G~~ssGKttLaL~~ia~--~q~~g~~~a~ID~e~~ld~~~-----a~~lGvdl~rllv~~P~~~E~al~~~e  124 (322)
T PF00154_consen   52 RGRIVEIYGPESSGKTTLALHAIAE--AQKQGGICAFIDAEHALDPEY-----AESLGVDLDRLLVVQPDTGEQALWIAE  124 (322)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH--HHHTT-EEEEEESSS---HHH-----HHHTT--GGGEEEEE-SSHHHHHHHHH
T ss_pred             cCceEEEeCCCCCchhhhHHHHHHh--hhcccceeEEecCcccchhhH-----HHhcCccccceEEecCCcHHHHHHHHH
Confidence            3569999999999999999888764  333344689999988877643     3333332111    2334555555555


Q ss_pred             HHcC-CCeEEEEEeCCCC
Q 043252          291 KQLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       291 ~~L~-~kr~LlVlDdv~~  307 (337)
                      ..++ +..-+||+|.|-.
T Consensus       125 ~lirsg~~~lVVvDSv~a  142 (322)
T PF00154_consen  125 QLIRSGAVDLVVVDSVAA  142 (322)
T ss_dssp             HHHHTTSESEEEEE-CTT
T ss_pred             HHhhcccccEEEEecCcc
Confidence            5554 4455999999843

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 ....

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=96.68  E-value=0.0013  Score=58.45  Aligned_cols=34  Identities=29%  Similarity=0.510  Sum_probs=26.1

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+++.+....       +-+.++|+.|+|||++++.....
T Consensus        23 ~~ll~~l~~~~-------~pvLl~G~~GtGKT~li~~~l~~   56 (272)
T PF12775_consen   23 SYLLDLLLSNG-------RPVLLVGPSGTGKTSLIQNFLSS   56 (272)
T ss_dssp             HHHHHHHHHCT-------EEEEEESSTTSSHHHHHHHHHHC
T ss_pred             HHHHHHHHHcC-------CcEEEECCCCCchhHHHHhhhcc
Confidence            45666666443       46799999999999999988754

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.67  E-value=0.013  Score=50.78  Aligned_cols=26  Identities=31%  Similarity=0.396  Sum_probs=23.0

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....+++|.|+.|.|||||++.+..-
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~   56 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEAL   56 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999988764

>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=96.67  E-value=0.016  Score=52.93  Aligned_cols=42  Identities=21%  Similarity=0.322  Sum_probs=32.5

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      .-.+.|.+.|....   .....+|+|.|.=|+||||+.+.+.+..
T Consensus         3 ~~a~~la~~I~~~~---~~~~~~IgL~G~WGsGKSs~l~~l~~~L   44 (325)
T PF07693_consen    3 PYAKALAEIIKNPD---SDDPFVIGLYGEWGSGKSSFLNMLKEEL   44 (325)
T ss_pred             HHHHHHHHHHhccC---CCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            44566777776543   2457899999999999999999998753

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 [].

>PRK07667 uridine kinase; Provisional

Probab=96.66  E-value=0.0032  Score=53.02  Aligned_cols=38  Identities=21%  Similarity=0.354  Sum_probs=29.1

Q ss_pred             HHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          198 KKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       198 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.|.+.+....    +...+|+|.|.+|+||||+|+.+...
T Consensus         3 ~~~~~~~~~~~~----~~~~iIgI~G~~gsGKStla~~L~~~   40 (193)
T PRK07667          3 TNELINIMKKHK----ENRFILGIDGLSRSGKTTFVANLKEN   40 (193)
T ss_pred             HHHHHHHHHhcC----CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            456666665443    23489999999999999999998764

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.66  E-value=0.0029  Score=64.44  Aligned_cols=51  Identities=25%  Similarity=0.221  Sum_probs=37.4

Q ss_pred             cccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|.+..++.|.+++..+-.       -+-...+.+.++|++|+|||+||+.+++.
T Consensus       178 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~  235 (733)
T TIGR01243       178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE  235 (733)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHH
Confidence            4588999999988877642210       01123457889999999999999999874

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.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.66  E-value=0.0082  Score=52.38  Aligned_cols=90  Identities=16%  Similarity=0.123  Sum_probs=52.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC-----CCCHHHHHHHHHHHhhCCC------CCCCCCHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD-----DFDVIRLTKSILLSIASDQ------NVDNHDLNK  284 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~-----~~~~~~~~~~il~~~~~~~------~~~~~~~~~  284 (337)
                      ..+++|||..|+|||||++.+..-   ...-...++..-.+     .....+-..++++.++...      +.+...-+.
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~L---~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQr  115 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILGL---EEPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQR  115 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHcC---cCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhh
Confidence            359999999999999999999863   22222333333111     1123344556666655332      112222222


Q ss_pred             HHHHHHHHcCCCeEEEEEeCCCCC
Q 043252          285 LQEELKKQLFGKKFLLVLDDVWNE  308 (337)
Q Consensus       285 ~~~~l~~~L~~kr~LlVlDdv~~~  308 (337)
                      -.-.+.+.|.-+.=|||.|..-+.
T Consensus       116 QRi~IARALal~P~liV~DEpvSa  139 (268)
T COG4608         116 QRIGIARALALNPKLIVADEPVSA  139 (268)
T ss_pred             hhHHHHHHHhhCCcEEEecCchhh
Confidence            223466777778889999988553

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.64  E-value=0.019  Score=58.33  Aligned_cols=118  Identities=14%  Similarity=0.175  Sum_probs=71.4

Q ss_pred             ccccchhHHHHHHHHHhcCCCCC-C-CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDSRN-D-GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~-~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      .++|.++.+..|.+.+....... + .....+.+.|+.|+|||-||+.+...  +-+..+..+-++++.      ...  
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~--~Fgse~~~IriDmse------~~e--  632 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEY--VFGSEENFIRLDMSE------FQE--  632 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHH--HcCCccceEEechhh------hhh--
Confidence            46788888888887776544211 1 25677888999999999999998763  323333344444443      222  


Q ss_pred             HHHhhCCCC--CCCCCHHHHHHHHHHHcCCCeE-EEEEeCCCCCChhcHHHhhccCC
Q 043252          268 LLSIASDQN--VDNHDLNKLQEELKKQLFGKKF-LLVLDDVWNENYTDWVHLSLPFQ  321 (337)
Q Consensus       268 l~~~~~~~~--~~~~~~~~~~~~l~~~L~~kr~-LlVlDdv~~~~~~~~~~l~~~l~  321 (337)
                      ...+.+..+  ......+    .|.+.++.+.| +|.||||...+......+...+.
T Consensus       633 vskligsp~gyvG~e~gg----~LteavrrrP~sVVLfdeIEkAh~~v~n~llq~lD  685 (898)
T KOG1051|consen  633 VSKLIGSPPGYVGKEEGG----QLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLLD  685 (898)
T ss_pred             hhhccCCCcccccchhHH----HHHHHHhcCCceEEEEechhhcCHHHHHHHHHHHh
Confidence            233322211  1222233    56666666666 77789998877777665555554

>TIGR00235 udk uridine kinase

Probab=96.64  E-value=0.0019  Score=55.01  Aligned_cols=25  Identities=40%  Similarity=0.481  Sum_probs=22.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|+|+|++|+|||||++.++..
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999999864

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK05439 pantothenate kinase; Provisional

Probab=96.62  E-value=0.018  Score=52.00  Aligned_cols=26  Identities=31%  Similarity=0.296  Sum_probs=22.7

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .....+|+|.|.+|+||||+|+.+..
T Consensus        83 ~~~~~iIgIaG~~gsGKSTla~~L~~  108 (311)
T PRK05439         83 QKVPFIIGIAGSVAVGKSTTARLLQA  108 (311)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            34578999999999999999988865

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.62  E-value=0.015  Score=56.01  Aligned_cols=24  Identities=33%  Similarity=0.376  Sum_probs=20.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|+|+|++|+||||++.++..
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa  372 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQ  372 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999988764

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=96.61  E-value=0.0049  Score=51.10  Aligned_cols=22  Identities=27%  Similarity=0.596  Sum_probs=20.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||++.+..
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G   48 (178)
T cd03229          27 EIVALLGPSGSGKSTLLRCIAG   48 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4999999999999999999975

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. 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.

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=96.61  E-value=0.003  Score=57.36  Aligned_cols=52  Identities=23%  Similarity=0.371  Sum_probs=44.7

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|.++.+++|++.|.+.....+..-+++.++|+.|.||||||..+.+-
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~  111 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRG  111 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999998765545667789999999999999999988764

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.60  E-value=0.0062  Score=50.22  Aligned_cols=113  Identities=16%  Similarity=0.140  Sum_probs=56.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhh--CCCCC--CC--------CCHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIA--SDQNV--DN--------HDLNK  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~--~~~~~--~~--------~~~~~  284 (337)
                      .+++|+|+.|.|||||.+.+....   ......+++.-....+..   ..+-..+.  .+...  ..        -+..+
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~~~~~~~---~~~~~~i~~~~q~~~~~~~~tv~~~~~LS~G~  100 (173)
T cd03230          27 EIYGLLGPNGAGKTTLIKIILGLL---KPDSGEIKVLGKDIKKEP---EEVKRRIGYLPEEPSLYENLTVRENLKLSGGM  100 (173)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCEEcccch---HhhhccEEEEecCCccccCCcHHHHhhcCHHH
Confidence            489999999999999999998642   122233333211000000   00001110  00000  00        11122


Q ss_pred             -HHHHHHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCC-CCCcEEEEEecC
Q 043252          285 -LQEELKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAG-AQGSKIIVTTRN  335 (337)
Q Consensus       285 -~~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~-~~gs~iivTTR~  335 (337)
                       ..-.+...|..+.=++++|+.-.. +......+...+..- ..|..||++|.+
T Consensus       101 ~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~  154 (173)
T cd03230         101 KQRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHI  154 (173)
T ss_pred             HHHHHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCC
Confidence             223455666677789999998653 333333444444321 236678888865

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.

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=96.60  E-value=0.0019  Score=51.27  Aligned_cols=22  Identities=36%  Similarity=0.480  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.++|++|+||||+|+.+...
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~   22 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKR   22 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999998753

...

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=96.60  E-value=0.012  Score=55.66  Aligned_cols=87  Identities=17%  Similarity=0.185  Sum_probs=48.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCC-----CCCCCCHH-----HHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQ-----NVDNHDLN-----KLQ  286 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~-----~~~~~~~~-----~~~  286 (337)
                      ..++|+|..|+|||||++.+....   .....+++..--..-++.++....+.......     ..+.....     ...
T Consensus       166 qri~I~G~SGsGKTTLL~~Ia~l~---~pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~a  242 (450)
T PRK06002        166 QRIGIFAGSGVGKSTLLAMLARAD---AFDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLTA  242 (450)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC---CCCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHHH
Confidence            489999999999999999887632   12223444433233445555444444331110     00111111     122


Q ss_pred             HHHHHHc--CCCeEEEEEeCCC
Q 043252          287 EELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       287 ~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      -.+.+++  +++..||++||+.
T Consensus       243 ~~iAEyfrd~G~~Vll~~DslT  264 (450)
T PRK06002        243 TAIAEYFRDRGENVLLIVDSVT  264 (450)
T ss_pred             HHHHHHHHHcCCCEEEeccchH
Confidence            2233443  5899999999993

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.60  E-value=0.012  Score=59.42  Aligned_cols=133  Identities=16%  Similarity=0.092  Sum_probs=72.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|....+..+.+.+..-..    .-.-|.|.|..|+|||++|+.++......  -...+.+++....  ...+... 
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~----~~~pVLI~GE~GTGK~~lA~~ih~~s~r~--~~~~v~i~c~~~~--~~~~~~~-  446 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQ----SDSTVLILGETGTGKELIARAIHNLSGRN--NRRMVKMNCAAMP--AGLLESD-  446 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhC----CCCCEEEECCCCcCHHHHHHHHHHhcCCC--CCCeEEEecccCC--hhHhhhh-
Confidence            4689998888887766653221    23478999999999999999998743211  1133445544322  1222211 


Q ss_pred             HHhhCCCCCCCCC-HHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC-----------CCcEEEEEecC
Q 043252          269 LSIASDQNVDNHD-LNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA-----------QGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~-~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~-----------~gs~iivTTR~  335 (337)
                        +.+........ .......+.   ....=.|+||+|..........|...+..+.           ...|||.||..
T Consensus       447 --lfg~~~~~~~g~~~~~~g~le---~a~~GtL~Ldei~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~  520 (686)
T PRK15429        447 --LFGHERGAFTGASAQRIGRFE---LADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNR  520 (686)
T ss_pred             --hcCcccccccccccchhhHHH---hcCCCeEEEechhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCC
Confidence              11111100000 001111121   1123468999998876666666666554321           23588888853

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

Probab=96.59  E-value=0.004  Score=50.37  Aligned_cols=117  Identities=15%  Similarity=0.137  Sum_probs=58.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEe---CCCCCHHHHHHHHHHHhh-----CCCCCCCCCH------
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV---SDDFDVIRLTKSILLSIA-----SDQNVDNHDL------  282 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v---~~~~~~~~~~~~il~~~~-----~~~~~~~~~~------  282 (337)
                      ..|-|++..|.||||+|-...-.. ....+. +.++..   ........++..+ ..+.     ....-...+.      
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra-~~~g~~-v~~vQFlKg~~~~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRA-LGHGYR-VGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-HHCCCe-EEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHH
Confidence            377888888999999996664321 111222 222222   1122333333332 0110     0000000111      


Q ss_pred             -HHHHHHHHHHcCCCeE-EEEEeCCCCC---ChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          283 -NKLQEELKKQLFGKKF-LLVLDDVWNE---NYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       283 -~~~~~~l~~~L~~kr~-LlVlDdv~~~---~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                       ....+..++.+....| |||||++-..   ..-..+.+...+.....+.-||+|.|+-
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence             1123334445555455 9999999432   2234455666665556677899999973

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.57  E-value=0.024  Score=52.91  Aligned_cols=25  Identities=28%  Similarity=0.275  Sum_probs=21.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.++|+.|+||||.+..+...
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~  197 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAI  197 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3569999999999999999888653

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.56  E-value=0.0069  Score=50.43  Aligned_cols=23  Identities=30%  Similarity=0.557  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|..|.|||||.+.+...
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          27 EIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999863

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. In members of 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.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=96.55  E-value=0.0063  Score=55.79  Aligned_cols=109  Identities=17%  Similarity=0.073  Sum_probs=66.4

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      .++|.+.....+...+....        -+.+.|++|+|||+||+.+...  ..   -..++|.+.......+++....-
T Consensus        25 ~~~g~~~~~~~~l~a~~~~~--------~vll~G~PG~gKT~la~~lA~~--l~---~~~~~i~~t~~l~p~d~~G~~~~   91 (329)
T COG0714          25 VVVGDEEVIELALLALLAGG--------HVLLEGPPGVGKTLLARALARA--LG---LPFVRIQCTPDLLPSDLLGTYAY   91 (329)
T ss_pred             eeeccHHHHHHHHHHHHcCC--------CEEEECCCCccHHHHHHHHHHH--hC---CCeEEEecCCCCCHHHhcCchhH
Confidence            37888888888777776543        6789999999999999999874  22   23466777777777665544333


Q ss_pred             HhhC---CCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccC
Q 043252          270 SIAS---DQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPF  320 (337)
Q Consensus       270 ~~~~---~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l  320 (337)
                      ....   ... ...+.     .+   +..-+.++.+|.++...+..-..+...+
T Consensus        92 ~~~~~~~~~~-~~~~g-----pl---~~~~~~ill~DEInra~p~~q~aLl~~l  136 (329)
T COG0714          92 AALLLEPGEF-RFVPG-----PL---FAAVRVILLLDEINRAPPEVQNALLEAL  136 (329)
T ss_pred             hhhhccCCeE-EEecC-----Cc---ccccceEEEEeccccCCHHHHHHHHHHH
Confidence            3221   000 00000     00   0011158999999887655555554444

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.55  E-value=0.011  Score=54.06  Aligned_cols=45  Identities=22%  Similarity=0.184  Sum_probs=32.9

Q ss_pred             cccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          191 VYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       191 ~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|....+.++.+.+..-..    .-.-|.|+|..|+||+++|+.++..
T Consensus         1 liG~S~~m~~~~~~~~~~a~----~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAP----LDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhC----CCCCEEEECCCCChHHHHHHHHHHh
Confidence            46777677776666654321    2246799999999999999999864

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

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.54  E-value=0.011  Score=51.35  Aligned_cols=117  Identities=15%  Similarity=0.227  Sum_probs=63.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcc-----ccc------ccc---cceEEEEeCC------CCCHH---------------
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDK-----QVE------DHF---DLKAWTCVSD------DFDVI---------------  261 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~-----~~~------~~F---~~~~wv~v~~------~~~~~---------------  261 (337)
                      .+++|+|+.|.|||||.+.+..-.     ++.      ..+   ..+.||.=..      +.++.               
T Consensus        31 ~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~~  110 (254)
T COG1121          31 EITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWFR  110 (254)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCcccccccc
Confidence            599999999999999999997621     110      001   1344543111      11222               


Q ss_pred             -------HHHHHHHHHhhCCC----CCCCCCHHHH-HHHHHHHcCCCeEEEEEeCCCCC-C---hhcHHHhhccCCCCCC
Q 043252          262 -------RLTKSILLSIASDQ----NVDNHDLNKL-QEELKKQLFGKKFLLVLDDVWNE-N---YTDWVHLSLPFQAGAQ  325 (337)
Q Consensus       262 -------~~~~~il~~~~~~~----~~~~~~~~~~-~~~l~~~L~~kr~LlVlDdv~~~-~---~~~~~~l~~~l~~~~~  325 (337)
                             +...+.++.++...    ....-+-.+. .-.|.+.|..+.=|++||.--.. +   ....-.+...+...  
T Consensus       111 ~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~e--  188 (254)
T COG1121         111 RLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQE--  188 (254)
T ss_pred             cccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHC--
Confidence                   22333344333211    1122222333 34567778888889999987542 1   22333344444432  


Q ss_pred             CcEEEEEecC
Q 043252          326 GSKIIVTTRN  335 (337)
Q Consensus       326 gs~iivTTR~  335 (337)
                      |..||++|.+
T Consensus       189 g~tIl~vtHD  198 (254)
T COG1121         189 GKTVLMVTHD  198 (254)
T ss_pred             CCEEEEEeCC
Confidence            7889998875

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=96.50  E-value=0.021  Score=48.09  Aligned_cols=23  Identities=30%  Similarity=0.494  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.|+.|.|||||.+.+..-
T Consensus        36 e~~~l~G~nGsGKStLl~~i~Gl   58 (194)
T cd03213          36 ELTAIMGPSGAGKSTLLNALAGR   58 (194)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999763

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.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.49  E-value=0.012  Score=53.88  Aligned_cols=132  Identities=14%  Similarity=0.063  Sum_probs=70.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc-ccccccceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|....+..+.+.+..-..    .-.-|.|+|..|+||+++|+.++.... -...   .+.|++... +...+-..+
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~----~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~p---fv~v~c~~~-~~~~~~~~l   77 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAP----LDKPVLIIGERGTGKELIASRLHYLSSRWQGP---FISLNCAAL-NENLLDSEL   77 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhC----CCCCEEEECCCCCcHHHHHHHHHHhCCccCCC---eEEEeCCCC-CHHHHHHHH
Confidence            3588998888888877764332    224688999999999999999986321 1222   334555542 222222222


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC-----------CCcEEEEEec
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA-----------QGSKIIVTTR  334 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~-----------~gs~iivTTR  334 (337)
                      ...-..... ...  ......+.   ....=.|+||+|..........|...+..+.           ...|||.||.
T Consensus        78 fg~~~~~~~-g~~--~~~~g~l~---~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~  149 (326)
T PRK11608         78 FGHEAGAFT-GAQ--KRHPGRFE---RADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATN  149 (326)
T ss_pred             ccccccccC-Ccc--cccCCchh---ccCCCeEEeCChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCc
Confidence            211100000 000  00001111   1122357899998776666666666554321           1258888875

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=96.49  E-value=0.0066  Score=49.17  Aligned_cols=110  Identities=17%  Similarity=0.145  Sum_probs=56.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC--CHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF--DVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF  294 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~--~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~  294 (337)
                      .+++|+|..|.|||||.+.+....   ......+++.-....  .....    ...+.-..  +...-+...-.+...+.
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~---~~~~G~i~~~~~~~~~~~~~~~----~~~i~~~~--qlS~G~~~r~~l~~~l~   96 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLL---KPTSGEILIDGKDIAKLPLEEL----RRRIGYVP--QLSGGQRQRVALARALL   96 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---CCCccEEEECCEEcccCCHHHH----HhceEEEe--eCCHHHHHHHHHHHHHh
Confidence            599999999999999999998742   223344444321111  11111    11111000  11122222333555555


Q ss_pred             CCeEEEEEeCCCCC-ChhcHHHhhccCCCC-CCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNE-NYTDWVHLSLPFQAG-AQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~-~~gs~iivTTR~  335 (337)
                      ...=+++||+.-.. +......+...+... ..+..+|++|.+
T Consensus        97 ~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~  139 (157)
T cd00267          97 LNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHD  139 (157)
T ss_pred             cCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence            56778999998643 233333444333321 124568888764

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.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.48  E-value=0.0097  Score=59.93  Aligned_cols=85  Identities=20%  Similarity=0.116  Sum_probs=56.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l~  290 (337)
                      .-+++-|+|++|+|||||+..++....  ..=..++|+...+.++..     .+++++.+..    ......+.....+.
T Consensus        59 ~GsiteI~G~~GsGKTtLal~~~~~a~--~~G~~v~yId~E~t~~~~-----~A~~lGvDl~~llv~~~~~~E~~l~~i~  131 (790)
T PRK09519         59 RGRVIEIYGPESSGKTTVALHAVANAQ--AAGGVAAFIDAEHALDPD-----YAKKLGVDTDSLLVSQPDTGEQALEIAD  131 (790)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH--HcCCcEEEECCccchhHH-----HHHHcCCChhHeEEecCCCHHHHHHHHH
Confidence            467999999999999999977654321  222457899888877743     4555544321    13344556666666


Q ss_pred             HHcCC-CeEEEEEeCCC
Q 043252          291 KQLFG-KKFLLVLDDVW  306 (337)
Q Consensus       291 ~~L~~-kr~LlVlDdv~  306 (337)
                      ..+.. +--|||+|.+-
T Consensus       132 ~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        132 MLIRSGALDIVVIDSVA  148 (790)
T ss_pred             HHhhcCCCeEEEEcchh
Confidence            66644 45589999985

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.48  E-value=0.049  Score=49.62  Aligned_cols=125  Identities=8%  Similarity=0.066  Sum_probs=67.0

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccc------cce--EEEEeCCCCCHHHHHHHHH
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF------DLK--AWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F------~~~--~wv~v~~~~~~~~~~~~il  268 (337)
                      ..+.|...+....     -...+.+.|+.|+||+++|+.+...---....      .|.  -++.....+|...      
T Consensus        10 ~~~~l~~~~~~~r-----l~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~------   78 (325)
T PRK06871         10 TYQQITQAFQQGL-----GHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHI------   78 (325)
T ss_pred             HHHHHHHHHHcCC-----cceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEE------
Confidence            3455666665433     24688899999999999998886431111100      000  0000111111100      


Q ss_pred             HHhhCCCCCCCCCHHHHH---HHHHHHc-CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQ---EELKKQL-FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~---~~l~~~L-~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                        +... .......++..   +.+...- .+++=++|+|++...+....+.|...|..-..++.+|++|.+
T Consensus        79 --i~p~-~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~  146 (325)
T PRK06871         79 --LEPI-DNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADL  146 (325)
T ss_pred             --Eccc-cCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECC
Confidence              0000 00112233322   2222111 356668889999888778888898888876777788887765

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.46  E-value=0.016  Score=51.40  Aligned_cols=124  Identities=16%  Similarity=0.069  Sum_probs=62.0

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEE---eCCCCCHHHHHHHHHHHhhC
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC---VSDDFDVIRLTKSILLSIAS  273 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---v~~~~~~~~~~~~il~~~~~  273 (337)
                      ..+.+...|...     ....-+.|+|+.|.|||||.+.+....   ......+++.   +.......++... ...+..
T Consensus        97 ~~~~~l~~l~~~-----~~~~~~~i~g~~g~GKttl~~~l~~~~---~~~~G~i~~~g~~v~~~d~~~ei~~~-~~~~~q  167 (270)
T TIGR02858        97 AADKLLPYLVRN-----NRVLNTLIISPPQCGKTTLLRDLARIL---STGISQLGLRGKKVGIVDERSEIAGC-VNGVPQ  167 (270)
T ss_pred             cHHHHHHHHHhC-----CCeeEEEEEcCCCCCHHHHHHHHhCcc---CCCCceEEECCEEeecchhHHHHHHH-hccccc
Confidence            445555566532     235689999999999999999998642   1222233332   1110011222211 111110


Q ss_pred             CC----CCCCCCHHHHHHHHHHHc-CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          274 DQ----NVDNHDLNKLQEELKKQL-FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       274 ~~----~~~~~~~~~~~~~l~~~L-~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..    ......... ...+...+ ....-+|++|.+...  +.+..+...+.   .|..||+||..
T Consensus       168 ~~~~~r~~v~~~~~k-~~~~~~~i~~~~P~villDE~~~~--e~~~~l~~~~~---~G~~vI~ttH~  228 (270)
T TIGR02858       168 HDVGIRTDVLDGCPK-AEGMMMLIRSMSPDVIVVDEIGRE--EDVEALLEALH---AGVSIIATAHG  228 (270)
T ss_pred             ccccccccccccchH-HHHHHHHHHhCCCCEEEEeCCCcH--HHHHHHHHHHh---CCCEEEEEech
Confidence            00    000011111 11122222 246779999998543  45555554442   46779999874

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.

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

Probab=96.45  E-value=0.0077  Score=55.12  Aligned_cols=26  Identities=27%  Similarity=0.344  Sum_probs=23.6

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .....+.|||++|+|||.+|+.+++.
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            45679999999999999999999986

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.45  E-value=0.0025  Score=43.95  Aligned_cols=22  Identities=36%  Similarity=0.570  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|.|..|+||||+++.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999988764

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.

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

Probab=96.45  E-value=0.0074  Score=59.06  Aligned_cols=70  Identities=24%  Similarity=0.266  Sum_probs=44.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHH----HHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEE----LKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~----l~~  291 (337)
                      ..-|.|.|+.|+|||+||+.+++... +++.-....|+++.-.                    ....+..+..    +..
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~--------------------~~~~e~iQk~l~~vfse  489 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLD--------------------GSSLEKIQKFLNNVFSE  489 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhcc--------------------chhHHHHHHHHHHHHHH
Confidence            35789999999999999999998644 3333334455555421                    1112332222    333


Q ss_pred             HcCCCeEEEEEeCCC
Q 043252          292 QLFGKKFLLVLDDVW  306 (337)
Q Consensus       292 ~L~~kr~LlVlDdv~  306 (337)
                      .+....-+|||||+.
T Consensus       490 ~~~~~PSiIvLDdld  504 (952)
T KOG0735|consen  490 ALWYAPSIIVLDDLD  504 (952)
T ss_pred             HHhhCCcEEEEcchh
Confidence            445667799999994

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.45  E-value=0.051  Score=49.38  Aligned_cols=41  Identities=12%  Similarity=0.126  Sum_probs=31.1

Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +++=++|||++...+...-+.|...|..-..++.+|++|.+
T Consensus       112 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~  152 (319)
T PRK08769        112 GIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQ  152 (319)
T ss_pred             CCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECC
Confidence            55668999999877667777788777765667778887764

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.44  E-value=0.053  Score=49.25  Aligned_cols=41  Identities=17%  Similarity=0.099  Sum_probs=32.2

Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +.+=++|+|++...+....+.|...|..-..++.+|++|.+
T Consensus       107 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~  147 (319)
T PRK06090        107 NGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHN  147 (319)
T ss_pred             CCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECC
Confidence            44558899999887778888998888776677877777765

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.44  E-value=0.047  Score=48.42  Aligned_cols=51  Identities=22%  Similarity=0.192  Sum_probs=32.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      -.++.|.|.+|+||||++..+.... ...+=..++|+++..+  ..++...++.
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~-~~~~g~~vl~iS~E~~--~~~~~~r~~~   80 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDL-ITQHGVRVGTISLEEP--VVRTARRLLG   80 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH-HHhcCceEEEEEcccC--HHHHHHHHHH
Confidence            3488899999999999998876542 1221234678876553  3444444433

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.43  E-value=0.02  Score=49.79  Aligned_cols=88  Identities=16%  Similarity=0.258  Sum_probs=53.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCC--------------------
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASD--------------------  274 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~--------------------  274 (337)
                      .-+++.|.|++|+|||+||..+.... . ..-+..+|++...  +..++...+.. ++-+                    
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~-~-~~ge~~lyvs~ee--~~~~i~~~~~~-~g~~~~~~~~~g~l~~~d~~~~~~   94 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNG-L-QMGEPGIYVALEE--HPVQVRRNMAQ-FGWDVRKYEEEGKFAIVDAFTGGI   94 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH-H-HcCCcEEEEEeeC--CHHHHHHHHHH-hCCCHHHHhhcCCEEEEecccccc
Confidence            46799999999999999997654321 1 1234577887665  44555554332 1110                    


Q ss_pred             -----CC----CCCCCHHHHHHHHHHHcCC-CeEEEEEeCCCC
Q 043252          275 -----QN----VDNHDLNKLQEELKKQLFG-KKFLLVLDDVWN  307 (337)
Q Consensus       275 -----~~----~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~  307 (337)
                           ..    ....+.+.+...+.+.+.. +.-+||+|.+..
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSls~  137 (237)
T TIGR03877        95 GEAAEREKYVVKDPTDVRELIDVLRQAIRDINAKRVVIDSVTT  137 (237)
T ss_pred             ccccccccccccCcccHHHHHHHHHHHHHHhCCCEEEEcChhH
Confidence                 00    0124566677777776643 333799999843

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.

>PRK06762 hypothetical protein; Provisional

Probab=96.43  E-value=0.0028  Score=51.81  Aligned_cols=23  Identities=39%  Similarity=0.525  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|++|+||||+|+.+.+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998764

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=96.41  E-value=0.0052  Score=59.57  Aligned_cols=118  Identities=19%  Similarity=0.204  Sum_probs=63.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhccc-ccccc-----cceEEEEeCC-CC----CH------------HHHHHHHHHHhhC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHF-----DLKAWTCVSD-DF----DV------------IRLTKSILLSIAS  273 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F-----~~~~wv~v~~-~~----~~------------~~~~~~il~~~~~  273 (337)
                      ..|+|+|+.|+|||||.+.+..... ..+..     -.+.|+.-.. ..    ++            ..-.+..+..+.-
T Consensus       349 ~riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~F  428 (530)
T COG0488         349 DRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFGF  428 (530)
T ss_pred             CEEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcCC
Confidence            4799999999999999999954311 01111     1122222111 00    11            2233333333332


Q ss_pred             CCCC------CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          274 DQNV------DNHDLNKLQEELKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       274 ~~~~------~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      ....      ..+.-+...-.|...+-.+.-|||||.-.+. +.+..+.|..+|.. -+|+ ||++|.++
T Consensus       429 ~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~-f~Gt-vl~VSHDr  496 (530)
T COG0488         429 TGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLD-FEGT-VLLVSHDR  496 (530)
T ss_pred             ChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHh-CCCe-EEEEeCCH
Confidence            2111      1122233334455566677889999999765 45566666666654 3465 77777654

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=96.38  E-value=0.017  Score=48.57  Aligned_cols=22  Identities=32%  Similarity=0.592  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||.+.+..
T Consensus        34 e~~~l~G~nGsGKSTLl~~l~G   55 (192)
T cd03232          34 TLTALMGESGAGKTTLLDVLAG   55 (192)
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            5999999999999999999985

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.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.38  E-value=0.031  Score=45.96  Aligned_cols=22  Identities=41%  Similarity=0.534  Sum_probs=19.3

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++.++|++|+||||++..+...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~   23 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALY   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999888653

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.

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=96.38  E-value=0.045  Score=46.45  Aligned_cols=22  Identities=36%  Similarity=0.585  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|.|..|.|||||.+.+..
T Consensus        35 ~~~~i~G~nGsGKSTLl~~l~G   56 (207)
T cd03369          35 EKIGIVGRTGAGKSTLILALFR   56 (207)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999964

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.36  E-value=0.0039  Score=49.97  Aligned_cols=24  Identities=38%  Similarity=0.382  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|.|++|+||||+++.+.+.
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~   28 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEK   28 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHH
Confidence            457899999999999999999864

>PRK14974 cell division protein FtsY; Provisional

Probab=96.36  E-value=0.031  Score=51.16  Aligned_cols=25  Identities=32%  Similarity=0.315  Sum_probs=21.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +..+|.++|+.|+||||++..+...
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~  163 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYY  163 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4679999999999999988777653

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=96.35  E-value=0.032  Score=47.90  Aligned_cols=22  Identities=27%  Similarity=0.537  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||++.+..
T Consensus        31 e~~~i~G~nGsGKSTLl~~l~G   52 (221)
T cd03244          31 EKVGIVGRTGSGKSSLLLALFR   52 (221)
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            4899999999999999999975

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.35  E-value=0.007  Score=50.53  Aligned_cols=22  Identities=41%  Similarity=0.539  Sum_probs=19.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999874

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.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.35  E-value=0.02  Score=55.74  Aligned_cols=134  Identities=12%  Similarity=0.123  Sum_probs=74.0

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc-ccccccceEEEEeCCCCCHHHHHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHFDLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~v~~~~~~~~~~~~  266 (337)
                      ...++|....+.++.+.+..-..    .-.-|.|+|..|+|||++|+.++.... ...   ..+.|++....+ ..+-..
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~----~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~---p~v~v~c~~~~~-~~~e~~  257 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAA----SDLNVLILGETGVGKELVARAIHAASPRADK---PLVYLNCAALPE-SLAESE  257 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhC----CCCcEEEECCCCccHHHHHHHHHHhCCcCCC---CeEEEEcccCCh-HHHHHH
Confidence            35689999998888887765332    234788999999999999999987422 222   334555554322 111111


Q ss_pred             HHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC-----------CCcEEEEEecC
Q 043252          267 ILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA-----------QGSKIIVTTRN  335 (337)
Q Consensus       267 il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~-----------~gs~iivTTR~  335 (337)
                      +.....+... ....  .....+.   ....=.|+||+|..........|...+..+.           ...|||.||..
T Consensus       258 lfG~~~g~~~-ga~~--~~~g~~~---~a~gGtL~ldeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~  331 (509)
T PRK05022        258 LFGHVKGAFT-GAIS--NRSGKFE---LADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNR  331 (509)
T ss_pred             hcCccccccC-CCcc--cCCcchh---hcCCCEEEecChhhCCHHHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCC
Confidence            1111111000 0000  0000011   1122247899998876666667766664321           13488888853

>PRK06547 hypothetical protein; Provisional

Probab=96.34  E-value=0.0039  Score=51.39  Aligned_cols=25  Identities=40%  Similarity=0.470  Sum_probs=22.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|.|++|+||||+|+.+...
T Consensus        14 ~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         14 GMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999999764

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.33  E-value=0.0054  Score=53.04  Aligned_cols=22  Identities=32%  Similarity=0.581  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|.|++|+||||+|+.+...
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~   29 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKK   29 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999998764

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.33  E-value=0.0034  Score=52.35  Aligned_cols=25  Identities=28%  Similarity=0.371  Sum_probs=21.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.++|.|+|++|+||||+++.+...
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3569999999999999999998753

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.

>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=96.32  E-value=0.011  Score=54.67  Aligned_cols=103  Identities=22%  Similarity=0.298  Sum_probs=58.2

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccc----cccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQV----EDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEEL  289 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~----~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l  289 (337)
                      ...+-+.|||..|.|||.|+-.+|+...+    +-||.              .+..++-+.+..... ....+..    +
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh--------------~Fm~~vh~~l~~~~~-~~~~l~~----v  120 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFH--------------EFMLDVHSRLHQLRG-QDDPLPQ----V  120 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHHHHHhCCcccccccccc--------------HHHHHHHHHHHHHhC-CCccHHH----H
Confidence            35678999999999999999999986433    22442              333444333332221 2233333    3


Q ss_pred             HHHcCCCeEEEEEeCCCCCChhcHHHhhccCCC-CCCCcEEEEEecCC
Q 043252          290 KKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQA-GAQGSKIIVTTRNQ  336 (337)
Q Consensus       290 ~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~-~~~gs~iivTTR~~  336 (337)
                      .+.+.++..||.||++.-.+..+=-.+...|.. ...|. |||+|-|.
T Consensus       121 a~~l~~~~~lLcfDEF~V~DiaDAmil~rLf~~l~~~gv-vlVaTSN~  167 (362)
T PF03969_consen  121 ADELAKESRLLCFDEFQVTDIADAMILKRLFEALFKRGV-VLVATSNR  167 (362)
T ss_pred             HHHHHhcCCEEEEeeeeccchhHHHHHHHHHHHHHHCCC-EEEecCCC
Confidence            344455667999999865544332222222221 13565 66666553

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

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.32  E-value=0.017  Score=56.64  Aligned_cols=134  Identities=14%  Similarity=0.121  Sum_probs=72.9

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc-ccccccceEEEEeCCCCCHHHHHH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ....++|....+.++.+.+..-..    .-..|.|+|..|+|||++|+.++.... ....|   +.|++.....  ..+.
T Consensus       194 ~~~~liG~s~~~~~~~~~~~~~a~----~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pf---v~i~c~~~~~--~~~~  264 (534)
T TIGR01817       194 KEDGIIGKSPAMRQVVDQARVVAR----SNSTVLLRGESGTGKELIAKAIHYLSPRAKRPF---VKVNCAALSE--TLLE  264 (534)
T ss_pred             ccCceEECCHHHHHHHHHHHHHhC----cCCCEEEECCCCccHHHHHHHHHHhCCCCCCCe---EEeecCCCCH--HHHH
Confidence            346789999999888887764321    233678999999999999999987422 22223   4455544221  2222


Q ss_pred             HHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC----C-------CcEEEEEec
Q 043252          266 SILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA----Q-------GSKIIVTTR  334 (337)
Q Consensus       266 ~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~----~-------gs~iivTTR  334 (337)
                      ..   +.+...........  ...........=.|+||+|..........|...+..+.    .       ..|||.||.
T Consensus       265 ~~---lfg~~~~~~~~~~~--~~~g~~~~a~~GtL~ldei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~  339 (534)
T TIGR01817       265 SE---LFGHEKGAFTGAIA--QRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATN  339 (534)
T ss_pred             HH---HcCCCCCccCCCCc--CCCCcccccCCCeEEEechhhCCHHHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCC
Confidence            21   11111100000000  00000001223468899998876666667766664321    1       247888774

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.

>PRK03839 putative kinase; Provisional

Probab=96.29  E-value=0.0034  Score=52.12  Aligned_cols=22  Identities=41%  Similarity=0.724  Sum_probs=20.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+++.+++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999874

>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=96.28  E-value=0.0067  Score=49.99  Aligned_cols=40  Identities=25%  Similarity=0.136  Sum_probs=28.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD  256 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~  256 (337)
                      ..++.+.|+.|+|||.||+.+.....+ +.....+-++++.
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~-~~~~~~~~~d~s~   42 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFV-GSERPLIRIDMSE   42 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT--SSCCEEEEEEGGG
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhcc-CCccchHHHhhhc
Confidence            568999999999999999998764211 2333445555554

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 ....

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.26  E-value=0.031  Score=52.66  Aligned_cols=24  Identities=33%  Similarity=0.408  Sum_probs=21.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|.++|..|+||||++..+..
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~  122 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAY  122 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999987754

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=96.25  E-value=0.019  Score=48.60  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=21.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|..|.|||||.+.+...
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          27 EVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            59999999999999999998764

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.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.23  E-value=0.0031  Score=47.65  Aligned_cols=21  Identities=48%  Similarity=0.608  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |-|+|++|+|||+||+.+..+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999998765

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

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.21  E-value=0.0033  Score=53.08  Aligned_cols=22  Identities=41%  Similarity=0.588  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|+|.|+.|+|||||++.+..-
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~   22 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQ   22 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998763

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.

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

Probab=96.19  E-value=0.026  Score=50.42  Aligned_cols=79  Identities=15%  Similarity=0.244  Sum_probs=47.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccc--cccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQV--EDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL  293 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L  293 (337)
                      -++|.++||+|.|||+|.+.++..-.+  .+.|....-+.+..    ..++..=...       ...-...+..++.+.+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins----hsLFSKWFsE-------SgKlV~kmF~kI~ELv  245 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS----HSLFSKWFSE-------SGKLVAKMFQKIQELV  245 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh----hHHHHHHHhh-------hhhHHHHHHHHHHHHH
Confidence            378999999999999999999986533  33444444444332    1222111111       2334455666677777


Q ss_pred             CCCeE--EEEEeCC
Q 043252          294 FGKKF--LLVLDDV  305 (337)
Q Consensus       294 ~~kr~--LlVlDdv  305 (337)
                      .++..  ++.+|.|
T Consensus       246 ~d~~~lVfvLIDEV  259 (423)
T KOG0744|consen  246 EDRGNLVFVLIDEV  259 (423)
T ss_pred             hCCCcEEEEEeHHH
Confidence            65544  5567888

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

Probab=96.19  E-value=0.0061  Score=52.70  Aligned_cols=53  Identities=28%  Similarity=0.330  Sum_probs=42.3

Q ss_pred             ccccccchhHHH---HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          188 EAKVYGRETEKK---EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       188 ~~~~vGr~~~~~---~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      -.+++|.++.+.   -|++.|.+++.=++...+-|..+|++|.|||.+|+.+.+..
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~  175 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA  175 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc
Confidence            356889887764   46777877654456778899999999999999999999853

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.18  E-value=0.016  Score=51.37  Aligned_cols=23  Identities=30%  Similarity=0.297  Sum_probs=18.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|+|.+|+||||+|+.+...
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~   24 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKY   24 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHH
Confidence            47899999999999999998764

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.18  E-value=0.025  Score=46.39  Aligned_cols=117  Identities=15%  Similarity=0.095  Sum_probs=59.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceE--EEEeCCCCCHHHHHHHHHHHhhCCCCC-----CCCC-------H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKA--WTCVSDDFDVIRLTKSILLSIASDQNV-----DNHD-------L  282 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~--wv~v~~~~~~~~~~~~il~~~~~~~~~-----~~~~-------~  282 (337)
                      ..|-|++-.|.||||.|-.+.-.. ....+.+.+  |+.-.........+..+  .+......     ...+       .
T Consensus         6 Gli~v~~g~GkGKtt~a~g~a~ra-~~~g~~v~ivQFlKg~~~~GE~~~l~~~--~~~~~~~g~g~~~~~~~~~~~~~~~   82 (173)
T TIGR00708         6 GIIIVHTGNGKGKTTAAFGMALRA-LGHGKKVGVIQFIKGAWPNGERAAFEPH--GVEFQVMGTGFTWETQNREADTAIA   82 (173)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHH-HHCCCeEEEEEEecCCcccChHHHHHhc--CcEEEECCCCCeecCCCcHHHHHHH
Confidence            578888889999999996654321 111222211  22222122333333332  11100000     0011       2


Q ss_pred             HHHHHHHHHHcCCCeE-EEEEeCCCCC---ChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          283 NKLQEELKKQLFGKKF-LLVLDDVWNE---NYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       283 ~~~~~~l~~~L~~kr~-LlVlDdv~~~---~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      ....+..++.+....| |||||.+-..   ..-+.+.+...|...+.+..||+|-|+-
T Consensus        83 ~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        83 KAAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            2233445555655555 9999999421   1223445666665556677899998863

Alternate name: corrinoid adenosyltransferase.

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=96.18  E-value=0.051  Score=51.49  Aligned_cols=21  Identities=48%  Similarity=0.714  Sum_probs=19.5

Q ss_pred             EEEEEEccCCCchHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .+++|+|+.|.||||||+.+.
T Consensus       363 ~~lgIIGPSgSGKSTLaR~lv  383 (580)
T COG4618         363 EALGIIGPSGSGKSTLARLLV  383 (580)
T ss_pred             ceEEEECCCCccHHHHHHHHH
Confidence            489999999999999999984

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.17  E-value=0.0096  Score=46.68  Aligned_cols=41  Identities=24%  Similarity=0.131  Sum_probs=28.5

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      ++.+++-+.|...-    ..-.+|.+.|.-|.|||||++.+....
T Consensus         6 ~~t~~l~~~l~~~l----~~~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150         6 KAMDKFGKAFAKPL----DFGTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             HHHHHHHHHHHHhC----CCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            34445555554321    123499999999999999999998753

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.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=96.17  E-value=0.022  Score=55.63  Aligned_cols=134  Identities=13%  Similarity=-0.007  Sum_probs=69.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|....+.++++.+..-..    .-.-|.|+|..|+||++||+.++....-  .-...+.++++...  ...+... 
T Consensus       204 ~~~ig~s~~~~~~~~~~~~~A~----~~~pvlI~GE~GtGK~~lA~aiH~~s~r--~~~pfv~inca~~~--~~~~e~e-  274 (520)
T PRK10820        204 SQIVAVSPKMRQVVEQARKLAM----LDAPLLITGDTGTGKDLLAYACHLRSPR--GKKPFLALNCASIP--DDVVESE-  274 (520)
T ss_pred             cceeECCHHHHHHHHHHHHHhC----CCCCEEEECCCCccHHHHHHHHHHhCCC--CCCCeEEeccccCC--HHHHHHH-
Confidence            4688988888777776653221    1235889999999999999998763211  11223455555432  2222221 


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC-----------CCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA-----------QGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~-----------~gs~iivTTR~  335 (337)
                        +.+...............+.+  ....=.|+||+|..........|...+..+.           ...|||.||..
T Consensus       275 --lFG~~~~~~~~~~~~~~g~~e--~a~~GtL~LdeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st~~  348 (520)
T PRK10820        275 --LFGHAPGAYPNALEGKKGFFE--QANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQK  348 (520)
T ss_pred             --hcCCCCCCcCCcccCCCChhh--hcCCCEEEEeChhhCCHHHHHHHHHHHhcCCcccCCCCcceeeeeEEEEecCC
Confidence              111111000000000000000  1122357899998776666666666554321           12378887754

>PF14516 AAA_35: AAA-like domain

Probab=96.16  E-value=0.1  Score=47.79  Aligned_cols=111  Identities=15%  Similarity=0.167  Sum_probs=68.3

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC-----CCHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD-----FDVIR  262 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~-----~~~~~  262 (337)
                      .+..|.|...-+++.+.|..+.       ..+.|.|+..+|||+|...+.+..+.. .|. .+++++..-     .+...
T Consensus        10 ~~~Yi~R~~~e~~~~~~i~~~G-------~~~~I~apRq~GKTSll~~l~~~l~~~-~~~-~v~id~~~~~~~~~~~~~~   80 (331)
T PF14516_consen   10 SPFYIERPPAEQECYQEIVQPG-------SYIRIKAPRQMGKTSLLLRLLERLQQQ-GYR-CVYIDLQQLGSAIFSDLEQ   80 (331)
T ss_pred             CCcccCchHHHHHHHHHHhcCC-------CEEEEECcccCCHHHHHHHHHHHHHHC-CCE-EEEEEeecCCCcccCCHHH
Confidence            3456788866677777776543       399999999999999999887753322 333 456766542     24555


Q ss_pred             HHHHHHHHhhCCCCC----------CCCCHHHHHHHHHHHc---CCCeEEEEEeCCCC
Q 043252          263 LTKSILLSIASDQNV----------DNHDLNKLQEELKKQL---FGKKFLLVLDDVWN  307 (337)
Q Consensus       263 ~~~~il~~~~~~~~~----------~~~~~~~~~~~l~~~L---~~kr~LlVlDdv~~  307 (337)
                      ++..+...+...-..          ...........+.+++   .+++.+|+||++..
T Consensus        81 f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~  138 (331)
T PF14516_consen   81 FLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDR  138 (331)
T ss_pred             HHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhh
Confidence            666665554332210          1112223334444432   26899999999964

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=96.16  E-value=0.06  Score=52.75  Aligned_cols=23  Identities=35%  Similarity=0.468  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -..++|+|+.|+|||||++.+..
T Consensus       361 G~~vaIvG~SGsGKSTLl~lL~g  383 (529)
T TIGR02868       361 GERVAILGPSGSGKSTLLMLLTG  383 (529)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999964

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.15  E-value=0.027  Score=49.78  Aligned_cols=41  Identities=20%  Similarity=0.275  Sum_probs=28.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD  257 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~  257 (337)
                      .-+++.|.|++|+|||+|+.++.... .+. =+.+++++...+
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~-a~~-Ge~vlyis~Ee~   75 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQ-ASR-GNPVLFVTVESP   75 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH-HhC-CCcEEEEEecCC
Confidence            45799999999999999998764431 111 235677877643

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK04040 adenylate kinase; Provisional

Probab=96.15  E-value=0.0049  Score=51.64  Aligned_cols=23  Identities=30%  Similarity=0.549  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|+|++|+||||+++.+...
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~   25 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEK   25 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH
Confidence            58999999999999999999764

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.13  E-value=0.0047  Score=51.20  Aligned_cols=23  Identities=30%  Similarity=0.470  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|+|+.|+|||||++.+...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            37899999999999999998664

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.

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=96.12  E-value=0.018  Score=49.18  Aligned_cols=83  Identities=23%  Similarity=0.376  Sum_probs=50.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC-CCHHHHHHHHHHHhhCCCC-----CCCCCH-H------
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD-FDVIRLTKSILLSIASDQN-----VDNHDL-N------  283 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~-~~~~~~~~~il~~~~~~~~-----~~~~~~-~------  283 (337)
                      .-++|.|..|+|||+|++.+.++..    -+..+++.+.+. ..+.++..++...-.....     ...... .      
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~~----~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~   91 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQD----ADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPY   91 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHCT----TTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhccc----ccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhc
Confidence            4789999999999999999987632    223477777654 3445555555433111100     011111 1      


Q ss_pred             ---HHHHHHHHHcCCCeEEEEEeCC
Q 043252          284 ---KLQEELKKQLFGKKFLLVLDDV  305 (337)
Q Consensus       284 ---~~~~~l~~~L~~kr~LlVlDdv  305 (337)
                         ...+.++.  +++..|+++||+
T Consensus        92 ~a~t~AEyfrd--~G~dVlli~Dsl  114 (215)
T PF00006_consen   92 TALTIAEYFRD--QGKDVLLIIDSL  114 (215)
T ss_dssp             HHHHHHHHHHH--TTSEEEEEEETH
T ss_pred             cchhhhHHHhh--cCCceeehhhhh
Confidence               12333444  799999999999

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 ....

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.12  E-value=0.071  Score=49.33  Aligned_cols=25  Identities=32%  Similarity=0.416  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...++.|+|+.|+||||++..+...
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~  229 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQ  229 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999888653

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.12  E-value=0.072  Score=44.15  Aligned_cols=55  Identities=11%  Similarity=0.238  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHcCCCeEEEEEeCCCCC-Ch-hcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          282 LNKLQEELKKQLFGKKFLLVLDDVWNE-NY-TDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       282 ~~~~~~~l~~~L~~kr~LlVlDdv~~~-~~-~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      -++-.-.+.+.+-++.-||+=|.-.-. ++ -.|+.+.-.-.-+..|..||+.|.+.
T Consensus       141 GEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~  197 (223)
T COG2884         141 GEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDL  197 (223)
T ss_pred             hHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccH
Confidence            344445566777788888888876321 22 35554433323456799999999764

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.12  E-value=0.02  Score=58.30  Aligned_cols=52  Identities=25%  Similarity=0.160  Sum_probs=36.2

Q ss_pred             ccccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.++.|.+..++.|.+.+.-+-.       .+-...+-+.++|++|+|||+||+.+.+.
T Consensus       452 ~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e  510 (733)
T TIGR01243       452 WSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE  510 (733)
T ss_pred             hhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            34577888887777766542110       01123456889999999999999999985

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.11  E-value=0.019  Score=52.93  Aligned_cols=106  Identities=14%  Similarity=0.166  Sum_probs=56.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      ..|.|.|+.|+||||+.+.+...  +..+...+++. +.++...  ..... ..+..... ...+.......++..|+..
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~--i~~~~~~~i~t-iEdp~E~--~~~~~-~~~i~q~e-vg~~~~~~~~~l~~~lr~~  195 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDY--INKNAAGHIIT-IEDPIEY--VHRNK-RSLINQRE-VGLDTLSFANALRAALRED  195 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh--hCcCCCCEEEE-EcCChhh--hccCc-cceEEccc-cCCCCcCHHHHHHHhhccC
Confidence            48999999999999999988763  33333444443 2222111  00000 00000000 1111223456677778778


Q ss_pred             eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          297 KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      .=.|++|++.+.  +.+.....   ....|-.|+.|+.
T Consensus       196 pd~i~vgEird~--~~~~~~l~---aa~tGh~v~~T~H  228 (343)
T TIGR01420       196 PDVILIGEMRDL--ETVELALT---AAETGHLVFGTLH  228 (343)
T ss_pred             CCEEEEeCCCCH--HHHHHHHH---HHHcCCcEEEEEc
Confidence            889999999653  44443222   2234555665554

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.11  E-value=0.0051  Score=50.47  Aligned_cols=24  Identities=33%  Similarity=0.484  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|+|++|+||||+|+.+...
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~   27 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKR   27 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999999999874

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.11  E-value=0.046  Score=49.89  Aligned_cols=24  Identities=25%  Similarity=0.351  Sum_probs=20.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -...+.++|+.|+||||+|+.+..
T Consensus        20 ~~hA~Lf~G~~G~GK~~la~~~a~   43 (325)
T PRK08699         20 RPNAWLFAGKKGIGKTAFARFAAQ   43 (325)
T ss_pred             cceEEEeECCCCCCHHHHHHHHHH
Confidence            345788999999999999988865

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.10  E-value=0.029  Score=52.18  Aligned_cols=83  Identities=18%  Similarity=0.148  Sum_probs=48.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~~  291 (337)
                      -.++.|.|.+|+|||||+..+....  ...-..++|++....  ...+.. -...++.....    ...+.+.+.+.+.+
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~--a~~g~~VlYvs~EEs--~~qi~~-Ra~rlg~~~~~l~l~~e~~le~I~~~i~~  156 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARL--AKRGGKVLYVSGEES--PEQIKL-RADRLGISTENLYLLAETNLEDILASIEE  156 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH--HhcCCeEEEEECCcC--HHHHHH-HHHHcCCCcccEEEEccCcHHHHHHHHHh
Confidence            4699999999999999998887542  122235677765443  333222 22333322111    22344555554432


Q ss_pred             HcCCCeEEEEEeCCC
Q 043252          292 QLFGKKFLLVLDDVW  306 (337)
Q Consensus       292 ~L~~kr~LlVlDdv~  306 (337)
                         .+.-+||+|.+.
T Consensus       157 ---~~~~lVVIDSIq  168 (372)
T cd01121         157 ---LKPDLVIIDSIQ  168 (372)
T ss_pred             ---cCCcEEEEcchH
Confidence               355689999984

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.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=96.10  E-value=0.023  Score=53.47  Aligned_cols=87  Identities=21%  Similarity=0.263  Sum_probs=47.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC-CCCHHHHHHHHHHHhhCCCCC------CCCCHHH-----
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD-DFDVIRLTKSILLSIASDQNV------DNHDLNK-----  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~-~~~~~~~~~~il~~~~~~~~~------~~~~~~~-----  284 (337)
                      ..++|+|..|+|||||++.+.....   .....+ +.+.. .-.+.++..+.+..-......      +......     
T Consensus       141 q~i~I~G~sG~GKTtLl~~I~~~~~---~~~gvi-~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~  216 (418)
T TIGR03498       141 QRLGIFAGSGVGKSTLLSMLARNTD---ADVVVI-ALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAY  216 (418)
T ss_pred             cEEEEECCCCCChHHHHHHHhCCCC---CCEEEE-EEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHH
Confidence            4899999999999999998886422   111222 22222 233444544443332111110      1111111     


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVWN  307 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~~  307 (337)
                      ..-.+.+++  ++++.||++||+..
T Consensus       217 ~a~~iAEyfrd~G~~Vll~~DslTr  241 (418)
T TIGR03498       217 TATAIAEYFRDQGKDVLLLMDSVTR  241 (418)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchhH
Confidence            222344444  58999999999943

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.

>COG3903 Predicted ATPase [General function prediction only]

Probab=96.09  E-value=0.0018  Score=59.46  Aligned_cols=113  Identities=18%  Similarity=0.222  Sum_probs=67.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL  293 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L  293 (337)
                      ..+.+.++|.|||||||++-.+..   +...|..-.|+.--.++ +...+.......+.....    +-+.....+....
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~----~g~~~~~~~~~~~   85 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQ----PGDSAVDTLVRRI   85 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhcccccc----cchHHHHHHHHHH
Confidence            357899999999999999988765   56667655555444444 444444444444554332    2233444566777


Q ss_pred             CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          294 FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       294 ~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      .++|.++|+||.-+- .+.-..+...+..+...-.|+.|+|.
T Consensus        86 ~~rr~llvldncehl-~~~~a~~i~all~~~~~~~~~atsre  126 (414)
T COG3903          86 GDRRALLVLDNCEHL-LDACAALIVALLGACPRLAILATSRE  126 (414)
T ss_pred             hhhhHHHHhcCcHHH-HHHHHHHHHHHHccchhhhhHHHhHh
Confidence            789999999998432 11222222233333334456666653

>TIGR03263 guanyl_kin guanylate kinase

Probab=96.09  E-value=0.0048  Score=51.12  Aligned_cols=23  Identities=35%  Similarity=0.590  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|.|+|+.|+|||||++.++..
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHcc
Confidence            48999999999999999999873

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.08  E-value=0.027  Score=53.04  Aligned_cols=86  Identities=17%  Similarity=0.229  Sum_probs=49.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC----CC-C-CHH-----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV----DN-H-DLN-----K  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~----~~-~-~~~-----~  284 (337)
                      ..++|+|..|+|||||++.++...    ..+..+.+-+.+.. .+.+++.+++..-......    .+ . ...     .
T Consensus       163 qrigI~G~sG~GKSTLL~~I~~~~----~~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~  238 (444)
T PRK08972        163 QRMGLFAGSGVGKSVLLGMMTRGT----TADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCE  238 (444)
T ss_pred             CEEEEECCCCCChhHHHHHhccCC----CCCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHH
Confidence            479999999999999999998632    12344455555543 3344555554331111100    11 1 111     1


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ..-.+.+++  ++++.||++||+.
T Consensus       239 ~A~tiAEyfrd~G~~VLl~~DslT  262 (444)
T PRK08972        239 TATTIAEYFRDQGLNVLLLMDSLT  262 (444)
T ss_pred             HHHHHHHHHHHcCCCEEEEEcChH
Confidence            222244444  6899999999993

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=96.08  E-value=0.038  Score=48.13  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=18.5

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +-.|+|++|+|||+|+..+.-
T Consensus         3 ~~ll~g~~G~GKS~lal~la~   23 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLAL   23 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHH
Confidence            667899999999999988864

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.

>PRK08149 ATP synthase SpaL; Validated

Probab=96.08  E-value=0.024  Score=53.40  Aligned_cols=87  Identities=18%  Similarity=0.307  Sum_probs=49.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC-CCCHHHHHHHHHHHhhCCCCC------CCCCH-----HH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD-DFDVIRLTKSILLSIASDQNV------DNHDL-----NK  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~-~~~~~~~~~~il~~~~~~~~~------~~~~~-----~~  284 (337)
                      ..++|+|..|+|||||++.++.....    +.++...+.. ..++.++..+++.........      +....     ..
T Consensus       152 q~i~I~G~sG~GKTTLl~~i~~~~~~----dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~~  227 (428)
T PRK08149        152 QRMGIFASAGCGKTSLMNMLIEHSEA----DVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAAL  227 (428)
T ss_pred             CEEEEECCCCCChhHHHHHHhcCCCC----CeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHHH
Confidence            48999999999999999999874221    2222333332 234556666666543221100      11111     11


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVWN  307 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~~  307 (337)
                      ....+.+++  ++++.||++||+..
T Consensus       228 ~a~tiAE~fr~~G~~Vll~~DslTr  252 (428)
T PRK08149        228 VATTVAEYFRDQGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHHHHHHHHcCCCEEEEccchHH
Confidence            223334444  58999999999943

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.08  E-value=0.047  Score=51.39  Aligned_cols=24  Identities=33%  Similarity=0.371  Sum_probs=20.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+++++|+.|+||||++..+..
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~  213 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAA  213 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            346999999999999999987754

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.07  E-value=0.068  Score=49.02  Aligned_cols=42  Identities=14%  Similarity=0.097  Sum_probs=33.4

Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      +++=++|+|++...+...++.|...|..-.+++.+|++|.+.
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~  172 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARI  172 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECCh
Confidence            455588999998888889999998888767778777777653

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=96.06  E-value=0.044  Score=49.54  Aligned_cols=23  Identities=22%  Similarity=0.481  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|.|||||.+.+...
T Consensus        29 ei~~l~G~NGaGKTTLl~~l~Gl   51 (301)
T TIGR03522        29 RIVGFLGPNGAGKSTTMKIITGY   51 (301)
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999753

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=96.06  E-value=0.13  Score=45.88  Aligned_cols=41  Identities=10%  Similarity=0.068  Sum_probs=32.7

Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +++=++|+|++.....+.++.+...|..-..++.+|++|.+
T Consensus        94 ~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~  134 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAK  134 (290)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCC
Confidence            55568899999888788999999888776677777777765

>PRK00625 shikimate kinase; Provisional

Probab=96.05  E-value=0.005  Score=50.81  Aligned_cols=22  Identities=23%  Similarity=0.326  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|+|++|+||||+++.+.+.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~   23 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKF   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999999764

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=96.05  E-value=0.0056  Score=46.77  Aligned_cols=22  Identities=32%  Similarity=0.604  Sum_probs=19.8

Q ss_pred             EEEEccCCCchHHHHHHHHhcc
Q 043252          219 IPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      |.|+|..|+|||||.+.++..+
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            7899999999999999998754

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=96.05  E-value=0.029  Score=53.29  Aligned_cols=89  Identities=21%  Similarity=0.257  Sum_probs=52.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCHH-----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDLN-----K  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~~-----~  284 (337)
                      .-++|.|..|+|||||+..+....... +=+.++++-+.+.. .+.+++.+++..-......      +.....     .
T Consensus       145 QR~gIfa~~GvGKt~Ll~~i~~~~~~~-~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~  223 (463)
T PRK09280        145 GKIGLFGGAGVGKTVLIQELINNIAKE-HGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVAL  223 (463)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhc-CCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            478999999999999998876543221 11346666665543 4456666666432111100      111111     1


Q ss_pred             HHHHHHHHc---CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL---FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L---~~kr~LlVlDdv~  306 (337)
                      ..-.+.+++   ++++.||++|++.
T Consensus       224 ~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        224 TGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHhcCCceEEEecchH
Confidence            233355555   6899999999993

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.04  E-value=0.029  Score=52.45  Aligned_cols=51  Identities=24%  Similarity=0.329  Sum_probs=36.7

Q ss_pred             cccccchhHHHHHHHHHhcC--------CCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKD--------DSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~--------~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.++.++.+.-.+...        ........+-|.++|++|+|||+||+.+...
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~   70 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKL   70 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHH
Confidence            45889988888886666531        0001122467899999999999999999875

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.04  E-value=0.007  Score=49.99  Aligned_cols=24  Identities=29%  Similarity=0.401  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|+|++|+||||+|+.+...
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            459999999999999999998864

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.02  E-value=0.0046  Score=51.38  Aligned_cols=22  Identities=27%  Similarity=0.418  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|+|++|+||||+|+.+...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999998763

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.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.01  E-value=0.065  Score=54.00  Aligned_cols=24  Identities=29%  Similarity=0.416  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++.++|+.|+||||++.++...
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~  208 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAAR  208 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhh
Confidence            479999999999999999888753

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=96.01  E-value=0.025  Score=53.44  Aligned_cols=87  Identities=20%  Similarity=0.227  Sum_probs=49.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCHH-----
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDLN-----  283 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~~-----  283 (337)
                      -..++|+|..|+|||||++.+++...    .+..+.+-+.+.. .+.++..+.+..-......      +.....     
T Consensus       158 Gqri~I~G~sG~GKTtLL~~I~~~~~----~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~  233 (442)
T PRK08927        158 GQRMGIFAGSGVGKSVLLSMLARNAD----ADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAA  233 (442)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccC----CCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHH
Confidence            34789999999999999999987432    1334445555433 3344554444332111100      111111     


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCC
Q 043252          284 KLQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       284 ~~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ...-.+.+++  +++..||++||+.
T Consensus       234 ~~a~tiAEyfrd~G~~Vll~~DslT  258 (442)
T PRK08927        234 YLTLAIAEYFRDQGKDVLCLMDSVT  258 (442)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCcH
Confidence            1222344444  5899999999993

>PRK05922 type III secretion system ATPase; Validated

Probab=96.01  E-value=0.048  Score=51.46  Aligned_cols=86  Identities=13%  Similarity=0.249  Sum_probs=48.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC-CCCHHHHHHHHHHHhhCCCCC----CCC--CHH-----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD-DFDVIRLTKSILLSIASDQNV----DNH--DLN-----K  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~-~~~~~~~~~~il~~~~~~~~~----~~~--~~~-----~  284 (337)
                      ..++|+|..|+|||||.+.+....    ..+....+.+.. .....+++.+...........    .+.  ...     .
T Consensus       158 qrigI~G~nG~GKSTLL~~Ia~~~----~~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~~  233 (434)
T PRK05922        158 QRIGVFSEPGSGKSSLLSTIAKGS----KSTINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAGR  233 (434)
T ss_pred             cEEEEECCCCCChHHHHHHHhccC----CCCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHHH
Confidence            478999999999999999998642    122333333332 223345555544333222110    111  111     1


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ..-.+.+++  ++++.||++||+.
T Consensus       234 ~a~tiAEyfrd~G~~VLl~~DslT  257 (434)
T PRK05922        234 AAMTIAEYFRDQGHRVLFIMDSLS  257 (434)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchh
Confidence            223344444  5899999999993

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=96.00  E-value=0.0074  Score=49.60  Aligned_cols=25  Identities=28%  Similarity=0.376  Sum_probs=22.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+++|+|..|+|||||++.+...
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~   29 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPA   29 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHH
Confidence            4569999999999999999998864

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.00  E-value=0.066  Score=51.32  Aligned_cols=24  Identities=29%  Similarity=0.383  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|++++|+.|+||||++.+++..
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~  279 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAAR  279 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHH
Confidence            479999999999999999988864

>PHA00729 NTP-binding motif containing protein

Probab=95.99  E-value=0.011  Score=50.64  Aligned_cols=25  Identities=48%  Similarity=0.566  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|.|.+|+||||||..+.+.
T Consensus        16 ~f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         16 GFVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHH
Confidence            3457899999999999999998764

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=95.98  E-value=0.05  Score=53.13  Aligned_cols=125  Identities=23%  Similarity=0.307  Sum_probs=68.2

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHH-HHHHHHhcccccccccceEEEEeCCCCCH--HHHHHHHHHHhh
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTT-LAQLVYNDKQVEDHFDLKAWTCVSDDFDV--IRLTKSILLSIA  272 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTt-La~~v~~~~~~~~~F~~~~wv~v~~~~~~--~~~~~~il~~~~  272 (337)
                      ...++|.+.+...        .||.|+|..|+|||| |+|.+|.+-     |...--|.+.++-.+  ..+.+.+.+.++
T Consensus       359 ~~R~~ll~~ir~n--------~vvvivgETGSGKTTQl~QyL~edG-----Y~~~GmIGcTQPRRvAAiSVAkrVa~EM~  425 (1042)
T KOG0924|consen  359 ACRDQLLSVIREN--------QVVVIVGETGSGKTTQLAQYLYEDG-----YADNGMIGCTQPRRVAAISVAKRVAEEMG  425 (1042)
T ss_pred             HHHHHHHHHHhhC--------cEEEEEecCCCCchhhhHHHHHhcc-----cccCCeeeecCchHHHHHHHHHHHHHHhC
Confidence            3445666666433        399999999999987 678888752     322224666666543  345555666654


Q ss_pred             CCCCC---------CC----------CCHHHHHHHHHHHcCCCeEEEEEeCCCCCC--hhcH-HHhhccCCCCCCCcEEE
Q 043252          273 SDQNV---------DN----------HDLNKLQEELKKQLFGKKFLLVLDDVWNEN--YTDW-VHLSLPFQAGAQGSKII  330 (337)
Q Consensus       273 ~~~~~---------~~----------~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~--~~~~-~~l~~~l~~~~~gs~ii  330 (337)
                      .....         +.          .+---|.+.|....-.|--.||+|......  .+-. ..+...+. ....-|+|
T Consensus       426 ~~lG~~VGYsIRFEdvT~~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~la-rRrdlKli  504 (1042)
T KOG0924|consen  426 VTLGDTVGYSIRFEDVTSEDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLA-RRRDLKLI  504 (1042)
T ss_pred             CccccccceEEEeeecCCCceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHH-hhccceEE
Confidence            32110         00          111223344444444455588999986542  1111 12222222 23356899


Q ss_pred             EEec
Q 043252          331 VTTR  334 (337)
Q Consensus       331 vTTR  334 (337)
                      |||-
T Consensus       505 VtSA  508 (1042)
T KOG0924|consen  505 VTSA  508 (1042)
T ss_pred             Eeec
Confidence            9974

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.97  E-value=0.0095  Score=50.58  Aligned_cols=22  Identities=23%  Similarity=0.122  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++.|.|+.|.||||+.+.+..
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999998864

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

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=95.97  E-value=0.015  Score=56.48  Aligned_cols=72  Identities=19%  Similarity=0.186  Sum_probs=44.5

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL  293 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L  293 (337)
                      ...+.+.++|++|.|||.||+.+.+.  ...+|-     .+..+    .    ++...      .......+...+....
T Consensus       274 ~~~~giLl~GpPGtGKT~lAkava~~--~~~~fi-----~v~~~----~----l~sk~------vGesek~ir~~F~~A~  332 (494)
T COG0464         274 RPPKGVLLYGPPGTGKTLLAKAVALE--SRSRFI-----SVKGS----E----LLSKW------VGESEKNIRELFEKAR  332 (494)
T ss_pred             CCCCeeEEECCCCCCHHHHHHHHHhh--CCCeEE-----EeeCH----H----Hhccc------cchHHHHHHHHHHHHH
Confidence            34568999999999999999999983  334442     22221    1    11100      1222333444455555


Q ss_pred             CCCeEEEEEeCCC
Q 043252          294 FGKKFLLVLDDVW  306 (337)
Q Consensus       294 ~~kr~LlVlDdv~  306 (337)
                      +...+.|.+|++.
T Consensus       333 ~~~p~iiFiDEiD  345 (494)
T COG0464         333 KLAPSIIFIDEID  345 (494)
T ss_pred             cCCCcEEEEEchh
Confidence            6788999999994

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=95.96  E-value=0.013  Score=58.08  Aligned_cols=74  Identities=15%  Similarity=0.087  Sum_probs=53.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|.++.++.|...+...        +.+.++|++|+||||+|+.+.... -..+|+..+|..-+ ..+...+++.+.
T Consensus        31 ~~vigq~~a~~~L~~~~~~~--------~~~l~~G~~G~GKttla~~l~~~l-~~~~~~~~~~~~np-~~~~~~~~~~v~  100 (637)
T PRK13765         31 DQVIGQEHAVEVIKKAAKQR--------RHVMMIGSPGTGKSMLAKAMAELL-PKEELQDILVYPNP-EDPNNPKIRTVP  100 (637)
T ss_pred             HHcCChHHHHHHHHHHHHhC--------CeEEEECCCCCcHHHHHHHHHHHc-ChHhHHHheEeeCC-CcchHHHHHHHH
Confidence            56889998888888777532        268899999999999999998642 22345667786553 345666777777


Q ss_pred             HHhh
Q 043252          269 LSIA  272 (337)
Q Consensus       269 ~~~~  272 (337)
                      .+++
T Consensus       101 ~~~G  104 (637)
T PRK13765        101 AGKG  104 (637)
T ss_pred             HhcC
Confidence            6553

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.96  E-value=0.02  Score=51.89  Aligned_cols=23  Identities=35%  Similarity=0.416  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.|+|..|.|||||++.+...
T Consensus       145 ~~ili~G~tGsGKTTll~al~~~  167 (308)
T TIGR02788       145 KNIIISGGTGSGKTTFLKSLVDE  167 (308)
T ss_pred             CEEEEECCCCCCHHHHHHHHHcc
Confidence            58999999999999999988764

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.95  E-value=0.061  Score=46.77  Aligned_cols=49  Identities=14%  Similarity=0.100  Sum_probs=30.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      -.++.|.|.+|+|||+++..+..+.- ..+=..++|++...  +..++...+
T Consensus        13 G~l~lI~G~~G~GKT~~~~~~~~~~~-~~~g~~vly~s~E~--~~~~~~~r~   61 (242)
T cd00984          13 GDLIIIAARPSMGKTAFALNIAENIA-KKQGKPVLFFSLEM--SKEQLLQRL   61 (242)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHH-HhCCCceEEEeCCC--CHHHHHHHH
Confidence            45999999999999999987765421 22112456666544  333444444

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.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=95.95  E-value=0.0071  Score=48.06  Aligned_cols=39  Identities=21%  Similarity=0.330  Sum_probs=27.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD  256 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~  256 (337)
                      ++|.|+|+.|+|||||++.+.+.. .+..+...+..+..+
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l-~~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINEL-KRRGYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHH-HHTT--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-hHcCCceEEEEEccC
Confidence            489999999999999999998863 234455555666655

>PRK04328 hypothetical protein; Provisional

Probab=95.94  E-value=0.025  Score=49.69  Aligned_cols=41  Identities=15%  Similarity=0.225  Sum_probs=29.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD  257 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~  257 (337)
                      .-+++.|.|.+|.|||+|+..+.... .+ .-+..+|++...+
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~-~~-~ge~~lyis~ee~   62 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNG-LQ-MGEPGVYVALEEH   62 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH-Hh-cCCcEEEEEeeCC
Confidence            45799999999999999997765431 22 2345778887663

>PF12061 DUF3542: Protein of unknown function (DUF3542); InterPro: IPR021929 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide

Probab=95.93  E-value=0.015  Score=51.44  Aligned_cols=75  Identities=19%  Similarity=0.251  Sum_probs=53.8

Q ss_pred             HHHHHHHHhhHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHcc-ccCChHHHHHHHHHHHHHHhhhhhhHHHH
Q 043252           13 VELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEK-KTTDDSVKLWLGELQNLAYDVEDLLDEFQ   87 (337)
Q Consensus        13 ~~~l~~kl~s~~~~~~~~~~~v~~~~~~L~~~L~~i~~~L~~ae~~-~~~~~~~~~Wl~~lr~~ayd~eD~lD~~~   87 (337)
                      ++.++++|-.+.-.......-++.+++-++.+|+.+|.||+..... ...-...+.+..++-..||++|+++|-+.
T Consensus       298 VdFlL~NLkdfq~rysdSlaflKnQiqvIQ~elesLqpFLk~V~ee~~nkh~~~ed~a~~ii~kAyevEYVVDaCi  373 (402)
T PF12061_consen  298 VDFLLKNLKDFQGRYSDSLAFLKNQIQVIQTELESLQPFLKHVVEEPHNKHDTNEDCATQIIRKAYEVEYVVDACI  373 (402)
T ss_pred             HHHHHhhHHHHhccccchHHHHHHHHHHHHHHHHHhhHHHHHHHhccchhhhhhhhHHHHHHHHHhheeeeeehhh
Confidence            3444455544322222223446899999999999999999997443 33333489999999999999999999874

The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain []. Most proteins matching this entry are found associated with PF00931 from PFAM.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=95.93  E-value=0.0064  Score=50.28  Aligned_cols=23  Identities=22%  Similarity=0.340  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|.+.|++|+||||+|+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            48999999999999999999764

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.93  E-value=0.02  Score=50.59  Aligned_cols=88  Identities=19%  Similarity=0.163  Sum_probs=56.4

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCC-------------------
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASD-------------------  274 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~-------------------  274 (337)
                      +..+++.|+|.+|+|||+++.++...  ...+...++||+....  ...++..+.+ ++-.                   
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~--~~~~ge~vlyvs~~e~--~~~l~~~~~~-~g~d~~~~~~~g~l~i~d~~~~~   95 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYE--GAREGEPVLYVSTEES--PEELLENARS-FGWDLEVYIEKGKLAILDAFLSE   95 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHH--HHhcCCcEEEEEecCC--HHHHHHHHHH-cCCCHHHHhhcCCEEEEEccccc
Confidence            34679999999999999999777653  3344788999998874  3444444422 1110                   


Q ss_pred             CC------CCCCCHHHHHHHHHHHcCC-CeEEEEEeCCC
Q 043252          275 QN------VDNHDLNKLQEELKKQLFG-KKFLLVLDDVW  306 (337)
Q Consensus       275 ~~------~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~  306 (337)
                      ..      ....+...+...+.+.... +..-+|+|.+-
T Consensus        96 ~~~~~~~~~~~~~~~~l~~~I~~~~~~~~~~~~ViDsi~  134 (260)
T COG0467          96 KGLVSIVVGDPLDLEELLDRIREIVEKEGADRVVIDSIT  134 (260)
T ss_pred             cccccccccCCccHHHHHHHHHHHHHHhCCCEEEEeCCc
Confidence            00      0123456666777666532 36678999985

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=95.92  E-value=0.024  Score=53.91  Aligned_cols=88  Identities=18%  Similarity=0.167  Sum_probs=54.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCH-----HH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDL-----NK  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~-----~~  284 (337)
                      .-++|.|.+|+|||||+..+...... .+-+.++++-+.+.. .+.+++.++...-......      +....     ..
T Consensus       144 QR~gIfa~~G~GKt~Ll~~~~~~~~~-~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~  222 (461)
T PRK12597        144 GKTGLFGGAGVGKTVLMMELIFNISK-QHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVL  222 (461)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHh-hCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHH
Confidence            47899999999999999888775332 245677777666543 4455666655432111100      11111     12


Q ss_pred             HHHHHHHHc---CCCeEEEEEeCC
Q 043252          285 LQEELKKQL---FGKKFLLVLDDV  305 (337)
Q Consensus       285 ~~~~l~~~L---~~kr~LlVlDdv  305 (337)
                      ..-.+.+++   ++++.||++|++
T Consensus       223 ~a~tiAEyfrd~~G~~VLl~~Dsl  246 (461)
T PRK12597        223 TGLTIAEYLRDEEKEDVLLFIDNI  246 (461)
T ss_pred             HHHHHHHHHHHhcCCceEEEeccc
Confidence            233455555   389999999999

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.92  E-value=0.007  Score=51.32  Aligned_cols=24  Identities=29%  Similarity=0.394  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|+|+|+.|+|||||++.++..
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            458999999999999999999874

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=95.92  E-value=0.0057  Score=49.05  Aligned_cols=22  Identities=27%  Similarity=0.616  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++.|.|++|+||||+|+.+...
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            3688999999999999998764

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=95.91  E-value=0.13  Score=47.13  Aligned_cols=125  Identities=12%  Similarity=0.137  Sum_probs=67.6

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccc---cce-----EEEEeCCCCCHHHHHHHHH
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF---DLK-----AWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~-----~wv~v~~~~~~~~~~~~il  268 (337)
                      .-+++...+..+.     -...+.+.|+.|+||+++|..+...---....   .|.     -++.....+|...+     
T Consensus        10 ~~~~l~~~~~~~r-----l~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i-----   79 (334)
T PRK07993         10 DYEQLVGSYQAGR-----GHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTL-----   79 (334)
T ss_pred             HHHHHHHHHHcCC-----cceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEE-----
Confidence            4456777775433     35688899999999999998875421000000   010     00001111111100     


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHc-----CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQL-----FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                         ...........++..+ +.+.+     .+++=++|+|++...+...-+.|...|..-..++-+|++|.+
T Consensus        80 ---~p~~~~~~I~idqiR~-l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~  147 (334)
T PRK07993         80 ---TPEKGKSSLGVDAVRE-VTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACRE  147 (334)
T ss_pred             ---ecccccccCCHHHHHH-HHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECC
Confidence               0000001122333222 22222     356668999999887777888888888776777878877765

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.91  E-value=0.058  Score=47.98  Aligned_cols=25  Identities=36%  Similarity=0.488  Sum_probs=21.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+++.++|++|+||||++.++...
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~   95 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANK   95 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4679999999999999999877643

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.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=95.91  E-value=0.0058  Score=48.62  Aligned_cols=22  Identities=41%  Similarity=0.625  Sum_probs=19.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|+|+.|+||||+|+.+...
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~   22 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKK   22 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998764

>COG3899 Predicted ATPase [General function prediction only]

Probab=95.91  E-value=0.027  Score=58.12  Aligned_cols=47  Identities=30%  Similarity=0.484  Sum_probs=39.6

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++||+.+.+.|...+..-.   .....++.+.|..|+|||+|++.|..-
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~---~g~~~~~lv~G~sGIGKsalv~ev~~~   47 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVS---KGRGEVVLVAGESGIGKSALVNEVHKP   47 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHh---CCCeEEEEEeecCCCcHHHHHHHHHHH
Confidence            37899999999999987543   234569999999999999999999874

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.90  E-value=0.059  Score=49.01  Aligned_cols=86  Identities=20%  Similarity=0.262  Sum_probs=47.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeC-CCCCHHHHHHHHHHHhhCCCCC------CCCCHH-----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVS-DDFDVIRLTKSILLSIASDQNV------DNHDLN-----K  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~-~~~~~~~~~~~il~~~~~~~~~------~~~~~~-----~  284 (337)
                      ..++|+|..|+|||||.+.+.....    -++.....+. ..-++.++....+..-......      +.....     .
T Consensus        70 qri~I~G~sG~GKTtLl~~Ia~~~~----~~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~~  145 (326)
T cd01136          70 QRLGIFAGSGVGKSTLLGMIARGTT----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAAY  145 (326)
T ss_pred             cEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHHH
Confidence            4789999999999999999987422    1223333333 2334555555554432211100      111111     1


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ..-.+.+++  +++..||++||+.
T Consensus       146 ~a~~~AEyfr~~g~~Vll~~Dslt  169 (326)
T cd01136         146 TATAIAEYFRDQGKDVLLLMDSLT  169 (326)
T ss_pred             HHHHHHHHHHHcCCCeEEEeccch
Confidence            222233333  5899999999983

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.

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=95.89  E-value=0.018  Score=51.86  Aligned_cols=23  Identities=30%  Similarity=0.508  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.++++.|+.|.|||||.+.+..
T Consensus        31 Gei~gllG~NGAGKTTllk~l~g   53 (293)
T COG1131          31 GEIFGLLGPNGAGKTTLLKILAG   53 (293)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhC
Confidence            35999999999999999999975

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

Probab=95.88  E-value=0.0094  Score=59.69  Aligned_cols=44  Identities=23%  Similarity=0.420  Sum_probs=34.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .-++||++|++++++.|.....    +-  -.++|.+|+|||+++.-+..
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~K----NN--PvLiGEpGVGKTAIvEGLA~  213 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTK----NN--PVLVGEPGVGKTAIVEGLAQ  213 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCC----CC--CeEecCCCCCHHHHHHHHHH
Confidence            3479999999999999986543    11  14689999999999865544

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.88  E-value=0.006  Score=50.67  Aligned_cols=22  Identities=45%  Similarity=0.613  Sum_probs=19.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|+|.|..|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998764

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.86  E-value=0.056  Score=46.23  Aligned_cols=22  Identities=27%  Similarity=0.449  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+|+.+...
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~   23 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEK   23 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999988753

>PRK06217 hypothetical protein; Validated

Probab=95.86  E-value=0.0067  Score=50.55  Aligned_cols=23  Identities=35%  Similarity=0.407  Sum_probs=20.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhcc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      .|.|.|.+|+||||||+.+....
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999998753

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=95.85  E-value=0.031  Score=52.26  Aligned_cols=51  Identities=24%  Similarity=0.334  Sum_probs=37.5

Q ss_pred             cccccchhHHHHHHHHHhcC--------CCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKD--------DSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~--------~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.++.++.+..++...        ..........|.++|+.|+|||+||+.+...
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~   73 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKL   73 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHH
Confidence            45899999999888777541        1001112367899999999999999999764

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=95.85  E-value=0.0084  Score=46.43  Aligned_cols=27  Identities=33%  Similarity=0.520  Sum_probs=18.2

Q ss_pred             EEEEccCCCchHHHHHHHHhccccccccc
Q 043252          219 IPIIGMGGLGKTTLAQLVYNDKQVEDHFD  247 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~  247 (337)
                      |.|+|.+|+||||+|+.+...  +...|.
T Consensus         2 vLleg~PG~GKT~la~~lA~~--~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARS--LGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHH--TT--EE
T ss_pred             EeeECCCccHHHHHHHHHHHH--cCCcee
Confidence            679999999999999999874  445563

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.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.85  E-value=0.0067  Score=48.64  Aligned_cols=22  Identities=45%  Similarity=0.616  Sum_probs=20.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|.|++|+||||+|+.+.+.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~   23 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEH   23 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHH
Confidence            7899999999999999999875

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=95.84  E-value=0.0085  Score=52.12  Aligned_cols=27  Identities=33%  Similarity=0.449  Sum_probs=23.4

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      ++..+|.++||+|+||||..|.++...
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~hl   43 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSHL   43 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHHH
Confidence            456789999999999999999998763

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.83  E-value=0.033  Score=52.58  Aligned_cols=87  Identities=18%  Similarity=0.273  Sum_probs=49.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC-CCCHHHHHHHHHHHhhCCC------CCCCCCHHH----
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD-DFDVIRLTKSILLSIASDQ------NVDNHDLNK----  284 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~-~~~~~~~~~~il~~~~~~~------~~~~~~~~~----  284 (337)
                      -..++|+|..|+|||||.+.+.+..    +.+..+++.+.. ...+.+++.+....-....      ..+......    
T Consensus       155 GqrigI~G~sG~GKSTLL~~I~~~~----~~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a~  230 (433)
T PRK07594        155 GQRVGIFSAPGVGKSTLLAMLCNAP----DADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRAL  230 (433)
T ss_pred             CCEEEEECCCCCCccHHHHHhcCCC----CCCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHHH
Confidence            3489999999999999999998642    233345555544 3344455555432110000      001111111    


Q ss_pred             -HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 -LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 -~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                       ..-.+.+++  ++++.||++||+.
T Consensus       231 ~~a~tiAEyfrd~G~~VLl~~Dslt  255 (433)
T PRK07594        231 FVATTIAEFFRDNGKRVVLLADSLT  255 (433)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCHH
Confidence             122344444  5899999999993

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.83  E-value=0.0096  Score=50.31  Aligned_cols=25  Identities=28%  Similarity=0.323  Sum_probs=22.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|+|++|+||||||+.+...
T Consensus        23 ~~~~i~i~G~~GsGKSTla~~l~~~   47 (198)
T PRK03846         23 KGVVLWFTGLSGSGKSTVAGALEEA   47 (198)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999999763

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=95.83  E-value=0.066  Score=51.77  Aligned_cols=23  Identities=39%  Similarity=0.712  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|.|||||.+.+...
T Consensus        51 EivgIiGpNGSGKSTLLkiLaGL   73 (549)
T PRK13545         51 EIVGIIGLNGSGKSTLSNLIAGV   73 (549)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            49999999999999999999864

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=95.82  E-value=0.079  Score=45.57  Aligned_cols=23  Identities=22%  Similarity=-0.018  Sum_probs=20.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++.|.|+.|.||||+.+.+..
T Consensus        31 g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            35889999999999999998876

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

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=95.81  E-value=0.097  Score=51.32  Aligned_cols=23  Identities=30%  Similarity=0.538  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.++..
T Consensus        28 e~~~liG~NGsGKSTLl~~l~Gl   50 (530)
T PRK15064         28 NRYGLIGANGCGKSTFMKILGGD   50 (530)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999864

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=95.81  E-value=0.066  Score=53.02  Aligned_cols=23  Identities=35%  Similarity=0.504  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -..++|+|+.|.|||||++.+..
T Consensus       366 G~~~aivG~sGsGKSTL~~ll~g  388 (574)
T PRK11160        366 GEKVALLGRTGCGKSTLLQLLTR  388 (574)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999975

>PRK13949 shikimate kinase; Provisional

Probab=95.79  E-value=0.0076  Score=49.58  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=19.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|++|+||||+++.+...
T Consensus         3 ~I~liG~~GsGKstl~~~La~~   24 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARE   24 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998864

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=95.79  E-value=0.037  Score=48.90  Aligned_cols=90  Identities=20%  Similarity=0.248  Sum_probs=54.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccc--cccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCHH----
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQV--EDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDLN----  283 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~~----  283 (337)
                      .-++|.|-.|+|||+|+..+.++...  +.+-+.++++-+.+.. +..+++.++...-......      +.....    
T Consensus        70 QR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a  149 (276)
T cd01135          70 QKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIIT  149 (276)
T ss_pred             CEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHH
Confidence            37899999999999999888765321  1234667888887654 4456666665432111100      111111    


Q ss_pred             -HHHHHHHHHc---CCCeEEEEEeCCC
Q 043252          284 -KLQEELKKQL---FGKKFLLVLDDVW  306 (337)
Q Consensus       284 -~~~~~l~~~L---~~kr~LlVlDdv~  306 (337)
                       ...-.+.+++   .+++.|+++||+.
T Consensus       150 ~~~a~aiAEyfrd~~g~~VLl~~D~lt  176 (276)
T cd01135         150 PRMALTTAEYLAYEKGKHVLVILTDMT  176 (276)
T ss_pred             HHHHHHHHHHHHhccCCeEEEEEcChh
Confidence             1223344554   3789999999994

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.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.78  E-value=0.0081  Score=50.20  Aligned_cols=23  Identities=26%  Similarity=0.413  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|+|+.|+|||||++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            37899999999999999999764

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

Probab=95.78  E-value=0.032  Score=45.79  Aligned_cols=79  Identities=14%  Similarity=0.142  Sum_probs=44.1

Q ss_pred             EEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCC--C
Q 043252          219 IPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFG--K  296 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~--k  296 (337)
                      +.|.|..|+|||++|.++...     .....+++.-...++.+ +...|...... .+ ......+....+.+.+..  +
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d~e-m~~rI~~H~~~-R~-~~w~t~E~~~~l~~~l~~~~~   73 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE-----LGGPVTYIATAEAFDDE-MAERIARHRKR-RP-AHWRTIETPRDLVSALKELDP   73 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCCHH-HHHHHHHHHHh-CC-CCceEeecHHHHHHHHHhcCC
Confidence            678999999999999888643     22356777777777653 33333332211 12 222222222233333311  2


Q ss_pred             eEEEEEeCC
Q 043252          297 KFLLVLDDV  305 (337)
Q Consensus       297 r~LlVlDdv  305 (337)
                      .-.|++|.+
T Consensus        74 ~~~VLIDcl   82 (169)
T cd00544          74 GDVVLIDCL   82 (169)
T ss_pred             CCEEEEEcH
Confidence            337999998

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.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=95.77  E-value=0.044  Score=45.73  Aligned_cols=21  Identities=33%  Similarity=0.207  Sum_probs=18.6

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++.|.|+.|.||||+.+.+.-
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHH
Confidence            467999999999999999873

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.77  E-value=0.038  Score=48.81  Aligned_cols=87  Identities=20%  Similarity=0.228  Sum_probs=47.7

Q ss_pred             EEEEEEccCCCchHHHH-HHHHhcccccccccce-EEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCHHH---
Q 043252          217 SVIPIIGMGGLGKTTLA-QLVYNDKQVEDHFDLK-AWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDLNK---  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~~-~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~~~---  284 (337)
                      .-++|.|..|+|||+|| ..+.+..    +-+.+ +++-+.+.. .+.++..++...-......      +......   
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~~----~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a  145 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQK----GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLA  145 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHhc----CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHH
Confidence            47899999999999996 6665431    22333 555565543 3455665555432111100      1111111   


Q ss_pred             --HHHHHHHHc--CCCeEEEEEeCCCC
Q 043252          285 --LQEELKKQL--FGKKFLLVLDDVWN  307 (337)
Q Consensus       285 --~~~~l~~~L--~~kr~LlVlDdv~~  307 (337)
                        ..-.+.+++  +++..||++||+..
T Consensus       146 ~~~a~aiAE~fr~~G~~Vlvl~DslTr  172 (274)
T cd01132         146 PYTGCAMGEYFMDNGKHALIIYDDLSK  172 (274)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEcChHH
Confidence              112233333  58999999999943

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.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=95.75  E-value=0.016  Score=46.94  Aligned_cols=36  Identities=25%  Similarity=0.428  Sum_probs=30.0

Q ss_pred             hhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       195 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.+++|.++|..         +++.++|..|+|||||...+..+
T Consensus        23 ~~g~~~l~~~l~~---------k~~vl~G~SGvGKSSLiN~L~~~   58 (161)
T PF03193_consen   23 GEGIEELKELLKG---------KTSVLLGQSGVGKSSLINALLPE   58 (161)
T ss_dssp             TTTHHHHHHHHTT---------SEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcCHHHHHHHhcC---------CEEEEECCCCCCHHHHHHHHHhh
Confidence            3567888888842         59999999999999999999875

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=95.75  E-value=0.013  Score=48.72  Aligned_cols=36  Identities=28%  Similarity=0.372  Sum_probs=27.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEE
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC  253 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  253 (337)
                      .++|.|+|+.|+|||||++.+...  ....|...++.+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~--~~~~~~~~v~~T   37 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQE--FPDKFGRVVSHT   37 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHH--STTTEEEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh--cccccccceeec
Confidence            358999999999999999999874  445564444443

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

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

Probab=95.75  E-value=0.071  Score=51.62  Aligned_cols=97  Identities=19%  Similarity=0.192  Sum_probs=55.8

Q ss_pred             ccccchhHHHHHHHHHhcCCCC-------CCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDSR-------NDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~  262 (337)
                      ++=|-++-+.+|.-.++.+-.+       +-....-|.+||++|+|||-||++|.|.  ....|     ++|-++    +
T Consensus       512 dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANE--ag~NF-----isVKGP----E  580 (802)
T KOG0733|consen  512 DIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANE--AGANF-----ISVKGP----E  580 (802)
T ss_pred             hcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhh--ccCce-----EeecCH----H
Confidence            3444556666666665544321       1223567899999999999999999995  44455     444432    1


Q ss_pred             HHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          263 LTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       263 ~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                      ++    ...      ...+...+..-+.+.=..-.|.|.||.+..
T Consensus       581 Ll----NkY------VGESErAVR~vFqRAR~saPCVIFFDEiDa  615 (802)
T KOG0733|consen  581 LL----NKY------VGESERAVRQVFQRARASAPCVIFFDEIDA  615 (802)
T ss_pred             HH----HHH------hhhHHHHHHHHHHHhhcCCCeEEEecchhh
Confidence            11    111      112222233333334346789999999843

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.74  E-value=0.0088  Score=50.20  Aligned_cols=24  Identities=50%  Similarity=0.523  Sum_probs=21.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|+|-||=|+||||||+.+.+.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~   27 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEH   27 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHH
Confidence            469999999999999999999774

>PRK15453 phosphoribulokinase; Provisional

Probab=95.73  E-value=0.073  Score=47.17  Aligned_cols=78  Identities=12%  Similarity=0.122  Sum_probs=42.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccc-eEEEEeCC--CCCHHHHHHHHH--HHhhCCC---CCCCCCHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDL-KAWTCVSD--DFDVIRLTKSIL--LSIASDQ---NVDNHDLNKLQ  286 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~v~~--~~~~~~~~~~il--~~~~~~~---~~~~~~~~~~~  286 (337)
                      ...+|+|.|.+|+||||+|+.+.....   +... .+.++...  .++....-..+.  +.-+.+.   .+++.+.+.+.
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~if~---~~~~~~~vi~~D~yh~ydr~~~~~~~~~~~r~g~nfdhf~PdAnd~dlL~   80 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEKIFR---RENINAAVVEGDSFHRYTRPEMKAAIAKARAAGRHFSHFGPEANLFDELE   80 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHh---hcCCCeEEEecccccccChhhHhhhhHHHHhcCCCCCCCCCCcccHHHHH
Confidence            356999999999999999998875211   1111 22233222  122222222221  1111111   13667788888


Q ss_pred             HHHHHHcCC
Q 043252          287 EELKKQLFG  295 (337)
Q Consensus       287 ~~l~~~L~~  295 (337)
                      +.++.+..+
T Consensus        81 ~~l~~l~~~   89 (290)
T PRK15453         81 QLFREYGET   89 (290)
T ss_pred             HHHHHHhcC
Confidence            888877653

>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]

Probab=95.73  E-value=0.042  Score=51.11  Aligned_cols=23  Identities=43%  Similarity=0.634  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -+.|+|||+.|+||+||.+.+..
T Consensus       613 dSRiaIVGPNGVGKSTlLkLL~G  635 (807)
T KOG0066|consen  613 DSRIAIVGPNGVGKSTLLKLLIG  635 (807)
T ss_pred             cceeEEECCCCccHHHHHHHHhc
Confidence            35799999999999999999874

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.73  E-value=0.041  Score=52.10  Aligned_cols=88  Identities=17%  Similarity=0.172  Sum_probs=48.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC------CCCCCHH-----H
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN------VDNHDLN-----K  284 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~------~~~~~~~-----~  284 (337)
                      -..++|.|..|+|||||.+.+.......   ..+++..-.....+.++...+...-.....      .+.....     .
T Consensus       163 Gq~~~I~G~sG~GKTtLl~~ia~~~~~d---~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~~  239 (441)
T PRK09099        163 GQRMGIFAPAGVGKSTLMGMFARGTQCD---VNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKAAY  239 (441)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCC---eEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHHH
Confidence            3589999999999999999998643221   123333323333445555555433211110      0111111     1


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ..-.+.+++  +++..||++||+.
T Consensus       240 ~a~tiAEyfrd~G~~VLl~~DslT  263 (441)
T PRK09099        240 VATAIAEYFRDRGLRVLLMMDSLT  263 (441)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchh
Confidence            222344444  5899999999993

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.72  E-value=0.014  Score=49.28  Aligned_cols=23  Identities=39%  Similarity=0.496  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.|++|+|+.|+|||||.+.+..
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~   50 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNG   50 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHC
Confidence            35999999999999999999865

>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=95.71  E-value=0.012  Score=47.55  Aligned_cols=88  Identities=18%  Similarity=0.097  Sum_probs=46.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEE-------eCC--CCCHH---HHHH---HHHHHhhCCCCC---
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC-------VSD--DFDVI---RLTK---SILLSIASDQNV---  277 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-------v~~--~~~~~---~~~~---~il~~~~~~~~~---  277 (337)
                      ..+|-|.|.+|+||||||+.+...  ....-....++.       ++.  .|+..   +-++   .+...+......   
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~--L~~~g~~~~~LDgD~lR~~l~~dl~fs~~dR~e~~rr~~~~A~ll~~~G~ivIv   79 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERR--LFARGIKVYLLDGDNLRHGLNADLGFSKEDREENIRRIAEVAKLLADQGIIVIV   79 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHH--HHHTTS-EEEEEHHHHCTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTTSEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEecCcchhhccCCCCCCCHHHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence            358999999999999999999874  222222233332       111  23322   1122   222222222110   


Q ss_pred             -CCCCHHHHHHHHHHHcCCCeEEEEEeCC
Q 043252          278 -DNHDLNKLQEELKKQLFGKKFLLVLDDV  305 (337)
Q Consensus       278 -~~~~~~~~~~~l~~~L~~kr~LlVlDdv  305 (337)
                       ......+..+..++.+...+|+-|.=+.
T Consensus        80 a~isp~~~~R~~~R~~~~~~~f~eVyv~~  108 (156)
T PF01583_consen   80 AFISPYREDREWARELIPNERFIEVYVDC  108 (156)
T ss_dssp             E----SHHHHHHHHHHHHTTEEEEEEEES
T ss_pred             eeccCchHHHHHHHHhCCcCceEEEEeCC
Confidence             2233456667777777666888777655

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 ....

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.71  E-value=0.008  Score=47.57  Aligned_cols=22  Identities=32%  Similarity=0.596  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|+|+.|+|||||++.+...
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhc
Confidence            3789999999999999999874

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.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.71  E-value=0.008  Score=48.76  Aligned_cols=20  Identities=45%  Similarity=0.748  Sum_probs=18.4

Q ss_pred             EEEEEccCCCchHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .|+|.|.+|+||||+++.+-
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            68999999999999998885

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=95.70  E-value=0.005  Score=52.21  Aligned_cols=22  Identities=23%  Similarity=0.158  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++.|+|+.|.|||||.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            5999999999999999999974

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=95.68  E-value=0.099  Score=53.29  Aligned_cols=102  Identities=15%  Similarity=0.229  Sum_probs=51.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHH--cCC
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQ--LFG  295 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~--L~~  295 (337)
                      +..|.|.+|.||||+++.+..-.+..   ...+....+..     .....+....+   ....++..+...+...  .-.
T Consensus       370 ~~il~G~aGTGKTtll~~i~~~~~~~---g~~V~~~ApTg-----~Aa~~L~~~~g---~~a~Ti~~~~~~~~~~~~~~~  438 (744)
T TIGR02768       370 IAVVVGRAGTGKSTMLKAAREAWEAA---GYRVIGAALSG-----KAAEGLQAESG---IESRTLASLEYAWANGRDLLS  438 (744)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHHHhC---CCeEEEEeCcH-----HHHHHHHhccC---CceeeHHHHHhhhccCcccCC
Confidence            78899999999999999987532111   12333333321     11111211111   1222333322111110  013


Q ss_pred             CeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          296 KKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       296 kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                      +.-|||+|++.-.+......|.....  ..|++||+.
T Consensus       439 ~~~llIvDEasMv~~~~~~~Ll~~~~--~~~~kliLV  473 (744)
T TIGR02768       439 DKDVLVIDEAGMVGSRQMARVLKEAE--EAGAKVVLV  473 (744)
T ss_pred             CCcEEEEECcccCCHHHHHHHHHHHH--hcCCEEEEE
Confidence            45699999997655455555543221  357888764

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.

>PRK13947 shikimate kinase; Provisional

Probab=95.68  E-value=0.0088  Score=49.08  Aligned_cols=22  Identities=41%  Similarity=0.530  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|++|+||||+|+.+.+.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~   24 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATT   24 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH
Confidence            4889999999999999999764

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.68  E-value=0.072  Score=46.13  Aligned_cols=48  Identities=19%  Similarity=0.191  Sum_probs=30.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      -.++.|.|..|+|||||+.++.... .+.. ...++++..  .+..+++..+
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~-~~~g-~~~~yi~~e--~~~~~~~~~~   71 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGF-LQNG-YSVSYVSTQ--LTTTEFIKQM   71 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH-HhCC-CcEEEEeCC--CCHHHHHHHH
Confidence            4599999999999999985544321 1222 234566533  3455666555

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.67  E-value=0.017  Score=45.63  Aligned_cols=70  Identities=21%  Similarity=0.205  Sum_probs=41.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFG  295 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~  295 (337)
                      .+-|.|.|.+|+|||||+..+...      | ..-|+++++-.....+..    ..........-+.+.+.+.|...+.+
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~------~-~~~~i~isd~vkEn~l~~----gyDE~y~c~i~DEdkv~D~Le~~m~~   75 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEK------T-GLEYIEISDLVKENNLYE----GYDEEYKCHILDEDKVLDELEPLMIE   75 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHH------h-CCceEehhhHHhhhcchh----cccccccCccccHHHHHHHHHHHHhc
Confidence            457899999999999999998753      1 134666665332222221    11111111344566777777777654


Q ss_pred             C
Q 043252          296 K  296 (337)
Q Consensus       296 k  296 (337)
                      .
T Consensus        76 G   76 (176)
T KOG3347|consen   76 G   76 (176)
T ss_pred             C
Confidence            3

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.67  E-value=0.048  Score=52.84  Aligned_cols=86  Identities=21%  Similarity=0.262  Sum_probs=47.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEE-eCCCCCHHHHHHHHHHHhhCCC---CCCCCC-----HHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC-VSDDFDVIRLTKSILLSIASDQ---NVDNHD-----LNKLQE  287 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-v~~~~~~~~~~~~il~~~~~~~---~~~~~~-----~~~~~~  287 (337)
                      .-..|+|++|+|||||++.+.+.. ...+-++.++|. +.+-..  ++ .+|-+.+....   ..+...     ...+.-
T Consensus       417 QR~LIvgpp~aGKTtLL~~IAn~i-~~n~~~~~~ivvLIgERpe--EV-tdm~rsVkgeVVasT~D~p~~~~~~~a~~ai  492 (672)
T PRK12678        417 QRGLIVSPPKAGKTTILQNIANAI-TTNNPECHLMVVLVDERPE--EV-TDMQRSVKGEVIASTFDRPPSDHTTVAELAI  492 (672)
T ss_pred             CEeEEeCCCCCCHHHHHHHHHHHH-hhcCCCeEEEEEEEeCchh--hH-HHHHHhccceEEEECCCCCHHHHHHHHHHHH
Confidence            478999999999999999998742 122334444433 333221  11 23333332110   001111     112233


Q ss_pred             HHHHHc--CCCeEEEEEeCCC
Q 043252          288 ELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       288 ~l~~~L--~~kr~LlVlDdv~  306 (337)
                      .+.++|  .++..||++|++.
T Consensus       493 ~~Ae~fre~G~dVlillDSlT  513 (672)
T PRK12678        493 ERAKRLVELGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHHHcCCCEEEEEeCch
Confidence            344444  6899999999994

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=95.66  E-value=0.011  Score=44.34  Aligned_cols=22  Identities=36%  Similarity=0.385  Sum_probs=19.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      -..++|+|+.|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            3589999999999999999976

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.65  E-value=0.039  Score=45.41  Aligned_cols=81  Identities=15%  Similarity=0.177  Sum_probs=43.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--CCCCCHHHHHHHHHHHcCC
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--VDNHDLNKLQEELKKQLFG  295 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--~~~~~~~~~~~~l~~~L~~  295 (337)
                      ++.|.|.+|+||||+|..+......     ..+++.....++. +....|-........  ........+...+.....+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~-----~~~~iat~~~~~~-e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~   76 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGL-----QVLYIATAQPFDD-EMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAP   76 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCC-----CcEeCcCCCCChH-HHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCC
Confidence            6899999999999999988754111     2334444444433 344444433322211  0111122344445443433


Q ss_pred             CeEEEEEeCC
Q 043252          296 KKFLLVLDDV  305 (337)
Q Consensus       296 kr~LlVlDdv  305 (337)
                      .. ++++|.+
T Consensus        77 ~~-~VlID~L   85 (170)
T PRK05800         77 GR-CVLVDCL   85 (170)
T ss_pred             CC-EEEehhH
Confidence            23 7889987

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=95.65  E-value=0.051  Score=54.54  Aligned_cols=130  Identities=15%  Similarity=0.116  Sum_probs=69.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc-ccccccceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|....+.++.+.+..-..    .-.-|.|+|..|+||+++|+.+++... -...|   +.|++.... ...+..++
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~----~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pf---v~vnc~~~~-~~~~~~el  396 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAK----SSFPVLLCGEEGVGKALLAQAIHNESERAAGPY---IAVNCQLYP-DEALAEEF  396 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhC----cCCCEEEECCCCcCHHHHHHHHHHhCCccCCCe---EEEECCCCC-hHHHHHHh
Confidence            3578888888777777654321    122478999999999999999987421 12223   344544432 22222333


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC---C--------CcEEEEEecC
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA---Q--------GSKIIVTTRN  335 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~---~--------gs~iivTTR~  335 (337)
                      +.............      .+.   ....=.|+||++..........|...|..+.   .        ..|||.||..
T Consensus       397 fg~~~~~~~~~~~g------~~~---~a~~GtL~ldei~~l~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~  466 (638)
T PRK11388        397 LGSDRTDSENGRLS------KFE---LAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTA  466 (638)
T ss_pred             cCCCCcCccCCCCC------cee---ECCCCEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccC
Confidence            32221100000000      000   1123358999998776666666766664321   1        2467777653

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=95.65  E-value=0.027  Score=43.51  Aligned_cols=47  Identities=21%  Similarity=0.355  Sum_probs=32.7

Q ss_pred             ccccchhHHHHHHH----HHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVE----LLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~----~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|..-..+.+++    .+..+   ...+.-|++.+|..|+|||.+++.+.+.
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~---~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANP---NPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCC---CCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            46666555554444    44333   3456789999999999999988777654

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PRK14530 adenylate kinase; Provisional

Probab=95.65  E-value=0.0093  Score=51.08  Aligned_cols=22  Identities=27%  Similarity=0.397  Sum_probs=19.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|+|++|+||||+|+.+...
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~   26 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEE   26 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999753

>PTZ00185 ATPase alpha subunit; Provisional

Probab=95.64  E-value=0.083  Score=50.60  Aligned_cols=91  Identities=15%  Similarity=0.198  Sum_probs=50.3

Q ss_pred             EEEEEEccCCCchHHHH-HHHHhcccc-----cccccceEEEEeCCCCCHHHHHHHHHHHhhC-CCCC----CCCC--HH
Q 043252          217 SVIPIIGMGGLGKTTLA-QLVYNDKQV-----EDHFDLKAWTCVSDDFDVIRLTKSILLSIAS-DQNV----DNHD--LN  283 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa-~~v~~~~~~-----~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~-~~~~----~~~~--~~  283 (337)
                      .-++|.|..|+|||+|| -.+.+...+     .++-..++++-+.+..+.-.-+.+.++.-+. ....    ...+  ..
T Consensus       190 QR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~~  269 (574)
T PTZ00185        190 QRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGL  269 (574)
T ss_pred             CEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHHH
Confidence            46899999999999997 555554322     1233467788887765433223333333221 1100    1111  11


Q ss_pred             H-----HHHHHHHHc--CCCeEEEEEeCCCC
Q 043252          284 K-----LQEELKKQL--FGKKFLLVLDDVWN  307 (337)
Q Consensus       284 ~-----~~~~l~~~L--~~kr~LlVlDdv~~  307 (337)
                      .     ..-.+.+++  +++..|||+||+..
T Consensus       270 r~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr  300 (574)
T PTZ00185        270 QYLAPYSGVTMGEYFMNRGRHCLCVYDDLSK  300 (574)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCEEEEEcCchH
Confidence            1     122233333  58999999999944

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.64  E-value=0.087  Score=44.01  Aligned_cols=41  Identities=27%  Similarity=0.284  Sum_probs=26.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccc--------cceEEEEeCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHF--------DLKAWTCVSDD  257 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--------~~~~wv~v~~~  257 (337)
                      .+..|.|++|+||||++..+....-....|        ..++|++...+
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            388999999999999998876543222122        25678876665

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=95.64  E-value=0.0095  Score=47.82  Aligned_cols=21  Identities=48%  Similarity=0.706  Sum_probs=19.0

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|++|+||||+|+.+...
T Consensus         2 i~l~G~~GsGKstla~~la~~   22 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKA   22 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            689999999999999999764

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.

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=95.63  E-value=0.04  Score=52.20  Aligned_cols=86  Identities=19%  Similarity=0.249  Sum_probs=47.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC-CCHHHHHHHHHHHhhCCCCC------CCCCHH-----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD-FDVIRLTKSILLSIASDQNV------DNHDLN-----K  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~-~~~~~~~~~il~~~~~~~~~------~~~~~~-----~  284 (337)
                      ..++|+|..|+|||||++.+....    ..+.++...+... .+..++...+...-......      +.....     .
T Consensus       169 qrigI~G~sG~GKSTLl~~I~g~~----~~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~~  244 (451)
T PRK05688        169 QRLGLFAGTGVGKSVLLGMMTRFT----EADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAAM  244 (451)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC----CCCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHHH
Confidence            479999999999999999987632    1223333333332 23444444444332111100      111111     1


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ....+.+++  ++++.||++||+.
T Consensus       245 ~a~aiAEyfrd~G~~VLl~~DslT  268 (451)
T PRK05688        245 YCTRIAEYFRDKGKNVLLLMDSLT  268 (451)
T ss_pred             HHHHHHHHHHHCCCCEEEEecchh
Confidence            222344444  6899999999993

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.63  E-value=0.012  Score=50.08  Aligned_cols=24  Identities=21%  Similarity=0.288  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....|.|+|++|+|||||++.+..
T Consensus        12 ~~~~ivi~GpsG~GK~tl~~~L~~   35 (206)
T PRK14738         12 KPLLVVISGPSGVGKDAVLARMRE   35 (206)
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHh
Confidence            567899999999999999999865

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=95.62  E-value=0.018  Score=47.36  Aligned_cols=25  Identities=32%  Similarity=0.491  Sum_probs=22.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      ...+.|.|+.|+|||||++.++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3588999999999999999999863

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.61  E-value=0.01  Score=50.87  Aligned_cols=23  Identities=39%  Similarity=0.559  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|..|+|||||++.+.-
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhc
Confidence            34899999999999999999963

>PHA02774 E1; Provisional

Probab=95.61  E-value=0.045  Score=53.13  Aligned_cols=38  Identities=13%  Similarity=0.046  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -+..|..+|..     .++...+.|+|++|.|||.+|..+.+-
T Consensus       420 fl~~lk~~l~~-----~PKknciv~~GPP~TGKS~fa~sL~~~  457 (613)
T PHA02774        420 FLTALKDFLKG-----IPKKNCLVIYGPPDTGKSMFCMSLIKF  457 (613)
T ss_pred             HHHHHHHHHhc-----CCcccEEEEECCCCCCHHHHHHHHHHH
Confidence            44556666632     234569999999999999999998874

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=95.60  E-value=0.043  Score=54.47  Aligned_cols=72  Identities=17%  Similarity=0.131  Sum_probs=45.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc-cccceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED-HFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|.++.++.+...+....        -+.++|++|+||||+++.+.+.  +.. .|...+++.-+ ..+...++..+
T Consensus        18 ~~viG~~~a~~~l~~a~~~~~--------~~ll~G~pG~GKT~la~~la~~--l~~~~~~~~~~~~n~-~~~~~~~~~~v   86 (608)
T TIGR00764        18 DQVIGQEEAVEIIKKAAKQKR--------NVLLIGEPGVGKSMLAKAMAEL--LPDEELEDILVYPNP-EDPNMPRIVEV   86 (608)
T ss_pred             hhccCHHHHHHHHHHHHHcCC--------CEEEECCCCCCHHHHHHHHHHH--cCchhheeEEEEeCC-CCCchHHHHHH
Confidence            568899988888877775322        4559999999999999999864  322 23333333222 12334455555


Q ss_pred             HHHh
Q 043252          268 LLSI  271 (337)
Q Consensus       268 l~~~  271 (337)
                      ..++
T Consensus        87 ~~~~   90 (608)
T TIGR00764        87 PAGE   90 (608)
T ss_pred             HHhh
Confidence            5444

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=95.60  E-value=0.017  Score=53.07  Aligned_cols=47  Identities=19%  Similarity=0.257  Sum_probs=38.0

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +-+.++|.++.+..|...+.++      .+.-|.|.|..|.||||+|+.+++-
T Consensus        15 pf~~ivGq~~~k~al~~~~~~p------~~~~vli~G~~GtGKs~~ar~~~~~   61 (350)
T CHL00081         15 PFTAIVGQEEMKLALILNVIDP------KIGGVMIMGDRGTGKSTTIRALVDL   61 (350)
T ss_pred             CHHHHhChHHHHHHHHHhccCC------CCCeEEEEcCCCCCHHHHHHHHHHH
Confidence            3467999998888888777654      3456779999999999999999764

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.59  E-value=0.012  Score=49.12  Aligned_cols=25  Identities=24%  Similarity=0.355  Sum_probs=22.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|+|++|+|||||++.+...
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3568999999999999999999764

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=95.59  E-value=0.04  Score=53.05  Aligned_cols=47  Identities=15%  Similarity=0.265  Sum_probs=35.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|....+..+...+..-..    .-..+.|.|..|+|||++|+.++..
T Consensus       138 ~~lig~s~~~~~l~~~~~~~~~----~~~~vli~Ge~GtGK~~lA~~ih~~  184 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRLSR----SSISVLINGESGTGKELVAHALHRH  184 (469)
T ss_pred             ccceecCHHHHHHHHHHHHHhc----cCCeEEEEeCCCCcHHHHHHHHHhc
Confidence            3588888887777766643221    2346889999999999999999875

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.59  E-value=0.047  Score=50.42  Aligned_cols=83  Identities=23%  Similarity=0.207  Sum_probs=49.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~~  291 (337)
                      -++|.|-|.+|+|||||.-.+....  ...- .+.||+-.+  +..++- --...++.....    ...+.+.+...+.+
T Consensus        93 Gs~iLIgGdPGIGKSTLLLQva~~l--A~~~-~vLYVsGEE--S~~Qik-lRA~RL~~~~~~l~l~aEt~~e~I~~~l~~  166 (456)
T COG1066          93 GSVILIGGDPGIGKSTLLLQVAARL--AKRG-KVLYVSGEE--SLQQIK-LRADRLGLPTNNLYLLAETNLEDIIAELEQ  166 (456)
T ss_pred             ccEEEEccCCCCCHHHHHHHHHHHH--HhcC-cEEEEeCCc--CHHHHH-HHHHHhCCCccceEEehhcCHHHHHHHHHh
Confidence            4699999999999999998888752  2222 466665444  333321 122334322221    23445555444444


Q ss_pred             HcCCCeEEEEEeCCCC
Q 043252          292 QLFGKKFLLVLDDVWN  307 (337)
Q Consensus       292 ~L~~kr~LlVlDdv~~  307 (337)
                         .+.-|+|+|.+..
T Consensus       167 ---~~p~lvVIDSIQT  179 (456)
T COG1066         167 ---EKPDLVVIDSIQT  179 (456)
T ss_pred             ---cCCCEEEEeccce
Confidence               5677999999944

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=95.57  E-value=0.047  Score=49.97  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.+.|++|.||||+++.+.+.
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~   22 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSAT   22 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999998864

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.

>TIGR01069 mutS2 MutS2 family protein

Probab=95.57  E-value=0.0079  Score=61.19  Aligned_cols=23  Identities=26%  Similarity=0.151  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++.|.|+.|.|||||.+.+..
T Consensus       322 ~~~liItGpNg~GKSTlLK~i~~  344 (771)
T TIGR01069       322 KRVLAITGPNTGGKTVTLKTLGL  344 (771)
T ss_pred             ceEEEEECCCCCCchHHHHHHHH
Confidence            46899999999999999998864

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PRK13975 thymidylate kinase; Provisional

Probab=95.56  E-value=0.012  Score=49.53  Aligned_cols=23  Identities=39%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|.|+.|+||||+++.+...
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999999999875

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.56  E-value=0.051  Score=51.33  Aligned_cols=87  Identities=20%  Similarity=0.282  Sum_probs=50.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC-----CCC-CHHH----
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV-----DNH-DLNK----  284 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~-----~~~-~~~~----  284 (337)
                      -..++|.|..|+|||||.+.+++...    -+.++++-+.+.. .+.+++...+..-......     ... ....    
T Consensus       162 Gq~~~I~G~sG~GKStLl~~Ia~~~~----~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (439)
T PRK06936        162 GQRMGIFAAAGGGKSTLLASLIRSAE----VDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAG  237 (439)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcCCC----CCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHH
Confidence            34899999999999999999987532    2456677666543 3344444433221111100     111 1111    


Q ss_pred             -HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 -LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 -~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                       ..-.+.+++  ++++.||++||+.
T Consensus       238 ~~a~tiAEyfrd~G~~Vll~~DslT  262 (439)
T PRK06936        238 FVATSIAEYFRDQGKRVLLLMDSVT  262 (439)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchh
Confidence             122233444  6999999999994

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=95.55  E-value=0.03  Score=48.68  Aligned_cols=63  Identities=25%  Similarity=0.226  Sum_probs=34.2

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHH
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRL  263 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~  263 (337)
                      +...+++.|....    .+..+|+|.|++|+|||||.-.+......+++=-.++=|.=|.+++--.+
T Consensus        14 ~~~~ll~~l~~~~----g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tGGAl   76 (266)
T PF03308_consen   14 EARELLKRLYPHT----GRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTGGAL   76 (266)
T ss_dssp             HHHHHHHHHGGGT----T-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC---S
T ss_pred             HHHHHHHHHHhhc----CCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCCCcc
Confidence            4456666665432    25679999999999999999877653222222222333444455544333

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.54  E-value=0.0088  Score=48.71  Aligned_cols=21  Identities=29%  Similarity=0.575  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|++|+||||+|+.+...
T Consensus         1 i~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999998764

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=95.54  E-value=0.044  Score=42.37  Aligned_cols=36  Identities=17%  Similarity=-0.086  Sum_probs=24.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEE
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC  253 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  253 (337)
                      .+.|.|+.|.|||+.+..+.............+|++
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~   37 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLA   37 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEc
Confidence            467999999999999977765432222344556654

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=95.53  E-value=0.025  Score=47.68  Aligned_cols=42  Identities=26%  Similarity=0.314  Sum_probs=31.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++++|.+..+..|.-....        ..-+.++|++|+|||+||+.+-.
T Consensus         3 ~dI~GQe~aKrAL~iAAaG--------~h~lLl~GppGtGKTmlA~~l~~   44 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAAG--------GHHLLLIGPPGTGKTMLARRLPS   44 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHHC--------C--EEEES-CCCTHHHHHHHHHH
T ss_pred             hhhcCcHHHHHHHHHHHcC--------CCCeEEECCCCCCHHHHHHHHHH
Confidence            4688988888777666643        24789999999999999999864

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.51  E-value=0.065  Score=51.86  Aligned_cols=87  Identities=17%  Similarity=0.175  Sum_probs=53.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCC--------------CCCCC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQ--------------NVDNH  280 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~--------------~~~~~  280 (337)
                      .-+++.|.|++|+|||||+.++.... .+ .=+.+++++..+  +..++...+ +.++-+.              .+...
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~-~~-~ge~~~y~s~eE--s~~~i~~~~-~~lg~~~~~~~~~g~l~~~~~~p~~~  336 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENA-CA-NKERAILFAYEE--SRAQLLRNA-YSWGIDFEEMEQQGLLKIICAYPESA  336 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH-HH-CCCeEEEEEeeC--CHHHHHHHH-HHcCCChHHHhhCCcEEEEEcccccC
Confidence            45799999999999999997776542 11 223456666554  445555443 3332111              11223


Q ss_pred             CHHHHHHHHHHHcCC-CeEEEEEeCCC
Q 043252          281 DLNKLQEELKKQLFG-KKFLLVLDDVW  306 (337)
Q Consensus       281 ~~~~~~~~l~~~L~~-kr~LlVlDdv~  306 (337)
                      ..+.....+.+.+.. +.-+||+|.+.
T Consensus       337 ~~~~~~~~i~~~i~~~~~~~vvIDsi~  363 (484)
T TIGR02655       337 GLEDHLQIIKSEIADFKPARIAIDSLS  363 (484)
T ss_pred             ChHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            446677777777643 44589999984

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.50  E-value=0.025  Score=47.26  Aligned_cols=36  Identities=28%  Similarity=0.212  Sum_probs=26.5

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +...+........       ..+.|+|+.|+|||||++.+...
T Consensus        13 ~~~~~l~~~v~~g-------~~i~I~G~tGSGKTTll~aL~~~   48 (186)
T cd01130          13 LQAAYLWLAVEAR-------KNILISGGTGSGKTTLLNALLAF   48 (186)
T ss_pred             HHHHHHHHHHhCC-------CEEEEECCCCCCHHHHHHHHHhh
Confidence            4444555554332       48999999999999999998763

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.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=95.49  E-value=0.043  Score=51.80  Aligned_cols=24  Identities=17%  Similarity=0.282  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|+|..|+|||||++.+...
T Consensus       155 GQ~igI~G~sGaGKSTLl~~I~g~  178 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRY  178 (434)
T ss_pred             ceEEEEECCCCCCccHHHHHHhcc
Confidence            458999999999999999998764

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=95.48  E-value=0.012  Score=48.37  Aligned_cols=21  Identities=48%  Similarity=0.602  Sum_probs=18.0

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|.|.+|+|||||++.+++.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~   22 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEE   22 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH
Confidence            689999999999999998764

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.

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=95.47  E-value=0.013  Score=46.13  Aligned_cols=22  Identities=32%  Similarity=0.603  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|..|+|||||.+.++.
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g   33 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAG   33 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTT
T ss_pred             CEEEEEccCCCccccceeeecc
Confidence            4899999999999999999975

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.47  E-value=0.041  Score=47.45  Aligned_cols=87  Identities=23%  Similarity=0.255  Sum_probs=51.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCC--------------CCCC--
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASD--------------QNVD--  278 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~--------------~~~~--  278 (337)
                      .-+++.|.|.+|+|||+|+.++.... .++.=+.++|++...+  ...+...+- +++-+              ....  
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~-~~~~ge~vlyvs~ee~--~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~   93 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNG-LKNFGEKVLYVSFEEP--PEELIENMK-SFGWDLEEYEDSGKLKIIDAFPERI   93 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH-HHHHT--EEEEESSS---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGS
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHh-hhhcCCcEEEEEecCC--HHHHHHHHH-HcCCcHHHHhhcCCEEEEecccccc
Confidence            45699999999999999997654321 2221234677777554  344444432 22110              0001  


Q ss_pred             ---CCCHHHHHHHHHHHcCC-CeEEEEEeCC
Q 043252          279 ---NHDLNKLQEELKKQLFG-KKFLLVLDDV  305 (337)
Q Consensus       279 ---~~~~~~~~~~l~~~L~~-kr~LlVlDdv  305 (337)
                         ..+.+.+...+.+.++. +...+|+|.+
T Consensus        94 ~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsl  124 (226)
T PF06745_consen   94 GWSPNDLEELLSKIREAIEELKPDRVVIDSL  124 (226)
T ss_dssp             T-TSCCHHHHHHHHHHHHHHHTSSEEEEETH
T ss_pred             cccccCHHHHHHHHHHHHHhcCCCEEEEECH
Confidence               35677777777777643 3469999988

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.47  E-value=0.011  Score=47.54  Aligned_cols=22  Identities=36%  Similarity=0.587  Sum_probs=19.5

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|+|.+|+||||||+.+...
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~   22 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEK   22 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            5789999999999999998764

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.46  E-value=0.03  Score=53.91  Aligned_cols=51  Identities=18%  Similarity=0.193  Sum_probs=33.0

Q ss_pred             cccccchhHHHHHHHHHhc---C-CCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLK---D-DSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~---~-~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.|.+..++.+......   . ..-+-...+-|.++|++|.|||.+|+.+.+.
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e  282 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAND  282 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            4567776666555442211   0 0001234567899999999999999999875

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=95.46  E-value=0.015  Score=46.93  Aligned_cols=24  Identities=33%  Similarity=0.602  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++.|+|.+|+||||+.+.+-..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~   27 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKE   27 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHH
Confidence            579999999999999999877653

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.46  E-value=0.013  Score=50.60  Aligned_cols=22  Identities=36%  Similarity=0.661  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++|+|+.|+|||||.+.+..
T Consensus        30 EfvsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          30 EFVAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999963

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=95.45  E-value=0.062  Score=47.23  Aligned_cols=77  Identities=16%  Similarity=0.110  Sum_probs=40.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC--CCHHHHHHHHHHHhh--CCC---CCCCCCHHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD--FDVIRLTKSILLSIA--SDQ---NVDNHDLNKLQEELK  290 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~--~~~~~~~~~il~~~~--~~~---~~~~~~~~~~~~~l~  290 (337)
                      +|+|.|..|+||||+++.+.......+  .....++...-  ++-...-..+.....  .+.   .+++.+.+.+.+.++
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~~~g--~~v~vI~~D~yyr~~r~~~~~~~~~a~~~~~nfdHf~PeAnd~dlL~~~l~   78 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFAREG--IHPAVVEGDSFHRYERMEMKMAIAEALDAGRNFSHFGPEANLFDLLEELFR   78 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhcC--CceEEEeccccccCCchhHHHHHHHHhhcCCCCCCCCcccccHHHHHHHHH
Confidence            589999999999999998875321111  01223332211  121122212222111  111   136677788888888


Q ss_pred             HHcCCC
Q 043252          291 KQLFGK  296 (337)
Q Consensus       291 ~~L~~k  296 (337)
                      .+.+++
T Consensus        79 ~L~~g~   84 (277)
T cd02029          79 TYGETG   84 (277)
T ss_pred             HHHcCC
Confidence            777655

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=95.45  E-value=0.095  Score=49.59  Aligned_cols=87  Identities=18%  Similarity=0.268  Sum_probs=47.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC-CCCHHHHHHHHHHHhhCCCC-----CCCCC-HH-----
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD-DFDVIRLTKSILLSIASDQN-----VDNHD-LN-----  283 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~-~~~~~~~~~~il~~~~~~~~-----~~~~~-~~-----  283 (337)
                      -..++|.|..|+|||||.+.+.....    .+....+.+.. ..++.++..+..........     ....+ ..     
T Consensus       145 Gq~~~I~G~sG~GKStLl~~I~~~~~----~~~~vi~~iG~~~~ev~~~~~~~~~~~~~~~tvvv~~~s~~p~~~r~~~~  220 (422)
T TIGR02546       145 GQRIGIFAGAGVGKSTLLGMIARGAS----ADVNVIALIGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPSLERLKAA  220 (422)
T ss_pred             CCEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEccCCcCHHHHHHHHhccccccceEEEeccccCCHHHHHHHH
Confidence            34789999999999999999987421    22233333333 33444554444332211110     01111 11     


Q ss_pred             HHHHHHHHHc--CCCeEEEEEeCCC
Q 043252          284 KLQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       284 ~~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ...-.+.+++  ++++.|+++|++.
T Consensus       221 ~~a~~~AE~f~~~g~~Vl~~~Dslt  245 (422)
T TIGR02546       221 YTATAIAEYFRDQGKRVLLMMDSLT  245 (422)
T ss_pred             HHHHHHHHHHHHCCCcEEEEEeCch
Confidence            1222334444  5789999999994

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.45  E-value=0.083  Score=45.59  Aligned_cols=113  Identities=12%  Similarity=0.088  Sum_probs=61.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCC--------C-----------
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASD--------Q-----------  275 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~--------~-----------  275 (337)
                      .-.++.|.|.+|+|||||+..+.... .+ .-+..+|++...+  ...+... ..+++..        .           
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~-~~-~g~~~~~is~e~~--~~~i~~~-~~~~g~~~~~~~~~~~l~i~d~~~~~~   93 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKG-LR-DGDPVIYVTTEES--RESIIRQ-AAQFGMDFEKAIEEGKLVIIDALMKEK   93 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHH-Hh-cCCeEEEEEccCC--HHHHHHH-HHHhCCCHHHHhhcCCEEEEEcccccc
Confidence            45799999999999999998765431 11 2245678876443  3333322 1111110        0           


Q ss_pred             ----CCCCCCHHHHHHHHHHHcCC---CeEEEEEeCCCCC---ChhcHHH----hhccCCCCCCCcEEEEEec
Q 043252          276 ----NVDNHDLNKLQEELKKQLFG---KKFLLVLDDVWNE---NYTDWVH----LSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       276 ----~~~~~~~~~~~~~l~~~L~~---kr~LlVlDdv~~~---~~~~~~~----l~~~l~~~~~gs~iivTTR  334 (337)
                          .....+.+++...+++.++.   +.-++|+|.+..-   .+..-..    +...+.  ..|..+|+|+.
T Consensus        94 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~vvIDsl~~l~~~~~~~~r~~~~~l~~~l~--~~~~tvil~~~  164 (229)
T TIGR03881        94 EDEWSLRELSIEELLNKVIEAKKYLGYGHARLVIDSMSAFWLDKPAMARKYSYYLKRVLN--RWNFTILLTSQ  164 (229)
T ss_pred             ccccccccCCHHHHHHHHHHHHHhhccCceEEEecCchhhhccChHHHHHHHHHHHHHHH--hCCCEEEEEec
Confidence                00123566677777766543   3458899998432   1111111    222222  35778888875

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.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.45  E-value=0.014  Score=49.59  Aligned_cols=27  Identities=30%  Similarity=0.501  Sum_probs=23.5

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++++|+++|+.|+|||||..++...
T Consensus        19 ~~~~~~i~~~G~~gsGKTTli~~l~~~   45 (207)
T TIGR00073        19 KHGLVVLNFMSSPGSGKTTLIEKLIDN   45 (207)
T ss_pred             hcCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            346899999999999999999888764

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.44  E-value=0.027  Score=46.94  Aligned_cols=119  Identities=17%  Similarity=0.079  Sum_probs=59.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceE--EEEeCCCCCHHHHHHHH--HHHh--hCCC-CCC-C-----CCH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKA--WTCVSDDFDVIRLTKSI--LLSI--ASDQ-NVD-N-----HDL  282 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~--wv~v~~~~~~~~~~~~i--l~~~--~~~~-~~~-~-----~~~  282 (337)
                      ...|-|+|..|-||||.|.-+.-.. ...-+.+.+  |+.-.........+..+  +...  +... ... .     ...
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~ra-~g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~  100 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMALRA-VGHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAA  100 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHHHH-HHCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHH
Confidence            3589999999999999996654321 111121111  11111122333333321  0000  0000 000 0     011


Q ss_pred             HHHHHHHHHHcCCCeE-EEEEeCCCCC---ChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          283 NKLQEELKKQLFGKKF-LLVLDDVWNE---NYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       283 ~~~~~~l~~~L~~kr~-LlVlDdv~~~---~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ....+..++.+....| |||||.+-..   ..-+.+++...|...+.+..||+|=|+
T Consensus       101 ~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~  157 (191)
T PRK05986        101 REGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRG  157 (191)
T ss_pred             HHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCC
Confidence            2233445555655555 9999999432   123445666666655667789999875

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.44  E-value=0.015  Score=49.07  Aligned_cols=24  Identities=25%  Similarity=0.411  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|.+|+||||+|+.+...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999874

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=95.44  E-value=0.044  Score=45.25  Aligned_cols=22  Identities=18%  Similarity=0.102  Sum_probs=17.4

Q ss_pred             EEEEEEccCCCchHH-HHHHHHh
Q 043252          217 SVIPIIGMGGLGKTT-LAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTt-La~~v~~  238 (337)
                      ..+.|.|..|.|||+ ++..++.
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~   47 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALE   47 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHH
Confidence            588999999999999 4455554

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=95.44  E-value=0.1  Score=49.53  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|+|..|+|||||++.+...
T Consensus       158 Gq~i~I~G~sG~GKStLl~~I~~~  181 (438)
T PRK07721        158 GQRVGIFAGSGVGKSTLMGMIARN  181 (438)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcc
Confidence            458999999999999999988864

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=95.42  E-value=0.13  Score=52.28  Aligned_cols=23  Identities=39%  Similarity=0.492  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -..++|+|..|.|||||++.+..
T Consensus       491 G~~iaIvG~sGsGKSTLlklL~g  513 (694)
T TIGR03375       491 GEKVAIIGRIGSGKSTLLKLLLG  513 (694)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999964

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.41  E-value=0.061  Score=51.22  Aligned_cols=90  Identities=17%  Similarity=0.223  Sum_probs=52.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhccccccccc--ceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCHH----
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD--LKAWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDLN----  283 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~~----  283 (337)
                      .-++|.|..|+|||||+..+.+.....+.+.  .++++-+.+.. .+.+++.+++..-......      +.....    
T Consensus       142 QR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a  221 (458)
T TIGR01041       142 QKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVT  221 (458)
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHH
Confidence            3789999999999999999887543321121  45666665543 4455666665332111110      111111    


Q ss_pred             -HHHHHHHHHc---CCCeEEEEEeCCC
Q 043252          284 -KLQEELKKQL---FGKKFLLVLDDVW  306 (337)
Q Consensus       284 -~~~~~l~~~L---~~kr~LlVlDdv~  306 (337)
                       ...-.+.+++   ++++.||++||+.
T Consensus       222 ~~~a~tiAEyfr~d~G~~VLli~DslT  248 (458)
T TIGR01041       222 PRMALTAAEYLAFEKDMHVLVILTDMT  248 (458)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcChh
Confidence             1223344555   4789999999993

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.41  E-value=0.014  Score=48.20  Aligned_cols=23  Identities=26%  Similarity=0.407  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|+|+.|+|||||++.+...
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHH
Confidence            46999999999999999999864

>PRK14527 adenylate kinase; Provisional

Probab=95.41  E-value=0.015  Score=48.87  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|+|++|+||||+|+.+...
T Consensus         6 ~~~i~i~G~pGsGKsT~a~~La~~   29 (191)
T PRK14527          6 NKVVIFLGPPGAGKGTQAERLAQE   29 (191)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998754

>PRK13409 putative ATPase RIL; Provisional

Probab=95.40  E-value=0.067  Score=53.02  Aligned_cols=23  Identities=48%  Similarity=0.709  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.+...
T Consensus       366 eiv~l~G~NGsGKSTLlk~L~Gl  388 (590)
T PRK13409        366 EVIGIVGPNGIGKTTFAKLLAGV  388 (590)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999864

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=95.40  E-value=0.079  Score=50.03  Aligned_cols=89  Identities=19%  Similarity=0.176  Sum_probs=50.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC------CCCCC-----HHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN------VDNHD-----LNK  284 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~------~~~~~-----~~~  284 (337)
                      -..++|+|..|+|||||.+.++.....   ....+...-.....+.+++...+..-+....      .+...     ...
T Consensus       156 Gqri~I~G~sG~GKTtLl~~Ia~~~~~---~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~~  232 (432)
T PRK06793        156 GQKIGIFAGSGVGKSTLLGMIAKNAKA---DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAAK  232 (432)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccCCC---CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHHH
Confidence            348899999999999999999875321   1122222222335666666655544221110      01111     112


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVWN  307 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~~  307 (337)
                      ....+.+++  +++..||++||+..
T Consensus       233 ~a~~iAEyfr~~G~~VLlilDslTr  257 (432)
T PRK06793        233 LATSIAEYFRDQGNNVLLMMDSVTR  257 (432)
T ss_pred             HHHHHHHHHHHcCCcEEEEecchHH
Confidence            223344444  58999999999954

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.40  E-value=0.18  Score=44.67  Aligned_cols=23  Identities=35%  Similarity=0.417  Sum_probs=20.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+++++|.+|+||||+++.+..
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~   97 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAW   97 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHH
Confidence            35999999999999999987754

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.38  E-value=0.16  Score=46.33  Aligned_cols=25  Identities=28%  Similarity=0.352  Sum_probs=21.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +..+|+|.|++|+|||||+..+...
T Consensus        55 ~~~~igi~G~~GaGKSTl~~~l~~~   79 (332)
T PRK09435         55 NALRIGITGVPGVGKSTFIEALGMH   79 (332)
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHH
Confidence            5679999999999999999887653

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=95.35  E-value=0.23  Score=41.07  Aligned_cols=22  Identities=36%  Similarity=0.579  Sum_probs=19.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+-|.|+.|+|||||.+.+.-
T Consensus        29 e~~~i~G~NG~GKTtLLRilaG   50 (209)
T COG4133          29 EALQITGPNGAGKTTLLRILAG   50 (209)
T ss_pred             CEEEEECCCCCcHHHHHHHHHc
Confidence            3788999999999999999964

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.34  E-value=0.055  Score=51.24  Aligned_cols=89  Identities=15%  Similarity=0.228  Sum_probs=54.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC------CCCCHH-----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV------DNHDLN-----K  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~------~~~~~~-----~  284 (337)
                      .-++|.|.+|+|||+|+..+..+.. +.+-+.++++-+.+.. .+.+++.++...-......      +.....     .
T Consensus       139 Qr~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~  217 (449)
T TIGR03305       139 GKAGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGH  217 (449)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHH
Confidence            4789999999999999988876532 2234677788776654 3455666655431111100      111111     1


Q ss_pred             HHHHHHHHc---CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL---FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L---~~kr~LlVlDdv~  306 (337)
                      ..-.+.+++   ++++.||++||+.
T Consensus       218 ~a~tiAEyfrd~~G~~VLl~~DslT  242 (449)
T TIGR03305       218 TALTMAEYFRDDEKQDVLLLIDNIF  242 (449)
T ss_pred             HHHHHHHHHHHhcCCceEEEecChH
Confidence            233445555   4789999999993

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.

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

Probab=95.32  E-value=0.035  Score=50.27  Aligned_cols=51  Identities=25%  Similarity=0.206  Sum_probs=37.8

Q ss_pred             cccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+=|-++.+++|.+...-+=.       -+-...+-|.++|++|.|||-||++|.+.
T Consensus       151 ~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~  208 (406)
T COG1222         151 EDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQ  208 (406)
T ss_pred             hhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhc
Confidence            3566788888888776532211       02345678999999999999999999985

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.32  E-value=0.085  Score=50.42  Aligned_cols=84  Identities=18%  Similarity=0.162  Sum_probs=48.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~  290 (337)
                      .-.++.|.|.+|+|||||+..+.....  ..-..++|++..+.  ...+... .+.++.....    ...+.+.+.+.+.
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~~a--~~g~~vlYvs~Ees--~~qi~~r-a~rlg~~~~~l~~~~e~~l~~i~~~i~  153 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAARLA--AAGGKVLYVSGEES--ASQIKLR-AERLGLPSDNLYLLAETNLEAILATIE  153 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEEcccc--HHHHHHH-HHHcCCChhcEEEeCCCCHHHHHHHHH
Confidence            356999999999999999988876421  11234677776543  3333222 3334321110    2234555555443


Q ss_pred             HHcCCCeEEEEEeCCC
Q 043252          291 KQLFGKKFLLVLDDVW  306 (337)
Q Consensus       291 ~~L~~kr~LlVlDdv~  306 (337)
                      +   .+.=+||+|.+.
T Consensus       154 ~---~~~~lVVIDSIq  166 (446)
T PRK11823        154 E---EKPDLVVIDSIQ  166 (446)
T ss_pred             h---hCCCEEEEechh
Confidence            3   244589999984

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=95.31  E-value=0.03  Score=47.82  Aligned_cols=20  Identities=55%  Similarity=0.863  Sum_probs=17.8

Q ss_pred             EEEEEccCCCchHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .|+|+|-||+||||+|..+.
T Consensus         2 kIaI~GKGG~GKTtiaalll   21 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLL   21 (255)
T ss_pred             eEEEecCCCccHHHHHHHHH
Confidence            68999999999999998744

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=95.30  E-value=0.03  Score=54.31  Aligned_cols=59  Identities=19%  Similarity=0.309  Sum_probs=41.7

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEE
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTC  253 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  253 (337)
                      +++--.+-++++..||...-. +....+++.+.|++|+||||.++.+++..    .|+..-|.+
T Consensus        20 eLavhkkKv~eV~~wl~~~~~-~~~~~~iLlLtGP~G~GKtttv~~La~el----g~~v~Ew~n   78 (519)
T PF03215_consen   20 ELAVHKKKVEEVRSWLEEMFS-GSSPKRILLLTGPSGCGKTTTVKVLAKEL----GFEVQEWIN   78 (519)
T ss_pred             HhhccHHHHHHHHHHHHHHhc-cCCCcceEEEECCCCCCHHHHHHHHHHHh----CCeeEEecC
Confidence            344445677888888875332 22335699999999999999999998752    355566754

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=95.27  E-value=0.024  Score=55.45  Aligned_cols=45  Identities=29%  Similarity=0.400  Sum_probs=36.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.+...+....      ..-+.|+|+.|+|||++|+.+++.
T Consensus        65 ~~iiGqs~~i~~l~~al~~~~------~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGPN------PQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCCC------CceEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999988775432      235679999999999999999864

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.

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=95.25  E-value=0.19  Score=50.71  Aligned_cols=22  Identities=36%  Similarity=0.653  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..|+|+|..|+|||||+|.+..
T Consensus       500 e~vaIvG~SGsGKSTL~KLL~g  521 (709)
T COG2274         500 EKVAIVGRSGSGKSTLLKLLLG  521 (709)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999954

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=95.24  E-value=0.016  Score=47.91  Aligned_cols=23  Identities=17%  Similarity=0.325  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|+|+.|.|||||++.++..
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~   26 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAAL   26 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh
Confidence            48999999999999999999864

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=95.23  E-value=0.017  Score=50.49  Aligned_cols=23  Identities=30%  Similarity=0.413  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|+|||||.+.++.
T Consensus        28 G~i~~iiGpNG~GKSTLLk~l~g   50 (258)
T COG1120          28 GEITGILGPNGSGKSTLLKCLAG   50 (258)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            45999999999999999999975

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=95.20  E-value=0.18  Score=46.04  Aligned_cols=48  Identities=17%  Similarity=0.187  Sum_probs=35.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSIL  268 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il  268 (337)
                      ..++|.|..|+|||+|++.+.+..    +-+.++++-+.+.. .+.+++.++-
T Consensus       158 qr~~I~G~~G~GKT~L~~~Iak~~----~~dvvVyv~iGERg~Ev~e~l~ef~  206 (369)
T cd01134         158 GTAAIPGPFGCGKTVIQQSLSKYS----NSDIVIYVGCGERGNEMTEVLEEFP  206 (369)
T ss_pred             CEEEEECCCCCChHHHHHHHHhCC----CCCEEEEEEeCCChHHHHHHHHHHH
Confidence            489999999999999999998752    23467788776643 3455665543

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.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=95.20  E-value=0.086  Score=49.63  Aligned_cols=86  Identities=20%  Similarity=0.254  Sum_probs=46.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCCCC------CCCCCHH-----H
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASDQN------VDNHDLN-----K  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~------~~~~~~~-----~  284 (337)
                      ..++|+|..|+|||||.+.+.+...    .+..+...+.... .+.++...+...-.....      .+.....     .
T Consensus       138 q~~~I~G~sG~GKTtLl~~I~~~~~----~~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~~  213 (411)
T TIGR03496       138 QRMGIFAGSGVGKSTLLGMMARYTE----ADVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAAF  213 (411)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCCC----CCEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHHH
Confidence            4799999999999999998886422    1233334444432 334444444332111100      0111111     1


Q ss_pred             HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          285 LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       285 ~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ..-.+.+++  ++++.||++||+.
T Consensus       214 ~a~tiAEyfr~~G~~Vll~~Dslt  237 (411)
T TIGR03496       214 YATAIAEYFRDQGKDVLLLMDSLT  237 (411)
T ss_pred             HHHHHHHHHHHCCCCEEEEEeChH
Confidence            222233444  5899999999993

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.

>cd04155 Arl3 Arl3 subfamily

Probab=95.20  E-value=0.018  Score=47.03  Aligned_cols=24  Identities=29%  Similarity=0.434  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|++|+|||||.+.+...
T Consensus        14 ~~~v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          14 EPRILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             ccEEEEEccCCCCHHHHHHHHhcC
Confidence            456999999999999999999874

Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.

>PRK11147 ABC transporter ATPase component; Reviewed

Probab=95.20  E-value=0.17  Score=50.70  Aligned_cols=23  Identities=26%  Similarity=0.576  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.+...
T Consensus        30 e~v~LvG~NGsGKSTLLriiaG~   52 (635)
T PRK11147         30 ERVCLVGRNGAGKSTLMKILNGE   52 (635)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCC
Confidence            48999999999999999999864

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=95.20  E-value=0.032  Score=51.12  Aligned_cols=44  Identities=16%  Similarity=0.307  Sum_probs=35.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +.+||.+..+..|.-.+..+.      ..-+.|.|..|.|||||++.+..
T Consensus         4 ~~ivgq~~~~~al~~~~~~~~------~g~vli~G~~G~gKttl~r~~~~   47 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVIDPK------IGGVMVMGDRGTGKSTAVRALAA   47 (337)
T ss_pred             cccccHHHHHHHHHHHhcCCC------CCeEEEEcCCCCCHHHHHHHHHH
Confidence            568999999988877776543      34577999999999999999964

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=95.19  E-value=0.015  Score=49.68  Aligned_cols=23  Identities=43%  Similarity=0.639  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|++|+|||||+..+..+
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~   28 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGD   28 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcC
Confidence            57889999999999999999865

>PLN02348 phosphoribulokinase

Probab=95.19  E-value=0.024  Score=52.53  Aligned_cols=26  Identities=27%  Similarity=0.342  Sum_probs=23.0

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +..-+|+|.|.+|+||||+|+.+.+.
T Consensus        47 ~~p~IIGIaG~SGSGKSTfA~~L~~~   72 (395)
T PLN02348         47 DGTVVIGLAADSGCGKSTFMRRLTSV   72 (395)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999999999864

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=95.18  E-value=0.16  Score=49.82  Aligned_cols=23  Identities=30%  Similarity=0.520  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -..++|+|+.|.|||||++.+..
T Consensus       348 G~~~~ivG~sGsGKSTL~~ll~g  370 (529)
T TIGR02857       348 GERVALVGPSGAGKSTLLNLLLG  370 (529)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999964

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.18  E-value=0.015  Score=47.03  Aligned_cols=22  Identities=36%  Similarity=0.504  Sum_probs=20.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |+.|+|+.|+|||||+..+...
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~   22 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKA   22 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999875

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=95.17  E-value=0.07  Score=53.03  Aligned_cols=23  Identities=35%  Similarity=0.524  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -..++|+|..|.|||||++.+..
T Consensus       361 G~~v~IvG~sGsGKSTLl~lL~g  383 (588)
T PRK13657        361 GQTVAIVGPTGAGKSTLINLLQR  383 (588)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999964

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=95.17  E-value=0.085  Score=50.39  Aligned_cols=116  Identities=21%  Similarity=0.294  Sum_probs=59.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhccc-----cc----cccc-----------ceEEEE--e---CCCCCHHHHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQ-----VE----DHFD-----------LKAWTC--V---SDDFDVIRLTKSILLSI  271 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~-----~~----~~F~-----------~~~wv~--v---~~~~~~~~~~~~il~~~  271 (337)
                      +-|++||+.|+|||||.+.+|-+..     +.    .+|.           ...|..  +   -..-...+..+.++..+
T Consensus       417 srvAlVGPNG~GKsTLlKl~~gdl~p~~G~vs~~~H~~~~~y~Qh~~e~ldl~~s~le~~~~~~~~~~~~e~~r~ilgrf  496 (614)
T KOG0927|consen  417 SRVALVGPNGAGKSTLLKLITGDLQPTIGMVSRHSHNKLPRYNQHLAEQLDLDKSSLEFMMPKFPDEKELEEMRSILGRF  496 (614)
T ss_pred             cceeEecCCCCchhhhHHHHhhccccccccccccccccchhhhhhhHhhcCcchhHHHHHHHhccccchHHHHHHHHHHh
Confidence            4789999999999999999987521     11    1111           111100  0   00012334555666665


Q ss_pred             hCCCCCCCCCHHHH-----HHH-HHHHcCCCeEEEEEeCCCCC-ChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          272 ASDQNVDNHDLNKL-----QEE-LKKQLFGKKFLLVLDDVWNE-NYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       272 ~~~~~~~~~~~~~~-----~~~-l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      +.....+.....++     ..- +....-...-|||||...+. +.+..+.+..++..- .|. ||++|.
T Consensus       497 gLtgd~q~~p~~~LS~Gqr~rVlFa~l~~kqP~lLlLDEPtnhLDi~tid~laeaiNe~-~Gg-vv~vSH  564 (614)
T KOG0927|consen  497 GLTGDAQVVPMSQLSDGQRRRVLFARLAVKQPHLLLLDEPTNHLDIETIDALAEAINEF-PGG-VVLVSH  564 (614)
T ss_pred             CCCccccccchhhcccccchhHHHHHHHhcCCcEEEecCCCcCCCchhHHHHHHHHhcc-CCc-eeeeec
Confidence            54422122222111     111 12222345679999998764 445566666666543 344 555554

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

Probab=95.16  E-value=0.053  Score=51.60  Aligned_cols=75  Identities=15%  Similarity=0.192  Sum_probs=43.5

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHH
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQ  292 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~  292 (337)
                      ...+..+.+.|++|+|||+||..+...    ..|..+=-+   .   ++++.       +..   +......+...+...
T Consensus       535 ~s~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKii---S---pe~mi-------G~s---EsaKc~~i~k~F~DA  594 (744)
T KOG0741|consen  535 RSPLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKII---S---PEDMI-------GLS---ESAKCAHIKKIFEDA  594 (744)
T ss_pred             cCcceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEe---C---hHHcc-------Ccc---HHHHHHHHHHHHHHh
Confidence            345778889999999999999988753    456533222   1   11100       000   111122333444445


Q ss_pred             cCCCeEEEEEeCCCC
Q 043252          293 LFGKKFLLVLDDVWN  307 (337)
Q Consensus       293 L~~kr~LlVlDdv~~  307 (337)
                      -+..--.||+||+..
T Consensus       595 YkS~lsiivvDdiEr  609 (744)
T KOG0741|consen  595 YKSPLSIIVVDDIER  609 (744)
T ss_pred             hcCcceEEEEcchhh
Confidence            556677999999944

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=95.14  E-value=0.028  Score=49.70  Aligned_cols=65  Identities=23%  Similarity=0.217  Sum_probs=41.6

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      .+|+..|...    .++..+|+|.|.+|+|||||.-.+-....-+.+=-.++=|.-|.+++--.++.+=
T Consensus        38 ~~ll~~l~p~----tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiLGDR  102 (323)
T COG1703          38 RELLRALYPR----TGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILGDR  102 (323)
T ss_pred             HHHHHHHhhc----CCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCccccccH
Confidence            4455555433    2357799999999999999997776543333443344555666666655555443

>PRK04182 cytidylate kinase; Provisional

Probab=95.14  E-value=0.019  Score=47.41  Aligned_cols=22  Identities=45%  Similarity=0.637  Sum_probs=20.3

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~   23 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            7899999999999999999864

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=95.13  E-value=0.093  Score=49.84  Aligned_cols=23  Identities=30%  Similarity=0.482  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|+|..|+|||||.+.+...
T Consensus       164 q~~~I~G~sG~GKStLl~~I~~~  186 (440)
T TIGR01026       164 QRIGIFAGSGVGKSTLLGMIARN  186 (440)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47899999999999999998864

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.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=95.11  E-value=0.018  Score=46.40  Aligned_cols=22  Identities=32%  Similarity=0.643  Sum_probs=19.5

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||++.++..
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~   23 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYD   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999988764

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=95.11  E-value=0.18  Score=50.10  Aligned_cols=24  Identities=29%  Similarity=0.376  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|+|+.|.|||||++.+...
T Consensus       376 G~~vaIvG~SGsGKSTL~~lL~g~  399 (588)
T PRK11174        376 GQRIALVGPSGAGKTSLLNALLGF  399 (588)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998653

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=95.10  E-value=0.027  Score=48.21  Aligned_cols=22  Identities=27%  Similarity=0.632  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||++.+..
T Consensus        30 e~~~i~G~nGsGKSTLl~~l~G   51 (216)
T TIGR00960        30 EMVFLVGHSGAGKSTFLKLILG   51 (216)
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999975

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.10  E-value=0.018  Score=48.27  Aligned_cols=22  Identities=41%  Similarity=0.593  Sum_probs=20.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|+|.|+.|+||||+++.+.+.
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~   23 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAER   23 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999874

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK08356 hypothetical protein; Provisional

Probab=95.10  E-value=0.023  Score=47.87  Aligned_cols=21  Identities=29%  Similarity=0.466  Sum_probs=19.2

Q ss_pred             EEEEEEccCCCchHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .+|.|+|++|+||||+|+.+-
T Consensus         6 ~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          6 MIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            579999999999999999983

>PLN02200 adenylate kinase family protein

Probab=95.09  E-value=0.022  Score=49.43  Aligned_cols=24  Identities=21%  Similarity=0.232  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|++|+||||+|+.+...
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~   66 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVET   66 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999988753

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.09  E-value=0.016  Score=47.22  Aligned_cols=21  Identities=38%  Similarity=0.377  Sum_probs=17.1

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |+|.|..|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999763

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

Probab=95.09  E-value=0.062  Score=52.39  Aligned_cols=58  Identities=22%  Similarity=0.177  Sum_probs=39.0

Q ss_pred             cccccccchhHHHHHHHHHhcCCCC-------CCCCcEEEEEEccCCCchHHHHHHHHhcccccccc
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSR-------NDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF  246 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  246 (337)
                      .-+++=|.|+-+.+|.+...-+-..       +-...+-|..+|++|+|||++|+.+.+.  ....|
T Consensus       432 ~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne--~~~nF  496 (693)
T KOG0730|consen  432 SWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANE--AGMNF  496 (693)
T ss_pred             ChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhh--hcCCe
Confidence            4455667777766666554322110       2245678999999999999999999985  34445

>TIGR01287 nifH nitrogenase iron protein

Probab=95.08  E-value=0.016  Score=51.58  Aligned_cols=22  Identities=41%  Similarity=0.614  Sum_probs=18.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +.|+|+|-||+||||++..+..
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~   22 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAA   22 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHH
Confidence            3789999999999999877754

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.

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=95.07  E-value=0.034  Score=42.95  Aligned_cols=24  Identities=33%  Similarity=0.274  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+|.+.|.=|.||||++|.+...
T Consensus        15 g~vi~L~GdLGaGKTtf~r~l~~~   38 (123)
T PF02367_consen   15 GDVILLSGDLGAGKTTFVRGLARA   38 (123)
T ss_dssp             -EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            369999999999999999999864

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.

>TIGR00416 sms DNA repair protein RadA

Probab=95.05  E-value=0.13  Score=49.29  Aligned_cols=85  Identities=14%  Similarity=0.172  Sum_probs=47.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l~  290 (337)
                      .-.++.|.|.+|+|||||+..+..... +. =..++|++..+.  ..++... ...++....    ....+.+.+...+.
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~~a-~~-g~kvlYvs~EEs--~~qi~~r-a~rlg~~~~~l~~~~e~~~~~I~~~i~  167 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQLA-KN-QMKVLYVSGEES--LQQIKMR-AIRLGLPEPNLYVLSETNWEQICANIE  167 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-hc-CCcEEEEECcCC--HHHHHHH-HHHcCCChHHeEEcCCCCHHHHHHHHH
Confidence            456999999999999999988865321 11 124677765443  3333221 222221110    02234555554443


Q ss_pred             HHcCCCeEEEEEeCCCC
Q 043252          291 KQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       291 ~~L~~kr~LlVlDdv~~  307 (337)
                      +   .+.-+||+|.+..
T Consensus       168 ~---~~~~~vVIDSIq~  181 (454)
T TIGR00416       168 E---ENPQACVIDSIQT  181 (454)
T ss_pred             h---cCCcEEEEecchh
Confidence            3   2444899999843

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)).

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=95.04  E-value=0.076  Score=51.73  Aligned_cols=47  Identities=19%  Similarity=0.255  Sum_probs=36.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|....+..+.+.+..-..    .-.-|.|.|..|.||+++|+.+++.
T Consensus       212 ~~iiG~S~~m~~~~~~i~~~A~----~~~pVLI~GE~GTGKe~lA~~IH~~  258 (526)
T TIGR02329       212 DDLLGASAPMEQVRALVRLYAR----SDATVLILGESGTGKELVAQAIHQL  258 (526)
T ss_pred             hheeeCCHHHHHHHHHHHHHhC----CCCcEEEECCCCcCHHHHHHHHHHh
Confidence            3589999888888877753321    2347899999999999999999974

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK13946 shikimate kinase; Provisional

Probab=95.03  E-value=0.019  Score=47.86  Aligned_cols=24  Identities=21%  Similarity=0.383  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.|.++|+.|+||||+++.+.+.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~   33 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATM   33 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            357999999999999999999864

>PRK14529 adenylate kinase; Provisional

Probab=95.03  E-value=0.094  Score=45.07  Aligned_cols=21  Identities=43%  Similarity=0.513  Sum_probs=18.9

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|.|++|+||||+++.+...
T Consensus         3 I~l~G~PGsGK~T~a~~La~~   23 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKK   23 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            788999999999999988764

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.03  E-value=0.066  Score=47.39  Aligned_cols=81  Identities=11%  Similarity=0.156  Sum_probs=42.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      ..+.|.|+.|.||||+++.+.+.  +...-..++.+.-+..+....     ..++..... ...   ...+.++..|+..
T Consensus        81 GlilisG~tGSGKTT~l~all~~--i~~~~~~iitiEdp~E~~~~~-----~~q~~v~~~-~~~---~~~~~l~~~lR~~  149 (264)
T cd01129          81 GIILVTGPTGSGKTTTLYSALSE--LNTPEKNIITVEDPVEYQIPG-----INQVQVNEK-AGL---TFARGLRAILRQD  149 (264)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhh--hCCCCCeEEEECCCceecCCC-----ceEEEeCCc-CCc---CHHHHHHHHhccC
Confidence            48999999999999999987653  211101122221111111110     011111110 111   2455666677666


Q ss_pred             eEEEEEeCCCCC
Q 043252          297 KFLLVLDDVWNE  308 (337)
Q Consensus       297 r~LlVlDdv~~~  308 (337)
                      .=.|+++++.+.
T Consensus       150 PD~i~vgEiR~~  161 (264)
T cd01129         150 PDIIMVGEIRDA  161 (264)
T ss_pred             CCEEEeccCCCH
Confidence            778899999764

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.

>PRK13236 nitrogenase reductase; Reviewed

Probab=95.02  E-value=0.023  Score=51.26  Aligned_cols=25  Identities=36%  Similarity=0.570  Sum_probs=21.4

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHH
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      +++.++|++.|-||+||||++-.+.
T Consensus         3 ~~~~~~~~~~GKGGVGKTt~a~NLA   27 (296)
T PRK13236          3 DENIRQIAFYGKGGIGKSTTSQNTL   27 (296)
T ss_pred             CcCceEEEEECCCcCCHHHHHHHHH
Confidence            4567999999999999999886664

>PRK13948 shikimate kinase; Provisional

Probab=95.01  E-value=0.024  Score=47.19  Aligned_cols=24  Identities=17%  Similarity=0.324  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.++|+.|+||||+++.+...
T Consensus        10 ~~~I~LiG~~GsGKSTvg~~La~~   33 (182)
T PRK13948         10 VTWVALAGFMGTGKSRIGWELSRA   33 (182)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999763

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=95.00  E-value=0.023  Score=43.31  Aligned_cols=21  Identities=33%  Similarity=0.544  Sum_probs=19.4

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |+|+|+.|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999973

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.00  E-value=0.049  Score=46.65  Aligned_cols=52  Identities=17%  Similarity=0.097  Sum_probs=30.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhccc-----ccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQ-----VEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~-----~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      +..|.|++|.||||++..+.....     ....-...+-++...+..+..++..+..
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            789999999999987766554320     1123344555555555566667666666

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.00  E-value=0.025  Score=51.43  Aligned_cols=25  Identities=32%  Similarity=0.421  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...++.++|++|+||||++..+...
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~  137 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHK  137 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4679999999999999999888653

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=94.99  E-value=0.021  Score=48.96  Aligned_cols=23  Identities=30%  Similarity=0.496  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.++.-
T Consensus        31 ~~~~l~G~nGsGKSTLl~~i~Gl   53 (218)
T cd03255          31 EFVAIVGPSGSGKSTLLNILGGL   53 (218)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            48999999999999999999753

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=94.99  E-value=0.021  Score=46.22  Aligned_cols=22  Identities=27%  Similarity=0.579  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||++.+.+.
T Consensus         2 ki~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        2 KLVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999988753

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=94.98  E-value=0.13  Score=48.71  Aligned_cols=24  Identities=25%  Similarity=0.378  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|+|..|+|||||++.+...
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i~~~  180 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMIVKG  180 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhc
Confidence            348999999999999999999864

>PRK14532 adenylate kinase; Provisional

Probab=94.98  E-value=0.02  Score=47.84  Aligned_cols=21  Identities=24%  Similarity=0.343  Sum_probs=18.9

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|.|++|+||||+|+.+...
T Consensus         3 i~~~G~pGsGKsT~a~~la~~   23 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEE   23 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            788999999999999999753

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=94.96  E-value=0.02  Score=47.92  Aligned_cols=21  Identities=33%  Similarity=0.426  Sum_probs=19.1

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|.|++|+||||+|+.+...
T Consensus         2 I~i~G~pGsGKst~a~~La~~   22 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKK   22 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            789999999999999999764

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=94.96  E-value=0.023  Score=46.48  Aligned_cols=22  Identities=41%  Similarity=0.619  Sum_probs=20.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|.|+.|+||||+|+.+.+.
T Consensus         2 iI~i~G~~GSGKstia~~la~~   23 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEK   23 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            7999999999999999999763

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=94.94  E-value=0.26  Score=51.46  Aligned_cols=102  Identities=12%  Similarity=0.207  Sum_probs=50.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHH--HcCC
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKK--QLFG  295 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~--~L~~  295 (337)
                      ++.|.|.+|.||||+.+.+..-.+..   ...+.......     ....-+..   .......++..+...+..  ..-.
T Consensus       364 v~vv~G~AGTGKTT~l~~~~~~~e~~---G~~V~~~ApTG-----kAA~~L~e---~tGi~a~TI~sll~~~~~~~~~l~  432 (988)
T PRK13889        364 LGVVVGYAGTGKSAMLGVAREAWEAA---GYEVRGAALSG-----IAAENLEG---GSGIASRTIASLEHGWGQGRDLLT  432 (988)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEecCcH-----HHHHHHhh---ccCcchhhHHHHHhhhcccccccc
Confidence            66799999999999988765421111   12333333221     11111111   111122222222111100  0112


Q ss_pred             CeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          296 KKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       296 kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                      +.-|||+|++--.+...+..|.....  ..|++||+.
T Consensus       433 ~~~vlIVDEASMv~~~~m~~LL~~a~--~~garvVLV  467 (988)
T PRK13889        433 SRDVLVIDEAGMVGTRQLERVLSHAA--DAGAKVVLV  467 (988)
T ss_pred             cCcEEEEECcccCCHHHHHHHHHhhh--hCCCEEEEE
Confidence            45599999997665555655543322  357888875

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=94.94  E-value=0.032  Score=47.45  Aligned_cols=23  Identities=26%  Similarity=0.508  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.+...
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          27 EIFGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999753

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. 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. 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.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=94.94  E-value=0.13  Score=51.07  Aligned_cols=113  Identities=19%  Similarity=0.146  Sum_probs=57.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcc-cccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCC--CCCHHHHHHHHHHHc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDK-QVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVD--NHDLNKLQEELKKQL  293 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~-~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~--~~~~~~~~~~l~~~L  293 (337)
                      ++..|.|.+|.||||++..+...- +....=...+.+..+..--...+...+-..+..-...+  .........-+.+.|
T Consensus       168 ~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiHrlL  247 (615)
T PRK10875        168 RISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEEASTLHRLL  247 (615)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccchhhhhcCCCchHHHHHHh
Confidence            488999999999999998887532 11111123555555544344444444432221100000  000000111222222


Q ss_pred             C----C--------Ce---EEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          294 F----G--------KK---FLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       294 ~----~--------kr---~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                      .    +        ..   =+||+|+..--+......+...++   +++|+|+.
T Consensus       248 g~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~al~---~~~rlIlv  298 (615)
T PRK10875        248 GAQPGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLIDALP---PHARVIFL  298 (615)
T ss_pred             CcCCCccchhhccccCCCCCeEEEChHhcccHHHHHHHHHhcc---cCCEEEEe
Confidence            1    1        11   289999986655555666666665   46788764

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=94.93  E-value=0.14  Score=45.32  Aligned_cols=94  Identities=20%  Similarity=0.210  Sum_probs=65.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      +...++|..|+|||+-++.+++..      .....+..+..++...+...+........   ..........+...+.+.
T Consensus        95 ~l~~vyg~~g~gKt~a~~~y~~s~------p~~~l~~~~p~~~a~~~i~~i~~~~~~~~---~~~~~d~~~~~~~~l~~~  165 (297)
T COG2842          95 SLVVVYGYAGLGKTQAAKNYAPSN------PNALLIEADPSYTALVLILIICAAAFGAT---DGTINDLTERLMIRLRDT  165 (297)
T ss_pred             ceEEEeccccchhHHHHHhhcccC------ccceeecCChhhHHHHHHHHHHHHHhccc---chhHHHHHHHHHHHHccC
Confidence            388899999999999999998741      22233456666676666666665554432   234455666677777888


Q ss_pred             eEEEEEeCCCCCChhcHHHhhcc
Q 043252          297 KFLLVLDDVWNENYTDWVHLSLP  319 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~l~~~  319 (337)
                      .=+|+.|+........++.++..
T Consensus       166 ~~~iivDEA~~L~~~ale~lr~i  188 (297)
T COG2842         166 VRLIIVDEADRLPYRALEELRRI  188 (297)
T ss_pred             cceeeeehhhccChHHHHHHHHH
Confidence            88999999877666666666543

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=94.93  E-value=0.024  Score=48.24  Aligned_cols=22  Identities=36%  Similarity=0.610  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||++.++.
T Consensus        28 ~~~~l~G~nGsGKSTLl~~l~G   49 (211)
T cd03225          28 EFVLIVGPNGSGKSTLLRLLNG   49 (211)
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            5899999999999999999975

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=94.93  E-value=0.033  Score=47.80  Aligned_cols=23  Identities=26%  Similarity=0.460  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|.|||||.+.+...
T Consensus        27 e~~~i~G~nGsGKSTLl~~i~G~   49 (220)
T cd03265          27 EIFGLLGPNGAGKTTTIKMLTTL   49 (220)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999753

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. 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. 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.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=94.92  E-value=0.041  Score=49.02  Aligned_cols=26  Identities=27%  Similarity=0.240  Sum_probs=23.2

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+..++.|.|.+|+|||||...+.+.
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~  127 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMR  127 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35789999999999999999988874

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.91  E-value=0.018  Score=50.48  Aligned_cols=22  Identities=27%  Similarity=0.578  Sum_probs=19.3

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.++|++|+||||+|+.+...
T Consensus         1 LIvl~G~pGSGKST~a~~La~~   22 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKK   22 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            3789999999999999998764

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.

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=94.91  E-value=0.019  Score=49.39  Aligned_cols=23  Identities=22%  Similarity=0.106  Sum_probs=20.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++.|.|+.|.||||+.+.+.-
T Consensus        30 ~~~~~l~G~n~~GKstll~~i~~   52 (222)
T cd03285          30 SRFLIITGPNMGGKSTYIRQIGV   52 (222)
T ss_pred             CeEEEEECCCCCChHHHHHHHHH
Confidence            46999999999999999988753

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

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=94.91  E-value=0.023  Score=45.06  Aligned_cols=24  Identities=46%  Similarity=0.598  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      +-|.++|..|+|||||++.+...+
T Consensus         2 krimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCCC
Confidence            357899999999999999997653

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=94.90  E-value=0.084  Score=49.98  Aligned_cols=24  Identities=17%  Similarity=0.228  Sum_probs=21.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|+|..|+|||||.+.+...
T Consensus       175 Gqri~I~G~sG~GKTTLL~~Ia~~  198 (455)
T PRK07960        175 GQRMGLFAGSGVGKSVLLGMMARY  198 (455)
T ss_pred             CcEEEEECCCCCCccHHHHHHhCC
Confidence            357999999999999999999864

>PRK06820 type III secretion system ATPase; Validated

Probab=94.90  E-value=0.096  Score=49.59  Aligned_cols=23  Identities=35%  Similarity=0.557  Sum_probs=20.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|+|..|+|||||++.+...
T Consensus       164 qri~I~G~sG~GKStLl~~I~~~  186 (440)
T PRK06820        164 QRIGIFAAAGVGKSTLLGMLCAD  186 (440)
T ss_pred             CEEEEECCCCCChHHHHHHHhcc
Confidence            37899999999999999988864

>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=94.89  E-value=0.058  Score=44.76  Aligned_cols=44  Identities=18%  Similarity=0.203  Sum_probs=28.5

Q ss_pred             EEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHH
Q 043252          219 IPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~  266 (337)
                      +.|.|++|+|||+|+..+.... .+.. ..++|++...  +...+...
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~-~~~g-~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAG-LARG-EPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH-HHCC-CcEEEEECCC--CHHHHHHH
Confidence            6789999999999998775532 1111 3466777654  34444443

A related protein is found in archaea.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=94.88  E-value=0.023  Score=47.52  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||.+.+..
T Consensus        19 e~~~i~G~nGsGKSTLl~~i~G   40 (190)
T TIGR01166        19 EVLALLGANGAGKSTLLLHLNG   40 (190)
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999975

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=94.87  E-value=0.23  Score=49.29  Aligned_cols=23  Identities=39%  Similarity=0.538  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -..++|+|+.|.|||||++.+..
T Consensus       361 G~~~~ivG~sGsGKSTL~~ll~g  383 (585)
T TIGR01192       361 GQTVAIVGPTGAGKTTLINLLQR  383 (585)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcc
Confidence            45899999999999999999864

This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=94.87  E-value=0.023  Score=45.91  Aligned_cols=21  Identities=19%  Similarity=0.412  Sum_probs=19.0

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||||+..+.+.
T Consensus         3 i~~vG~~~vGKTsli~~l~~~   23 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEG   23 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999988764

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>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=94.86  E-value=0.02  Score=49.83  Aligned_cols=20  Identities=35%  Similarity=0.405  Sum_probs=17.1

Q ss_pred             EEccCCCchHHHHHHHHhcc
Q 043252          221 IIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       221 I~G~gGiGKTtLa~~v~~~~  240 (337)
                      |+|++|+||||+++.+.+..
T Consensus         1 ViGpaGSGKTT~~~~~~~~~   20 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWL   20 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH
Confidence            68999999999999998753

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=94.86  E-value=0.028  Score=45.69  Aligned_cols=23  Identities=39%  Similarity=0.557  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +++.|+|..|+|||||+..+...
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~   24 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPA   24 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998864

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=94.86  E-value=0.023  Score=46.59  Aligned_cols=22  Identities=27%  Similarity=0.425  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|+|+.|+||||+++.+...
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~   25 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQA   25 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5888999999999999999764

---

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	337
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	1e-63
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-49
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-31
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	2e-11
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	3e-11

>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 =  211 bits (538), Expect = 1e-63
 Identities = 45/284 (15%), Positives = 95/284 (33%), Gaps = 36/284 (12%)

Query: 65  VKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKLI 124
           ++      +++      ++D   ++ F             + ++   +  + + +   LI
Sbjct: 10  LQHREALEKDI--KTSYIMDHMISDGFLTI----------SEEEKVRNEPTQQQRAAMLI 57

Query: 125 PTCCPTFTLQSIQFDYSMM-SKIKKINDRFRDIEEEIGSLKLIKSSAGGSKKARQRRDTT 183
                      + F  +++    K +     D    + S     S +G +   R      
Sbjct: 58  KMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEG 117

Query: 184 SLVEEAKVY-GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV 242
            + +   V+  R+     I + L K           + I GM G GK+ LA     D  +
Sbjct: 118 GVPQRPVVFVTRKKLVNAIQQKLSKLKGEP----GWVTIHGMAGCGKSVLAAEAVRDHSL 173

Query: 243 EDHF--DLKAWTCVSDDFDVIRLTK-----SILLSIASDQNVDNHDLNKLQEELKKQLFG 295
            +        W  V        L K     + L    S       ++ + ++ L+  +  
Sbjct: 174 LEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLR 233

Query: 296 K--KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQD 337
           K  + LL+LDDVW+             +A     +I++TTR++ 
Sbjct: 234 KHPRSLLILDDVWDSWV---------LKAFDSQCQILLTTRDKS 268

>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 =  172 bits (437), Expect = 2e-49
 Identities = 47/302 (15%), Positives = 95/302 (31%), Gaps = 45/302 (14%)

Query: 49  KAVLDDAEEKKTTDDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQ 108
              L  A  +   D   +  L  L+      ED  +     + R + +            
Sbjct: 7   CRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERI------------ 54

Query: 109 PSSSRTSTKSKFRKLIPTCCPTFTLQSIQFDYSMMSKIKKINDRFRDIEEEIGSL--KLI 166
                    + F ++              F+Y+  S +    + + D       L   ++
Sbjct: 55  ---------ANFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVV 105

Query: 167 KSSAGGSKKARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGG 226
            +     +   ++    ++ ++   Y RE     +++ L +     D     + + G  G
Sbjct: 106 IAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEM---CDLDSFFLFLHGRAG 162

Query: 227 LGKTTLAQLVYND--KQVEDHFDLKAWTCVS-----DDFDVIRLTKSILLSIASDQN--- 276
            GK+ +A    +   + +  ++D   W   S       FD+      +L S     N   
Sbjct: 163 SGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPS 222

Query: 277 VDNHDLNKLQEELKKQLF-GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN 335
           V++     L+  +   L      L V DDV  E    W        A     + +VTTR+
Sbjct: 223 VEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRW--------AQELRLRCLVTTRD 274

Query: 336 QD 337
            +
Sbjct: 275 VE 276

>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 =  124 bits (312), Expect = 1e-31
 Identities = 63/304 (20%), Positives = 106/304 (34%), Gaps = 73/304 (24%)

Query: 69  LGELQNLAYDVEDLLDEFQTEAFRRKL-----------LLGNGEPAAAHDQPSSSRTSTK 117
            GE Q   Y  +D+L  F+ +AF               +L   E                
Sbjct: 11  TGEHQ---YQYKDILSVFE-DAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKD-----AV 61

Query: 118 SKFRKLIPTCCPT-------FTLQSIQFDYS-MMSKIKK-INDRFRDIEEEIGSLKLIKS 168
           S   +L  T           F  + ++ +Y  +MS IK             I        
Sbjct: 62  SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI-------- 113

Query: 169 SAGGSKKARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLG 228
                ++ R   D   +  +  V  R     ++ + LL+     +     + I G+ G G
Sbjct: 114 ----EQRDRLYNDN-QVFAKYNVS-RLQPYLKLRQALLELRPAKN-----VLIDGVLGSG 162

Query: 229 KTTLAQLVYNDKQVEDHFDLKA-W----TCVSDDFDVIRLTKSILLSIASD--QNVDN-- 279
           KT +A  V    +V+   D K  W     C S +  V+ + + +L  I  +     D+  
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPE-TVLEMLQKLLYQIDPNWTSRSDHSS 221

Query: 280 ---HDLNKLQEELKKQLFGKKF---LLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTT 333
                ++ +Q EL++ L  K +   LLVL +V N     W   +L         KI++TT
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK--AWNAFNL-------SCKILLTT 272

Query: 334 RNQD 337
           R + 
Sbjct: 273 RFKQ 276

>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 = 41.4 bits (96), Expect = 4e-04
 Identities = 50/344 (14%), Positives = 107/344 (31%), Gaps = 102/344 (29%)

Query: 10  TASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKK---------- 59
           +++++L ++ + +E  RL   +         ++  L+    VL + +  K          
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSK--------PYENCLL----VLLNVQNAKAWNAFNLSCK 267

Query: 60  ---TT-DDSVKLWLGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTS 115
              TT    V  +L         ++       T    + LL                   
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTL-TPDEVKSLL------------------- 307

Query: 116 TKSKFRKLIPTCCPTFTLQSIQFDYSMMSKIKKIN----DRFRDIEEEIGSLKL---IKS 168
              K+    P   P   L +     S++++  +      D ++ +  +    KL   I+S
Sbjct: 308 --LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD----KLTTIIES 361

Query: 169 SAGGSKKARQRRDTTSLV---EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMG 225
           S    + A  R+    L      A +         ++ L+  D  ++D       ++ + 
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAHI----PTI--LLSLIWFDVIKSD------VMVVVN 409

Query: 226 GLGKTTLAQLVYNDKQVEDH---FDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHD- 281
            L K +L +    +  +       +LK       + +   L +SI+      +  D+ D 
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKV----KLE-NEYALHRSIVDHYNIPKTFDSDDL 464

Query: 282 ----------------LNKLQEELKKQLFGKKFLLVLDDVWNEN 309
                           L  ++   +  LF   F   LD  + E 
Sbjct: 465 IPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF---LDFRFLEQ 505

>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 = 64.5 bits (157), Expect = 2e-11
 Identities = 33/156 (21%), Positives = 62/156 (39%), Gaps = 24/156 (15%)

Query: 192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQ-LVYNDKQVEDHF-DLK 249
             R+     I + L K +         + I GM G GK+ LA   V +   +E  F    
Sbjct: 127 VTRKKLVHAIQQKLWKLNGEP----GWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGV 182

Query: 250 AWTCV--SDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFG------KKFLLV 301
            W  +   D   ++   +++ + +  +++        + EE K +L         + LL+
Sbjct: 183 HWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNI-EEAKDRLRVLMLRKHPRSLLI 241

Query: 302 LDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQD 337
           LDDVW+             +A     +I++TTR++ 
Sbjct: 242 LDDVWDPWV---------LKAFDNQCQILLTTRDKS 268

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare} Length = 115

 Score = 58.7 bits (142), Expect = 3e-11
 Identities = 24/115 (20%), Positives = 48/115 (41%), Gaps = 9/115 (7%)

Query: 11  ASVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEKKT--TDDSVKLW 68
           A++  L+ KL       F     +K ++    K+L ++ A L    E      D   KLW
Sbjct: 1   AAISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLW 60

Query: 69  LGELQNLAYDVEDLLDEFQTEAFRRKLLLGNGEPAAAHDQPSSSRTSTKSKFRKL 123
             E++ L+Y +ED++D+F        + +   +    +++       T    +K+
Sbjct: 61  ADEVRELSYVIEDVVDKFL-------VQVDGIKSDDNNNKFKGLMKRTTELLKKV 108

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	337
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.92
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.84
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.82
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.77
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.77
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.34
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.24
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.21
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.2
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.17
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.11
2fna_A	357	Conserved hypothetical protein; structural genomic	99.05
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.01
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.0
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.8
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.79
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.64
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.61
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.45
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.42
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.36
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.34
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.34
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.29
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.28
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.25
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.18
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.16
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.12
3co5_A	143	Putative two-component system transcriptional RES	98.11
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.07
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.05
3bos_A	242	Putative DNA replication factor; P-loop containing	98.01
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.01
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.99
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.98
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.97
3pvs_A	447	Replication-associated recombination protein A; ma	97.95
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.94
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.9
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.86
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.85
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.83
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.82
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.8
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.8
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.79
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.79
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.77
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.73
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.69
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.64
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.64
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.61
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.61
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.58
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.56
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.56
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.5
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.49
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.47
2qgz_A	308	Helicase loader, putative primosome component; str	97.45
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.4
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.38
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.34
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.3
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.27
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.18
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.18
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.16
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.16
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.14
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.14
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.11
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.1
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.1
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.08
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.06
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.03
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.01
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.01
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	97.01
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.99
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.98
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.98
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.95
3io5_A	333	Recombination and repair protein; storage dimer, i	96.95
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.9
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.88
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.87
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.86
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.79
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.78
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.75
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.7
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.67
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.64
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.63
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.56
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.56
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.55
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.54
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.53
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.51
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.48
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.48
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.47
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.43
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	96.42
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.4
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.39
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.38
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.36
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.35
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.34
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.33
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.32
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.3
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.23
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.22
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.18
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.18
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.17
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	96.16
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.16
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.15
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.15
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.15
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.14
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.14
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.13
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.12
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.1
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	96.09
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.08
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.07
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	96.07
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.05
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.05
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.03
2xxa_A	433	Signal recognition particle protein; protein trans	96.01
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.0
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.0
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.99
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.97
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.95
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.93
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.93
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.92
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.91
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.89
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	95.87
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.87
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.86
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.85
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.84
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.84
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.83
1via_A	175	Shikimate kinase; structural genomics, transferase	95.83
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.82
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.81
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.8
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.8
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.79
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.79
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.77
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.77
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.76
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.76
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	95.76
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.76
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.76
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.76
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.75
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.73
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.73
3ice_A	422	Transcription termination factor RHO; transcriptio	95.73
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.73
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.72
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.72
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.7
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.7
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.69
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.66
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.65
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.61
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.61
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.59
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.59
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.57
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.56
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.56
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.56
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.55
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.54
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.53
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.52
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.51
2ged_A	193	SR-beta, signal recognition particle receptor beta	95.47
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.46
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.45
2og2_A	359	Putative signal recognition particle receptor; nuc	95.44
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.43
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.43
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	95.41
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.4
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	95.4
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.4
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.39
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.39
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	95.39
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	95.39
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.39
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	95.38
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.38
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	95.37
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.36
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.35
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	95.35
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	95.29
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.28
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.28
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.26
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	95.25
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.25
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.25
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.24
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.23
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.23
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.22
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.21
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	95.18
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.18
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.17
1b0u_A	262	Histidine permease; ABC transporter, transport pro	95.16
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	95.16
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.16
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.14
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.14
1ji0_A	240	ABC transporter; ATP binding protein, structural g	95.1
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.1
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.08
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.07
1g6h_A	257	High-affinity branched-chain amino acid transport	95.07
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	95.07
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.06
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.06
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.06
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	95.05
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	95.04
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	95.04
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.01
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	95.0
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.98
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.98
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.97
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.95
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.94
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	94.94
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.9
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.88
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.88
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.88
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.86
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	94.86
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.85
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.84
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.83
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	94.82
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.81
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.81
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.8
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	94.8
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	94.78
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.77
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.76
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.76
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	94.74
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.73
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.73
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.72
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.71
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.69
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	94.66
3end_A	307	Light-independent protochlorophyllide reductase ir	94.64
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.61
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.6
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.53
3l0o_A	427	Transcription termination factor RHO; helicase, RH	94.5
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.5
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.5
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.49
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	94.48
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.42
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.42
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	94.4
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.35
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	94.35
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	94.34
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.34
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.33
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.32
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.3
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.28
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	94.26
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	94.26
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	94.24
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.24
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	94.22
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.2
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.19
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	94.18
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	94.17
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	94.14
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	94.13
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.12
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	94.11
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.1
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.06
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	94.06
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	94.06
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	94.03
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.03
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	94.03
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	94.02
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	94.01
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.97
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.96
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.96
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.96
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.96
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	93.96
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.95
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.91
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.91
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	93.9
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.89
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.89
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	93.87
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.87
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.84
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.84
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.83
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	93.82
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.82
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.82
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	93.81
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.79
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.78
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	93.78
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	93.77
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	93.77
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	93.76
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.75
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	93.75
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.75
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	93.75
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.74
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	93.72
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.71
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.7
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.67
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	93.66
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	93.65
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.64
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.64
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.62
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.62
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	93.61
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	93.59
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.58
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	93.58
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	93.58
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	93.56
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	93.56
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	93.54
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.53
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	93.51
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	93.51
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	93.49
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	93.48
2ewv_A	372	Twitching motility protein PILT; pilus retraction	93.47
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	93.47
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	93.46
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.44
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.44
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	93.43
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.43
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	93.43
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	93.43
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	93.43
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	93.4
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.39
3llu_A	196	RAS-related GTP-binding protein C; structural geno	93.38
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	93.38
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	93.36
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	93.35
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	93.35
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	93.32
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	93.3
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	93.29
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	93.29
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	93.28
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	93.27
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	93.26
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	93.26
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	93.25
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	93.24
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	93.23
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	93.22
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	93.22
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	93.21
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	93.21
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	93.19
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	93.18
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	93.15
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	93.14
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	93.13
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	93.13
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	93.12
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.11
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	93.11
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	93.08
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	93.07
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	93.07
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	93.04
1p9r_A	418	General secretion pathway protein E; bacterial typ	93.04
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	93.02
2fh5_B	214	SR-beta, signal recognition particle receptor beta	93.02
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	93.0
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	92.98
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	92.97
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	92.96
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	92.96
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	92.95
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	92.94
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	92.92
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	92.92
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.92
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	92.9
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	92.89
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	92.88
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	92.87
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	92.87
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.87
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	92.87
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	92.86
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	92.85
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	92.84
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	92.82
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	92.8
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	92.74
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	92.73
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	92.72
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	92.72
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	92.71
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	92.7
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	92.68
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	92.66
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	92.65
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	92.64
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	92.63
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	92.62
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	92.6
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	92.6
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	92.59
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	92.55
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	92.55
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	92.53
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	92.52
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	92.5
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	92.49
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	92.46
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	92.43
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	92.42
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	92.39
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	92.38
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	92.35
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	92.31
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	92.29
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	92.28
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	92.25
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	92.24
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	92.24
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	92.23
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	92.23
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	92.2
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	92.06
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	92.05
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	92.01
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	92.0
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.99
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	91.96
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	91.94
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	91.85
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	91.85
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	91.84
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	91.83
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	91.81
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	91.77

>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=99.92  E-value=1.1e-24  Score=211.51  Aligned_cols=134  Identities=25%  Similarity=0.337  Sum_probs=111.3

Q ss_pred             ccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh--cccccccccceEEEEeCCCC--CHHHHHHHH
Q 043252          192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN--DKQVEDHFDLKAWTCVSDDF--DVIRLTKSI  267 (337)
Q Consensus       192 vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~--~~~~~~~F~~~~wv~v~~~~--~~~~~~~~i  267 (337)
                      |||+.++++|.++|....   +...++|+|+||||+||||||+++|+  +.+++.+|++++||++++.+  +...++..|
T Consensus       131 ~GR~~~~~~l~~~L~~~~---~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~i  207 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMC---DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDI  207 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHT---TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhccc---CCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHH
Confidence            699999999999997542   23579999999999999999999998  67899999999999999985  889999999


Q ss_pred             HHHhhCCCC------CCCCCHHHHHHHHHHHcCCC-eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          268 LLSIASDQN------VDNHDLNKLQEELKKQLFGK-KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       268 l~~~~~~~~------~~~~~~~~~~~~l~~~L~~k-r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      +.++.....      ....+...+...+++.|.++ ||||||||||+.....|..        .+||+||||||++
T Consensus       208 l~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~~~~~--------~~gs~ilvTTR~~  275 (549)
T 2a5y_B          208 LLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQ--------ELRLRCLVTTRDV  275 (549)
T ss_dssp             HHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHH--------HTTCEEEEEESBG
T ss_pred             HHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhhcccc--------cCCCEEEEEcCCH
Confidence            999976521      02335677899999999996 9999999999863223432        2699999999985

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.84  E-value=6.3e-21  Score=190.93  Aligned_cols=132  Identities=23%  Similarity=0.217  Sum_probs=105.6

Q ss_pred             cccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccc-eEEEEeCCCCCHHHHHHHHHH
Q 043252          191 VYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDL-KAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       191 ~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~v~~~~~~~~~~~~il~  269 (337)
                      .|||+.++++|.++|...+     ..++|+|+||||+||||||+.+|++.++..+|+. ++|+++++.++...++..|+.
T Consensus       130 ~VGRe~eLeeL~elL~~~d-----~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~  204 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELR-----PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK  204 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCC-----SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhccC-----CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHH
Confidence            4999999999999998532     3679999999999999999999998888999997 899999999998888888877


Q ss_pred             HhhCCC---CCC-------CCCHHHHHHHHHHHc---CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          270 SIASDQ---NVD-------NHDLNKLQEELKKQL---FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       270 ~~~~~~---~~~-------~~~~~~~~~~l~~~L---~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      .+....   ...       ..+.+.+...+++.|   .++||||||||+|+.  +.|..+    +   +||+||||||++
T Consensus       205 lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~--eqLe~f----~---pGSRILVTTRd~  275 (1221)
T 1vt4_I          205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA--KAWNAF----N---LSCKILLTTRFK  275 (1221)
T ss_dssp             HHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCH--HHHHHH----H---SSCCEEEECSCS
T ss_pred             HHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChH--HHHHhh----C---CCeEEEEeccCh
Confidence            543211   101       113455667777766   789999999999984  667654    2   689999999985

>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=99.82  E-value=2.8e-20  Score=196.22  Aligned_cols=138  Identities=22%  Similarity=0.364  Sum_probs=107.5

Q ss_pred             ccccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc-cccc-cceEEEEeCCCCC--HH
Q 043252          186 VEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV-EDHF-DLKAWTCVSDDFD--VI  261 (337)
Q Consensus       186 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F-~~~~wv~v~~~~~--~~  261 (337)
                      .....||||++++++|.++|....    ...++|+|+||||+||||||+++|++.+. ..+| +.++|+++++..+  ..
T Consensus       121 ~~~~~~vgR~~~~~~l~~~l~~~~----~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~  196 (1249)
T 3sfz_A          121 QRPVIFVTRKKLVHAIQQKLWKLN----GEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLL  196 (1249)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHTTT----TSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHH
T ss_pred             CCCceeccHHHHHHHHHHHHhhcc----CCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHH
Confidence            345679999999999999997543    35789999999999999999999987543 4555 5677999998544  34


Q ss_pred             HHHHHHHHHhhCCCC---CCCCCHHHHHHHHHHHcCCC--eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          262 RLTKSILLSIASDQN---VDNHDLNKLQEELKKQLFGK--KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       262 ~~~~~il~~~~~~~~---~~~~~~~~~~~~l~~~L~~k--r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      ..+..++..+.....   ....+.+.+.+.++..|.++  ||||||||+|+.  ..|..+       .+||+||||||++
T Consensus       197 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~--~~~~~~-------~~~~~ilvTtR~~  267 (1249)
T 3sfz_A          197 MKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP--WVLKAF-------DNQCQILLTTRDK  267 (1249)
T ss_dssp             HHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCH--HHHTTT-------CSSCEEEEEESST
T ss_pred             HHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCH--HHHHhh-------cCCCEEEEEcCCH
Confidence            456677777765432   13467888999999999877  999999999975  444432       5689999999986

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=170.94  Aligned_cols=135  Identities=25%  Similarity=0.372  Sum_probs=100.7

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc-ccccc-ceEEEEeCCCCCHHHHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV-EDHFD-LKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F~-~~~wv~v~~~~~~~~~~~  265 (337)
                      ...||||+.+++.|.++|....    ...++|+|+||||+||||||+.+|++.++ ..+|. .++|++++.. +...++.
T Consensus       123 ~~~~vGR~~~l~~L~~~L~~~~----~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~  197 (591)
T 1z6t_A          123 PVVFVTRKKLVNAIQQKLSKLK----GEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLM  197 (591)
T ss_dssp             CSSCCCCHHHHHHHHHHHTTST----TSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHH
T ss_pred             CCeecccHHHHHHHHHHHhccc----CCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHH
Confidence            3569999999999999997532    34689999999999999999999987655 78894 7999999875 3444444


Q ss_pred             HH---HHHhhCCC---CCCCCCHHHHHHHHHHHcCC--CeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          266 SI---LLSIASDQ---NVDNHDLNKLQEELKKQLFG--KKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       266 ~i---l~~~~~~~---~~~~~~~~~~~~~l~~~L~~--kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      .+   +..+....   .....+.+.+...+...+.+  +++||||||+|+.  ..+.    .+   .+||+||||||+.
T Consensus       198 ~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~--~~l~----~l---~~~~~ilvTsR~~  267 (591)
T 1z6t_A          198 KLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS--WVLK----AF---DSQCQILLTTRDK  267 (591)
T ss_dssp             HHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH--HHHH----TT---CSSCEEEEEESCG
T ss_pred             HHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH--HHHH----Hh---cCCCeEEEECCCc
Confidence            44   33443211   11345677888888888865  7899999999874  3332    23   4689999999975

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.77  E-value=4.7e-19  Score=134.97  Aligned_cols=79  Identities=27%  Similarity=0.426  Sum_probs=74.0

Q ss_pred             HHHHHHHHHhhHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHcc--ccCChHHHHHHHHHHHHHHhhhhhhHHHHHH
Q 043252           12 SVELLVNKLASEGIRLFARQGRIKDDLVKWKKKLVTIKAVLDDAEEK--KTTDDSVKLWLGELQNLAYDVEDLLDEFQTE   89 (337)
Q Consensus        12 ~~~~l~~kl~s~~~~~~~~~~~v~~~~~~L~~~L~~i~~~L~~ae~~--~~~~~~~~~Wl~~lr~~ayd~eD~lD~~~~~   89 (337)
                      +++.+++||++.+.+|+.++.||++++++|+++|++|++||.+|+.+  +..++.++.|+++||++|||+|||||+|.++
T Consensus         2 ~v~~ll~KL~~ll~~E~~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD~f~~~   81 (115)
T 3qfl_A            2 AISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDKFLVQ   81 (115)
T ss_dssp             TTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45678899999999999999999999999999999999999999987  5689999999999999999999999999987


Q ss_pred             H
Q 043252           90 A   90 (337)
Q Consensus        90 ~   90 (337)
                      .
T Consensus        82 ~   82 (115)
T 3qfl_A           82 V   82 (115)
T ss_dssp             H
T ss_pred             h
Confidence            6

>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=99.34  E-value=2.2e-12  Score=120.25  Aligned_cols=147  Identities=15%  Similarity=0.142  Sum_probs=96.0

Q ss_pred             cccccchhHHHHHHHHH-hcCCCCCCCCcEEEEE--EccCCCchHHHHHHHHhccccc---cccc-ceEEEEeCCCCCHH
Q 043252          189 AKVYGRETEKKEIVELL-LKDDSRNDGGFSVIPI--IGMGGLGKTTLAQLVYNDKQVE---DHFD-LKAWTCVSDDFDVI  261 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L-~~~~~~~~~~~~vi~I--~G~gGiGKTtLa~~v~~~~~~~---~~F~-~~~wv~v~~~~~~~  261 (337)
                      ..++||+.+++.|..+| .............+.|  +|++|+|||||++.+++.....   ..|. ..+|+.+....+..
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY  101 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHH
Confidence            67999999999999998 4211000012346666  9999999999999999753211   0122 35788877777888


Q ss_pred             HHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcC--CCeEEEEEeCCCCCC------hhcHHHhhccCCCC---C--CCcE
Q 043252          262 RLTKSILLSIASDQNVDNHDLNKLQEELKKQLF--GKKFLLVLDDVWNEN------YTDWVHLSLPFQAG---A--QGSK  328 (337)
Q Consensus       262 ~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~~------~~~~~~l~~~l~~~---~--~gs~  328 (337)
                      .++..++.+++........+...+...+.+.+.  +++++|||||++...      ...+..+...+...   .  ....
T Consensus       102 ~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~  181 (412)
T 1w5s_A          102 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIG  181 (412)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEE
T ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEE
Confidence            999999999865433223445666677777764  779999999997631      23343333333211   1  3345


Q ss_pred             EEEEecC
Q 043252          329 IIVTTRN  335 (337)
Q Consensus       329 iivTTR~  335 (337)
                      ||+||+.
T Consensus       182 lI~~~~~  188 (412)
T 1w5s_A          182 FLLVASD  188 (412)
T ss_dssp             EEEEEEE
T ss_pred             EEEEecc
Confidence            7878864

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.24  E-value=1.4e-11  Score=113.64  Aligned_cols=146  Identities=11%  Similarity=0.047  Sum_probs=97.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccc----cc--ccceEEEEeCCCC-CHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVE----DH--FDLKAWTCVSDDF-DVI  261 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~--F~~~~wv~v~~~~-~~~  261 (337)
                      ..++||+.+++.+..+|.....  ......+.|+|++|+||||||+.+++...-.    ..  ....+|++++... +..
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~--~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   97 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVK--NEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQ   97 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHT--TCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHc--CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHH
Confidence            6799999999999988864211  1234589999999999999999998752111    11  2346788877777 888


Q ss_pred             HHHHHHHHHhhCCCC-CCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhc-HHHhhccCCCCCCCcEEEEEecCC
Q 043252          262 RLTKSILLSIASDQN-VDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTD-WVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       262 ~~~~~il~~~~~~~~-~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~-~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      .++..++..+..... ....+...+...+.+.+..++.+|||||++...... .+.+...|.....+..||+||+..
T Consensus        98 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~  174 (384)
T 2qby_B           98 AVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDI  174 (384)
T ss_dssp             HHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSST
T ss_pred             HHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCC
Confidence            899999988854322 123445667778888887777799999996532111 112011121111567888888753

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.21  E-value=1e-10  Score=108.00  Aligned_cols=146  Identities=14%  Similarity=0.058  Sum_probs=101.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++||+.+++.|..++...........+.+.|+|++|+|||||++.+++....... ...+|++++...+...++..++
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHHHH
Confidence            679999999999999986521001112348999999999999999999875321111 2457788778788889999999


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcC--CCeEEEEEeCCCCCChhcHHHhhccCCCCC----CCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLF--GKKFLLVLDDVWNENYTDWVHLSLPFQAGA----QGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~----~gs~iivTTR~  335 (337)
                      ..++........+...+...+...+.  +++.+||||+++..+......+...+....    .+..||+||+.
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~  168 (389)
T 1fnn_A           96 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHN  168 (389)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESS
T ss_pred             HHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECC
Confidence            98865433233456666666666663  668899999998765555666655553211    35678888764

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.20  E-value=7.2e-11  Score=108.77  Aligned_cols=118  Identities=19%  Similarity=0.228  Sum_probs=87.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccc----ccccceEEEEeCCCCCHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVE----DHFDLKAWTCVSDDFDVIRLT  264 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~v~~~~~~~~~~  264 (337)
                      ..++||+.+++.+..+|...-  .......+.|+|++|+||||||+.+++.....    ..-...+|+++....+...++
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~--~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   96 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPAL--RGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVA   96 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGT--SSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHH--cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHH
Confidence            679999999999999985431  12235688999999999999999998753111    001235788888888889999


Q ss_pred             HHHHHHhhCCCCCCCCCHHHHHHHHHHHc--CCCeEEEEEeCCCCC
Q 043252          265 KSILLSIASDQNVDNHDLNKLQEELKKQL--FGKKFLLVLDDVWNE  308 (337)
Q Consensus       265 ~~il~~~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  308 (337)
                      ..++.+++........+...+...+.+.+  .+++.+||||+++..
T Consensus        97 ~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l  142 (387)
T 2v1u_A           97 SAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFL  142 (387)
T ss_dssp             HHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHH
T ss_pred             HHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhh
Confidence            99999986654433445667777777777  456889999999753

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.17  E-value=5.3e-11  Score=108.13  Aligned_cols=133  Identities=17%  Similarity=0.269  Sum_probs=87.3

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC------CH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF------DV  260 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~------~~  260 (337)
                      ....|+||+.+++.|.+++...        +++.|+|++|+|||||++.+++..      . .+|+++....      +.
T Consensus        10 ~~~~~~gR~~el~~L~~~l~~~--------~~v~i~G~~G~GKT~Ll~~~~~~~------~-~~~~~~~~~~~~~~~~~~   74 (350)
T 2qen_A           10 RREDIFDREEESRKLEESLENY--------PLTLLLGIRRVGKSSLLRAFLNER------P-GILIDCRELYAERGHITR   74 (350)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHHC--------SEEEEECCTTSSHHHHHHHHHHHS------S-EEEEEHHHHHHTTTCBCH
T ss_pred             ChHhcCChHHHHHHHHHHHhcC--------CeEEEECCCcCCHHHHHHHHHHHc------C-cEEEEeecccccccCCCH
Confidence            3467999999999999998642        499999999999999999998752      1 6777765432      55


Q ss_pred             HHHHHHHHHHhhC-----------------CCCCCCCCHHHHHHHHHHHcCC-CeEEEEEeCCCCCCh-------hcHHH
Q 043252          261 IRLTKSILLSIAS-----------------DQNVDNHDLNKLQEELKKQLFG-KKFLLVLDDVWNENY-------TDWVH  315 (337)
Q Consensus       261 ~~~~~~il~~~~~-----------------~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~~~~-------~~~~~  315 (337)
                      ..++..+...+..                 .......+...+...+.+.+.. ++++|||||++....       ..+..
T Consensus        75 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~  154 (350)
T 2qen_A           75 EELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLAL  154 (350)
T ss_dssp             HHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHH
Confidence            6666666665432                 0000124566666667666542 389999999976321       22333


Q ss_pred             hhccCCCCCCCcEEEEEecC
Q 043252          316 LSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       316 l~~~l~~~~~gs~iivTTR~  335 (337)
                      +...+.. ..+.++|+|++.
T Consensus       155 L~~~~~~-~~~~~~il~g~~  173 (350)
T 2qen_A          155 FAYAYDS-LPNLKIILTGSE  173 (350)
T ss_dssp             HHHHHHH-CTTEEEEEEESS
T ss_pred             HHHHHHh-cCCeEEEEECCc
Confidence            3322222 246788888764

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.11  E-value=8.2e-11  Score=108.28  Aligned_cols=144  Identities=19%  Similarity=0.182  Sum_probs=93.7

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccc---cceEEEEeCCCCCHHHHH
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF---DLKAWTCVSDDFDVIRLT  264 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~v~~~~~~~~~~  264 (337)
                      +..++||+.+++.|.+++...-.  ......+.|+|++|+|||||++.+++.  ....+   ...+|+++....+...++
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~--~~~~~~vli~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~i~~~~~~~~~~~~   94 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYR--EEKPNNIFIYGLTGTGKTAVVKFVLSK--LHKKFLGKFKHVYINTRQIDTPYRVL   94 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGG--TCCCCCEEEEECTTSSHHHHHHHHHHH--HHHHTCSSCEEEEEEHHHHCSHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHc--CCCCCeEEEECCCCCCHHHHHHHHHHH--HHHHhcCCceEEEEECCCCCCHHHHH
Confidence            36799999999999999874210  123458899999999999999999875  22222   245778877767777888


Q ss_pred             HHHHHHhhCCCCCCCCCHHHHHHHHHHHcC--CCeEEEEEeCCCCCC----hhcHHHhhccCCC-CCCCcEEEEEecC
Q 043252          265 KSILLSIASDQNVDNHDLNKLQEELKKQLF--GKKFLLVLDDVWNEN----YTDWVHLSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       265 ~~il~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~~----~~~~~~l~~~l~~-~~~gs~iivTTR~  335 (337)
                      ..++..++........+...+...+.+.+.  +++.+||||+++...    ...+..+...+.. ...+..+|+||+.
T Consensus        95 ~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~  172 (386)
T 2qby_A           95 ADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITND  172 (386)
T ss_dssp             HHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESC
T ss_pred             HHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECC
Confidence            888877754432223345666666666663  458999999996521    2233334332211 1234567777764

>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=99.05  E-value=8.5e-10  Score=100.32  Aligned_cols=133  Identities=13%  Similarity=0.152  Sum_probs=82.4

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC-----CCHH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD-----FDVI  261 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~-----~~~~  261 (337)
                      ....|+||+.+++.|.+ +..         +++.|+|++|+|||||++.+++...  .   ..+|+.+...     .+..
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---------~~v~i~G~~G~GKT~L~~~~~~~~~--~---~~~~~~~~~~~~~~~~~~~   75 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---------PITLVLGLRRTGKSSIIKIGINELN--L---PYIYLDLRKFEERNYISYK   75 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---------SEEEEEESTTSSHHHHHHHHHHHHT--C---CEEEEEGGGGTTCSCCCHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC---------CcEEEECCCCCCHHHHHHHHHHhcC--C---CEEEEEchhhccccCCCHH
Confidence            34679999999999999 732         4999999999999999999987532  1   2578887643     3445


Q ss_pred             HHHHHHHHHhhC-------------CC-----CC----------CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCCh---
Q 043252          262 RLTKSILLSIAS-------------DQ-----NV----------DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENY---  310 (337)
Q Consensus       262 ~~~~~il~~~~~-------------~~-----~~----------~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~---  310 (337)
                      .++..+...+..             ..     +.          .......+...+.+... ++++|||||++..+.   
T Consensus        76 ~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~  154 (357)
T 2fna_A           76 DFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRG  154 (357)
T ss_dssp             HHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTT
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCc
Confidence            555554443311             00     00          12345566666655433 499999999965321   


Q ss_pred             hcHHHhhccCCCCCCCcEEEEEecC
Q 043252          311 TDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       311 ~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..|..+...+.+...+.++|+|++.
T Consensus       155 ~~~~~~l~~~~~~~~~~~~i~~g~~  179 (357)
T 2fna_A          155 VNLLPALAYAYDNLKRIKFIMSGSE  179 (357)
T ss_dssp             CCCHHHHHHHHHHCTTEEEEEEESS
T ss_pred             hhHHHHHHHHHHcCCCeEEEEEcCc
Confidence            2222222222222236789999875

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.01  E-value=1.8e-09  Score=92.31  Aligned_cols=134  Identities=16%  Similarity=0.169  Sum_probs=76.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++||+..++.|..++....     ....+.|+|++|+||||||+.+++.......+...      ....... ...+.
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~-----~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~------~~~~~~~-~~~~~   90 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR-----IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITAT------PCGVCDN-CREIE   90 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC-----CCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSS------CCSCSHH-HHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-----CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC------CCcccHH-HHHHh
Confidence            468999999999999997543     23488999999999999999998753211111000      0000000 00000


Q ss_pred             HHhhCC----CCCCCCCHHHHHHHHHHHc-----CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASD----QNVDNHDLNKLQEELKKQL-----FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~----~~~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ......    ..........+. .+.+.+     .+++.+|||||++..+...+..+...+.....+..+|+||+.
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~  165 (250)
T 1njg_A           91 QGRFVDLIEIDAASRTKVEDTR-DLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTD  165 (250)
T ss_dssp             TTCCSSEEEEETTCGGGHHHHH-HHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESC
T ss_pred             ccCCcceEEecCcccccHHHHH-HHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCC
Confidence            000000    000001111121 222221     356899999999876666777777766655567888888864

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=99.00  E-value=3.1e-09  Score=89.66  Aligned_cols=124  Identities=13%  Similarity=0.088  Sum_probs=77.7

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|++..++.+.+++....      ...+.|+|++|+|||+||+.+++... ...+. ..+.+..+.......+.. .
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~------~~~~ll~G~~G~GKT~l~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~   88 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERKN------IPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGIDVVRH-K   88 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC------CCCEEEECSTTSSHHHHHHHHHHHHH-GGGGGGGEEEEETTCTTCHHHHHH-H
T ss_pred             HHHcCcHHHHHHHHHHHhCCC------CCeEEEECCCCCCHHHHHHHHHHHHh-ccccccceEEeccccccChHHHHH-H
Confidence            468999999999999997543      22489999999999999999987421 11121 233344444333322222 2


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +..+.....               ...+++.+|||||++......+..+...+.....+.++|+||+.
T Consensus        89 ~~~~~~~~~---------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~  141 (226)
T 2chg_A           89 IKEFARTAP---------------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNY  141 (226)
T ss_dssp             HHHHHTSCC---------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHhcccC---------------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCC
Confidence            222111100               01257889999999876555666666666554567788888864

>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=98.80  E-value=9.8e-09  Score=92.08  Aligned_cols=124  Identities=15%  Similarity=0.198  Sum_probs=78.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|++..++.|..++....      ...+.|+|++|+||||+|+.+++... ...+. ..++++.+...... .+.++
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~~------~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~~-~i~~~   92 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDGN------MPHMIISGMPGIGKTTSVHCLAHELL-GRSYADGVLELNASDDRGID-VVRNQ   92 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCC------CCCEEEECSTTSSHHHHHHHHHHHHH-GGGHHHHEEEECTTSCCSHH-HHHTH
T ss_pred             HHHHCCHHHHHHHHHHHHcCC------CCeEEEECcCCCCHHHHHHHHHHHhc-CCcccCCEEEecCccccChH-HHHHH
Confidence            568999999999999997543      22389999999999999999987521 11111 23444444332322 22223


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHc-CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQL-FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +..+.....               .+ .+++.+|||||++......+..+...+.....++++|+||..
T Consensus        93 ~~~~~~~~~---------------~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~  146 (323)
T 1sxj_B           93 IKHFAQKKL---------------HLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQ  146 (323)
T ss_dssp             HHHHHHBCC---------------CCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHHhccc---------------cCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCC
Confidence            322221000               11 356889999999876556666676666555567788888854

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.79  E-value=2.3e-08  Score=89.34  Aligned_cols=117  Identities=12%  Similarity=0.033  Sum_probs=80.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc------cccceEEEEeCCCCCHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED------HFDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~------~F~~~~wv~v~~~~~~~~  262 (337)
                      ..+.||++|+++|...|...-  .......+.|+|++|+|||++++.|++......      .| ..+++++....+...
T Consensus        20 ~~L~~Re~E~~~i~~~L~~~i--~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~-~~v~INc~~~~t~~~   96 (318)
T 3te6_A           20 ELLKSQVEDFTRIFLPIYDSL--MSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIF-DYIHIDALELAGMDA   96 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH--HTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCE-EEEEEETTCCC--HH
T ss_pred             cccCCHHHHHHHHHHHHHHHh--cCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCce-EEEEEeccccCCHHH
Confidence            348899999999988876432  123456889999999999999999998632111      12 356777777788889


Q ss_pred             HHHHHHHHhhCCCCCCCCCHHHHHHHHHHH--cCCCeEEEEEeCCCCC
Q 043252          263 LTKSILLSIASDQNVDNHDLNKLQEELKKQ--LFGKKFLLVLDDVWNE  308 (337)
Q Consensus       263 ~~~~il~~~~~~~~~~~~~~~~~~~~l~~~--L~~kr~LlVlDdv~~~  308 (337)
                      ++..|++++.+...........+...+...  -.++.++|+||++..-
T Consensus        97 ~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l  144 (318)
T 3te6_A           97 LYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENL  144 (318)
T ss_dssp             HHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSS
T ss_pred             HHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHh
Confidence            999999999765432233344444444432  2467899999999764

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.64  E-value=4.5e-08  Score=80.41  Aligned_cols=45  Identities=24%  Similarity=0.397  Sum_probs=38.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+++++.+.+++....      ...+.|+|++|+|||+||+.+++.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~------~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQRRT------KNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS------SCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHhcCC------CCceEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999996532      346789999999999999999874

>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=98.61  E-value=4.8e-08  Score=87.70  Aligned_cols=124  Identities=14%  Similarity=0.102  Sum_probs=75.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccc-cceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF-DLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|++..++.|..++....      ...+.|+|++|+||||+|+.+++.... ..+ ...+.+..+..... ..+...
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~~------~~~~ll~G~~G~GKT~la~~l~~~l~~-~~~~~~~~~~~~~~~~~~-~~~~~~   96 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTGS------MPHLLFAGPPGVGKTTAALALARELFG-ENWRHNFLELNASDERGI-NVIREK   96 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC------CCEEEEESCTTSSHHHHHHHHHHHHHG-GGHHHHEEEEETTCHHHH-HTTHHH
T ss_pred             HHhhCCHHHHHHHHHHHHcCC------CCeEEEECcCCCCHHHHHHHHHHHhcC-CcccCceEEeeccccCch-HHHHHH
Confidence            458999999999999987543      234899999999999999999875211 111 12233333321111 111111


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +..+....+               ...+++.+||+||++......+..+...+.....++++|+||..
T Consensus        97 ~~~~~~~~~---------------~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~  149 (327)
T 1iqp_A           97 VKEFARTKP---------------IGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNY  149 (327)
T ss_dssp             HHHHHHSCC---------------GGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHHhhCC---------------cCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCC
Confidence            111110000               11256889999999876666677777666555567788888754

>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=98.45  E-value=5.6e-07  Score=80.31  Aligned_cols=121  Identities=13%  Similarity=0.121  Sum_probs=74.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|++..++.|.+++....      ...+.++|++|+|||++|+.+++... ...+. ..+.++.+....        
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~------~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~--------   81 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERKN------IPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERG--------   81 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTTC------CCCEEEESSSSSSHHHHHHHHHHHHH-TTCHHHHCEEEETTSTTC--------
T ss_pred             HHHhCCHHHHHHHHHHHhCCC------CCeEEEECcCCcCHHHHHHHHHHHhc-CCcccCCeEEEeCccccC--------
Confidence            458999999999988885432      23489999999999999999987421 11111 123333333111        


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHH--c-CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQ--L-FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~--L-~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                                 ..........+...  + .+++.+||||++..........+...+.....++++|+||..
T Consensus        82 -----------~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~  141 (319)
T 2chq_A           82 -----------IDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNY  141 (319)
T ss_dssp             -----------TTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESC
T ss_pred             -----------hHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCC
Confidence                       11111111111111  1 256889999999776556667777777655567788888754

>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=98.42  E-value=9.2e-07  Score=80.84  Aligned_cols=135  Identities=18%  Similarity=0.205  Sum_probs=75.7

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|++..++.|...+....     ....+.|+|++|+||||+|+.+.+.......+..       .++........+.
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~-----~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~-------~~~~~~~~~~~~~   83 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR-----IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA-------TPCGVCDNCREIE   83 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC-----CCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCS-------SCCSSSHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHHhCC-----CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC-------CCCcccHHHHHHh
Confidence            358999999999999997543     2347889999999999999999864321111100       0000000001111


Q ss_pred             HH-------hhCCCCCCCCCHHHHHHHHHHH-cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LS-------IASDQNVDNHDLNKLQEELKKQ-LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~-------~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..       +.............+...+... ..+++.+|||||+...+...++.+...+.....+..+|++|..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~  158 (373)
T 1jr3_A           84 QGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTD  158 (373)
T ss_dssp             TSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESC
T ss_pred             ccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCC
Confidence            00       0000000122333333322211 1356789999999776656677777666554556777777753

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.36  E-value=5.1e-07  Score=73.76  Aligned_cols=45  Identities=24%  Similarity=0.376  Sum_probs=38.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|++.+++.+.+.+....      ...+.|+|++|+|||+||+.+++.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~------~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRRT------KNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS------SCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCCC------CCceEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999996532      346789999999999999999874

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.34  E-value=1.1e-06  Score=71.99  Aligned_cols=121  Identities=19%  Similarity=0.197  Sum_probs=65.2

Q ss_pred             chhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhC
Q 043252          194 RETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIAS  273 (337)
Q Consensus       194 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~  273 (337)
                      .+..++.+.+++.+-..   .....+.|+|++|+|||||++.+++.......+ ..+++      +..++...+......
T Consensus        19 ~~~~~~~~~~~~~~~~~---~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~-~~~~~------~~~~~~~~~~~~~~~   88 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNP---EEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGI-RGYFF------DTKDLIFRLKHLMDE   88 (180)
T ss_dssp             HHHHHHHHHHHHHSCCG---GGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCC-CCCEE------EHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccc---cCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCC-eEEEE------EHHHHHHHHHHHhcC
Confidence            44555566666544321   124589999999999999999998753211122 12333      344555555544433


Q ss_pred             CCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHH--HhhccCCCC-CCCcEEEEEecC
Q 043252          274 DQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWV--HLSLPFQAG-AQGSKIIVTTRN  335 (337)
Q Consensus       274 ~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~--~l~~~l~~~-~~gs~iivTTR~  335 (337)
                      ...   .   .....+.     +.-+|||||++....+.|.  .+...+... ..|..||+||..
T Consensus        89 ~~~---~---~~~~~~~-----~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~  142 (180)
T 3ec2_A           89 GKD---T---KFLKTVL-----NSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNY  142 (180)
T ss_dssp             TCC---S---HHHHHHH-----TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCC
T ss_pred             chH---H---HHHHHhc-----CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCC
Confidence            221   1   2222221     4568999999843223333  233323211 246678888864

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.34  E-value=1.8e-06  Score=68.12  Aligned_cols=113  Identities=15%  Similarity=0.046  Sum_probs=67.6

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc-ccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ-VEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .++|+...+.++.+.+..-..    ...-|.|+|++|+|||++|+.+++... ....|   + ++++...+.        
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~----~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~---v-~~~~~~~~~--------   65 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSE----TDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEF---V-YRELTPDNA--------   65 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTT----CCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCC---E-EEECCTTTS--------
T ss_pred             CceeCCHHHHHHHHHHHHHhC----CCCCEEEECCCCCCHHHHHHHHHHhCCccCCCE---E-EECCCCCcc--------
Confidence            478999999998888754221    122478999999999999999987421 12222   2 555543221        


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                                 .....   .+...   +.-.|+||++..........+...+.......+||.||..
T Consensus        66 -----------~~~~~---~~~~a---~~g~l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           66 -----------PQLND---FIALA---QGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             -----------SCHHH---HHHHH---TTSCEEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             -----------hhhhc---HHHHc---CCcEEEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCc
Confidence                       11111   11111   2347899999877655556666555444445678888753

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.29  E-value=1.2e-06  Score=72.97  Aligned_cols=119  Identities=18%  Similarity=0.187  Sum_probs=62.4

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCC
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQ  275 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~  275 (337)
                      ..++.+..++.....  ......+.|+|++|+|||+||+.+++..  .......+|++++      .+...+...+..  
T Consensus        36 ~~~~~~~~~~~~~~~--~~~~~~~~l~G~~GtGKT~la~~i~~~~--~~~~~~~~~~~~~------~~~~~~~~~~~~--  103 (202)
T 2w58_A           36 KAIRFAERFVAEYEP--GKKMKGLYLHGSFGVGKTYLLAAIANEL--AKRNVSSLIVYVP------ELFRELKHSLQD--  103 (202)
T ss_dssp             HHHHHHHHHHHHCCS--SCCCCEEEEECSTTSSHHHHHHHHHHHH--HTTTCCEEEEEHH------HHHHHHHHC-----
T ss_pred             HHHHHHHHHHHHhhh--ccCCCeEEEECCCCCCHHHHHHHHHHHH--HHcCCeEEEEEhH------HHHHHHHHHhcc--
Confidence            345566666654421  1112588999999999999999999753  2222345566543      344444332211  


Q ss_pred             CCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHH--hhc-cCCCC-CCCcEEEEEecC
Q 043252          276 NVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVH--LSL-PFQAG-AQGSKIIVTTRN  335 (337)
Q Consensus       276 ~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~--l~~-~l~~~-~~gs~iivTTR~  335 (337)
                          .....+...+.+     .-+|||||++......|..  +.. .+... ..+.++|+||..
T Consensus       104 ----~~~~~~~~~~~~-----~~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~  158 (202)
T 2w58_A          104 ----QTMNEKLDYIKK-----VPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNF  158 (202)
T ss_dssp             ----CCCHHHHHHHHH-----SSEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESS
T ss_pred             ----chHHHHHHHhcC-----CCEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Confidence                122333333322     2399999997643333321  221 12111 235578888864

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.28  E-value=1.7e-06  Score=78.38  Aligned_cols=134  Identities=11%  Similarity=0.057  Sum_probs=75.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|++..++.|..++....      ...+.|+|++|+||||+|+.+.+.......+. ....++.+....... +.+.
T Consensus        37 ~~i~g~~~~~~~l~~~l~~~~------~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~  109 (353)
T 1sxj_D           37 DEVTAQDHAVTVLKKTLKSAN------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISI-VREK  109 (353)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTT------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHH-HTTH
T ss_pred             HHhhCCHHHHHHHHHHHhcCC------CCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHH-HHHH
Confidence            468999999999999986442      22389999999999999999987521111121 123344443323322 2222


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      +..+...........     .....-.++.-+|++|++..........+...+.......++|++|.
T Consensus       110 ~~~~~~~~~~~~~~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          110 VKNFARLTVSKPSKH-----DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             HHHHHHSCCCCCCTT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             HHHHhhhcccccchh-----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeC
Confidence            222221111011000     00111124556999999976655555666666554445567777764

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=98.25  E-value=3e-06  Score=76.09  Aligned_cols=119  Identities=22%  Similarity=0.209  Sum_probs=73.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      ..++|.+..++.|..++....     ...++.+.|++|+|||++|+.+.+..  ..   ..+.++.+. .. ...+..++
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~~-----~~~~~L~~G~~G~GKT~la~~la~~l--~~---~~~~i~~~~-~~-~~~i~~~~   93 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKGK-----IPHIILHSPSPGTGKTTVAKALCHDV--NA---DMMFVNGSD-CK-IDFVRGPL   93 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTTC-----CCSEEEECSSTTSSHHHHHHHHHHHT--TE---EEEEEETTT-CC-HHHHHTHH
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-----CCeEEEeeCcCCCCHHHHHHHHHHHh--CC---CEEEEcccc-cC-HHHHHHHH
Confidence            568999999999999997543     23578889999999999999998752  11   233444333 22 22222222


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCC-hhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNEN-YTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~-~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..+.....                ..+++-+|+|||+.... ......|...+.......++|+||..
T Consensus        94 ~~~~~~~~----------------~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~  145 (324)
T 3u61_B           94 TNFASAAS----------------FDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANN  145 (324)
T ss_dssp             HHHHHBCC----------------CSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESS
T ss_pred             HHHHhhcc----------------cCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCC
Confidence            22211110                12467899999997754 44555555555433345678887754

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=98.18  E-value=1.4e-06  Score=78.10  Aligned_cols=50  Identities=26%  Similarity=0.400  Sum_probs=37.7

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|++..++.+..++..... .......+.|+|++|+|||+||+.+++.
T Consensus        12 ~~~ig~~~~~~~l~~~l~~~~~-~~~~~~~vll~G~~GtGKT~la~~i~~~   61 (324)
T 1hqc_A           12 DEYIGQERLKQKLRVYLEAAKA-RKEPLEHLLLFGPPGLGKTTLAHVIAHE   61 (324)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHH-HCSCCCCCEEECCTTCCCHHHHHHHHHH
T ss_pred             HHhhCHHHHHHHHHHHHHHHHc-cCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            5689999999988888753110 0112347889999999999999999874

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.16  E-value=7e-06  Score=72.99  Aligned_cols=128  Identities=17%  Similarity=0.100  Sum_probs=67.9

Q ss_pred             ccccchhHHHHHHHHHhcCC---------CCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCH
Q 043252          190 KVYGRETEKKEIVELLLKDD---------SRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDV  260 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~---------~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~  260 (337)
                      .++|.+..++.|.+++....         .........+.|+|++|+|||+||+.+.+...........-++.++..   
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~---  108 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRD---  108 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGG---
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHH---
Confidence            47888888888776654210         001223457899999999999999988764221111111123333211   


Q ss_pred             HHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCC---------ChhcHHHhhccCCCCCCCcEEEE
Q 043252          261 IRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNE---------NYTDWVHLSLPFQAGAQGSKIIV  331 (337)
Q Consensus       261 ~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---------~~~~~~~l~~~l~~~~~gs~iiv  331 (337)
                               .+....  .......+...+...   +..+|+||++...         .......|...+.....+..||.
T Consensus       109 ---------~l~~~~--~g~~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~  174 (309)
T 3syl_A          109 ---------DLVGQY--IGHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVIL  174 (309)
T ss_dssp             ---------GTCCSS--TTCHHHHHHHHHHHH---TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEE
T ss_pred             ---------Hhhhhc--ccccHHHHHHHHHhc---CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEE
Confidence                     010000  111112222223222   3459999999732         33444556655555455667777


Q ss_pred             Eec
Q 043252          332 TTR  334 (337)
Q Consensus       332 TTR  334 (337)
                      ||.
T Consensus       175 ~~~  177 (309)
T 3syl_A          175 AGY  177 (309)
T ss_dssp             EEC
T ss_pred             eCC
Confidence            774

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.12  E-value=2.6e-06  Score=74.98  Aligned_cols=52  Identities=27%  Similarity=0.205  Sum_probs=38.5

Q ss_pred             ccccccchhHHHHHHHHHhcCCCC-------CCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSR-------NDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|.+..++.|.+.+...-..       +-.....+.|+|++|+|||+||+.+++.
T Consensus        16 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~   74 (285)
T 3h4m_A           16 YEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE   74 (285)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            456899999999998887432000       0012356899999999999999999875

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.11  E-value=1.7e-06  Score=68.14  Aligned_cols=110  Identities=13%  Similarity=0.114  Sum_probs=61.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      -.++|++..+.++.+.+.....    ...-|.|+|..|+|||++|+.+++...        -++.+.-..-....     
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~----~~~~vll~G~~GtGKt~lA~~i~~~~~--------~~~~~~~~~~~~~~-----   66 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAK----RTSPVFLTGEAGSPFETVARYFHKNGT--------PWVSPARVEYLIDM-----   66 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHT----CSSCEEEEEETTCCHHHHHGGGCCTTS--------CEECCSSTTHHHHC-----
T ss_pred             cCceeCCHHHHHHHHHHHHHhC----CCCcEEEECCCCccHHHHHHHHHHhCC--------CeEEechhhCChHh-----
Confidence            3578999888888887753211    112478999999999999999987422        22222211100110     


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCC-CCCcEEEEEec
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAG-AQGSKIIVTTR  334 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~-~~gs~iivTTR  334 (337)
                                       ...+.+..  +.-.|+||++..........+...+... ..+.+||.||.
T Consensus        67 -----------------~~~~~~~a--~~~~l~lDei~~l~~~~q~~Ll~~l~~~~~~~~~iI~~tn  114 (143)
T 3co5_A           67 -----------------PMELLQKA--EGGVLYVGDIAQYSRNIQTGITFIIGKAERCRVRVIASCS  114 (143)
T ss_dssp             -----------------HHHHHHHT--TTSEEEEEECTTCCHHHHHHHHHHHHHHTTTTCEEEEEEE
T ss_pred             -----------------hhhHHHhC--CCCeEEEeChHHCCHHHHHHHHHHHHhCCCCCEEEEEecC
Confidence                             11111111  2347899999876655555555544432 23467887775

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.07  E-value=1e-05  Score=73.38  Aligned_cols=44  Identities=18%  Similarity=0.127  Sum_probs=34.8

Q ss_pred             cccccchhHHHHHHHHH-hcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          189 AKVYGRETEKKEIVELL-LKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L-~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++|.+...+.+..++ ....     ... +.|+|+.|+||||+++.+..
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~~-----~~~-~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPRD-----LPH-LLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTC-----CCC-EEEECSTTSSHHHHHHTHHH
T ss_pred             HHhcCCHHHHHHHHHHHhhCCC-----CCe-EEEECCCCCCHHHHHHHHHH
Confidence            45889998888888877 3222     223 89999999999999998876

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=98.05  E-value=1.1e-05  Score=69.70  Aligned_cols=51  Identities=25%  Similarity=0.240  Sum_probs=35.2

Q ss_pred             cccccchhHHHHHHHHHh---cCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLL---KDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~---~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+..++.|.+++.   .+..   .+......+.|+|++|+|||+||+.+++.
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~   62 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE   62 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            568899888777755542   2211   00123456889999999999999999874

>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=98.01  E-value=1.3e-06  Score=74.41  Aligned_cols=60  Identities=13%  Similarity=0.079  Sum_probs=38.4

Q ss_pred             cccccc---hhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC
Q 043252          189 AKVYGR---ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD  256 (337)
Q Consensus       189 ~~~vGr---~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~  256 (337)
                      ..++|.   +..++.+..++...      ....+.|+|++|+||||||+.+++...  .......|+.++.
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~------~~~~~ll~G~~G~GKT~la~~l~~~~~--~~~~~~~~~~~~~   90 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD------GVQAIYLWGPVKSGRTHLIHAACARAN--ELERRSFYIPLGI   90 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC------SCSEEEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEEEGGG
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC------CCCeEEEECCCCCCHHHHHHHHHHHHH--HcCCeEEEEEHHH
Confidence            346653   35556666666432      235889999999999999999987522  2223456666544

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.01  E-value=1.5e-05  Score=71.99  Aligned_cols=123  Identities=15%  Similarity=0.157  Sum_probs=68.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++|.+..++.|..++....      +..+.++|+.|+||||+|+.+..... ...+. ...-++.+....... .+++
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~------~~~~ll~Gp~G~GKTtla~~la~~l~-~~~~~~~~~~~~~~~~~~~~~-ir~~   96 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGK------LPHLLFYGPPGTGKTSTIVALAREIY-GKNYSNMVLELNASDDRGIDV-VRNQ   96 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC------CCCEEEECSSSSSHHHHHHHHHHHHH-TTSHHHHEEEECTTSCCSHHH-HHTH
T ss_pred             HHhcCcHHHHHHHHHHHhcCC------CceEEEECCCCCCHHHHHHHHHHHHc-CCCccceEEEEcCcccccHHH-HHHH
Confidence            457898888888888886433      22388999999999999999987421 11111 112222222222221 1122


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      +..+.....               .+.+.+-++|+|++........+.|...+......+++|++|.
T Consensus        97 i~~~~~~~~---------------~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n  148 (340)
T 1sxj_C           97 IKDFASTRQ---------------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLAN  148 (340)
T ss_dssp             HHHHHHBCC---------------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             HHHHHhhcc---------------cCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEec
Confidence            222110000               0123467889999866554555666555544344566776653

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.99  E-value=2.2e-05  Score=71.60  Aligned_cols=48  Identities=19%  Similarity=0.304  Sum_probs=36.2

Q ss_pred             ccccccchhHHHH---HHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKE---IVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~---l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|++..++.   +...+.....    ....+.|+|++|+|||+||+.+.+.
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~----~~~~vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKI----AGRAVLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCC----TTCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCC----CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            3569999988766   4555543321    2368999999999999999999875

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.98  E-value=1.7e-05  Score=71.45  Aligned_cols=50  Identities=28%  Similarity=0.404  Sum_probs=38.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|++..++.+..++..... .......+.|+|++|+|||+||+.+.+.
T Consensus        29 ~~iiG~~~~~~~l~~~l~~~~~-~~~~~~~vll~G~~GtGKT~la~~ia~~   78 (338)
T 3pfi_A           29 DGYIGQESIKKNLNVFIAAAKK-RNECLDHILFSGPAGLGKTTLANIISYE   78 (338)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHH-TTSCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHhCChHHHHHHHHHHHHHHHh-cCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            5699999999999888864311 0123456899999999999999999764

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.97  E-value=3.1e-05  Score=65.01  Aligned_cols=87  Identities=21%  Similarity=0.100  Sum_probs=53.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhh-----------CCCCCCCCCHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIA-----------SDQNVDNHDLNK  284 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~-----------~~~~~~~~~~~~  284 (337)
                      -.++.|+|++|+|||||+..+..     ..-..++|+.....++...+.. +...+.           ............
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~-----~~~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL-----LSGKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQRR   93 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH-----HHCSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-----HcCCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHHH
Confidence            35999999999999999999876     1123577887776556655443 332221           111112222234


Q ss_pred             HHHHHHHHcCCCeEEEEEeCCCCC
Q 043252          285 LQEELKKQLFGKKFLLVLDDVWNE  308 (337)
Q Consensus       285 ~~~~l~~~L~~kr~LlVlDdv~~~  308 (337)
                      ....++..+..+.-+||||.+...
T Consensus        94 ~~~~~~~l~~~~~~lliiD~~~~~  117 (220)
T 2cvh_A           94 VIGSLKKTVDSNFALVVVDSITAH  117 (220)
T ss_dssp             HHHHHHHHCCTTEEEEEEECCCCC
T ss_pred             HHHHHHHHhhcCCCEEEEcCcHHH
Confidence            555666666545679999998653

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.95  E-value=3e-05  Score=72.75  Aligned_cols=103  Identities=17%  Similarity=0.198  Sum_probs=59.0

Q ss_pred             cccccchhHH---HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC-CCHHHHH
Q 043252          189 AKVYGRETEK---KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD-FDVIRLT  264 (337)
Q Consensus       189 ~~~vGr~~~~---~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~-~~~~~~~  264 (337)
                      ..++|.+..+   ..|...+....      ...+.|+|++|+||||||+.+.+.  ....|     +.++.. ..... +
T Consensus        26 ~~ivGq~~~~~~~~~L~~~i~~~~------~~~vLL~GppGtGKTtlAr~ia~~--~~~~f-----~~l~a~~~~~~~-i   91 (447)
T 3pvs_A           26 AQYIGQQHLLAAGKPLPRAIEAGH------LHSMILWGPPGTGKTTLAEVIARY--ANADV-----ERISAVTSGVKE-I   91 (447)
T ss_dssp             TTCCSCHHHHSTTSHHHHHHHHTC------CCEEEEECSTTSSHHHHHHHHHHH--TTCEE-----EEEETTTCCHHH-H
T ss_pred             HHhCCcHHHHhchHHHHHHHHcCC------CcEEEEECCCCCcHHHHHHHHHHH--hCCCe-----EEEEeccCCHHH-H
Confidence            4688988877   67777775433      468999999999999999999875  22222     222221 12221 1


Q ss_pred             HHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCC
Q 043252          265 KSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQA  322 (337)
Q Consensus       265 ~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~  322 (337)
                      ..++...                 ......+++.+|+||++........+.|...+..
T Consensus        92 r~~~~~a-----------------~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~  132 (447)
T 3pvs_A           92 REAIERA-----------------RQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIED  132 (447)
T ss_dssp             HHHHHHH-----------------HHHHHTTCCEEEEEETTTCC------CCHHHHHT
T ss_pred             HHHHHHH-----------------HHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc
Confidence            1111111                 0111146788999999977654455555555543

>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=97.94  E-value=3.6e-05  Score=72.15  Aligned_cols=102  Identities=24%  Similarity=0.248  Sum_probs=59.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhccccccccc--ceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD--LKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL  293 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L  293 (337)
                      ...+.|+|++|+||||||+.+++.  ....|.  ..++++.      ..+..++...+...      ...    .+...+
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~--l~~~~~~~~v~~v~~------~~~~~~~~~~~~~~------~~~----~~~~~~  191 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYITS------EKFLNDLVDSMKEG------KLN----EFREKY  191 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHH--HHHHCCSSCEEEEEH------HHHHHHHHHHHHTT------CHH----HHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEeeH------HHHHHHHHHHHHcc------cHH----HHHHHh
Confidence            567899999999999999999874  222221  2344443      33444555554322      111    233444


Q ss_pred             CCCeEEEEEeCCCCCCh--hcHHHhhccCCC-CCCCcEEEEEecC
Q 043252          294 FGKKFLLVLDDVWNENY--TDWVHLSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       294 ~~kr~LlVlDdv~~~~~--~~~~~l~~~l~~-~~~gs~iivTTR~  335 (337)
                      ..+.-+|+|||+.....  .....+...+.. ...|..||+||.+
T Consensus       192 ~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          192 RKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             TTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             cCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            43667999999965422  222334333321 1346788888875

>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=97.90  E-value=2.6e-05  Score=74.67  Aligned_cols=135  Identities=19%  Similarity=0.199  Sum_probs=71.9

Q ss_pred             cccccchhHHHHHHHHHhcCC-----------CCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC
Q 043252          189 AKVYGRETEKKEIVELLLKDD-----------SRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD  257 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~-----------~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~  257 (337)
                      ..++|++..++.|..||....           ....+..+.+.|+|++|+||||+|+.+++..    .+ ..+.++++..
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l----~~-~~i~in~s~~  113 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL----GY-DILEQNASDV  113 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT----TC-EEEEECTTSC
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc----CC-CEEEEeCCCc
Confidence            568999999999999997511           0001234689999999999999999998753    11 2334555544


Q ss_pred             CCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCCh---hcHHHhhccCCCCCCCcEEEEEec
Q 043252          258 FDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENY---TDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       258 ~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~---~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ... .++...+........ ...-......  .....+++.+|+||++.....   ..+..+...+..  .+..||+++.
T Consensus       114 ~~~-~~~~~~i~~~~~~~~-~~~~~~~~~~--~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~--~~~~iIli~~  187 (516)
T 1sxj_A          114 RSK-TLLNAGVKNALDNMS-VVGYFKHNEE--AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLILICN  187 (516)
T ss_dssp             CCH-HHHHHTGGGGTTBCC-STTTTTC------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEEEES
T ss_pred             chH-HHHHHHHHHHhcccc-HHHHHhhhhh--hhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHh--cCCCEEEEEc
Confidence            333 233333322211110 0000000000  001235788999999965422   223444443332  2334666554

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.86  E-value=3.7e-05  Score=68.24  Aligned_cols=123  Identities=11%  Similarity=0.181  Sum_probs=66.8

Q ss_pred             ccccchhHHHHHHHHHhcCC---CCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDD---SRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKS  266 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~  266 (337)
                      .++|.+..++.+...+....   .........+.|+|++|+|||++|+.++...  ...-...+.+.++...... ....
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~--~~~~~~~~~~~~~~~~~~~-~~~~   94 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL--FDTEEAMIRIDMTEYMEKH-AVSR   94 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHH--HSCGGGEEEEEGGGCCSTT-HHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHH--cCCCcceEEeecccccccc-cHHH
Confidence            47899888888877776421   0012234689999999999999999998742  1111123455554432211 1111


Q ss_pred             HHHHhhCCCCC-CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCC
Q 043252          267 ILLSIASDQNV-DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQ  321 (337)
Q Consensus       267 il~~~~~~~~~-~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~  321 (337)
                      ++   +..... .......+...+..   ...-+|+||++..........|...+.
T Consensus        95 l~---g~~~~~~~~~~~~~~~~~~~~---~~~~vl~lDEi~~l~~~~~~~Ll~~le  144 (311)
T 4fcw_A           95 LI---GAPPGYVGYEEGGQLTEAVRR---RPYSVILFDAIEKAHPDVFNILLQMLD  144 (311)
T ss_dssp             HH---CCCTTSTTTTTCCHHHHHHHH---CSSEEEEEETGGGSCHHHHHHHHHHHH
T ss_pred             hc---CCCCccccccccchHHHHHHh---CCCeEEEEeChhhcCHHHHHHHHHHHh
Confidence            11   111100 11111222222222   234699999997766666666655543

>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=97.85  E-value=7e-05  Score=66.54  Aligned_cols=119  Identities=8%  Similarity=-0.019  Sum_probs=72.6

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc-cccccccceEEEEeCC-CCCHHHHHHHHHHH
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK-QVEDHFDLKAWTCVSD-DFDVIRLTKSILLS  270 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~-~~~~~F~~~~wv~v~~-~~~~~~~~~~il~~  270 (337)
                      |-++-++.|...+...      ..+...++|+.|+||||+|+.+.+.. .....+....++..++ ...+.. .++++..
T Consensus         1 g~~~~~~~L~~~i~~~------~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~-ir~li~~   73 (305)
T 2gno_A            1 GAKDQLETLKRIIEKS------EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDD-IRTIKDF   73 (305)
T ss_dssp             ---CHHHHHHHHHHTC------SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHH-HHHHHHH
T ss_pred             ChHHHHHHHHHHHHCC------CCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHH-HHHHHHH
Confidence            3455566777777532      25689999999999999999997631 1111122234454432 233332 3344444


Q ss_pred             hhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          271 IASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       271 ~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +.....                 .+++-++|+|++........+.|...+....+.+.+|++|.+
T Consensus        74 ~~~~p~-----------------~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~  121 (305)
T 2gno_A           74 LNYSPE-----------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRR  121 (305)
T ss_dssp             HTSCCS-----------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESC
T ss_pred             Hhhccc-----------------cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECC
Confidence            432111                 245678999999877667778888877766667888887743

>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=97.83  E-value=4.5e-05  Score=68.39  Aligned_cols=52  Identities=29%  Similarity=0.279  Sum_probs=38.7

Q ss_pred             ccccccchhHHHHHHHHHhcC----C--CCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKD----D--SRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~----~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|.+..++.|.+.+..+    .  .......+.+.|+|++|+|||+||+.+++.
T Consensus        17 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~   74 (322)
T 3eie_A           17 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE   74 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHH
T ss_pred             HHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            357899999999998877311    0  001223467999999999999999999875

>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=97.82  E-value=3.7e-05  Score=67.07  Aligned_cols=47  Identities=15%  Similarity=0.167  Sum_probs=33.6

Q ss_pred             ccccchhHHHHHHH-------HHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVE-------LLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~-------~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|.....+++..       .+....   ......+.|+|++|+|||+||+.+++.
T Consensus        34 ~~i~~~~~~~~i~~~~~~l~~~l~~~~---~~~~~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           34 GIIKWGDPVTRVLDDGELLVQQTKNSD---RTPLVSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHHHCS---SCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHHHHHHHHHhccC---CCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            46777666665555       333221   234678999999999999999999875

>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=97.80  E-value=0.00017  Score=64.96  Aligned_cols=117  Identities=12%  Similarity=0.106  Sum_probs=67.1

Q ss_pred             hhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc--------------------cccceEEEEe
Q 043252          195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED--------------------HFDLKAWTCV  254 (337)
Q Consensus       195 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~F~~~~wv~v  254 (337)
                      ++..+.+...+....     -...+.++|+.|+|||++|+.+.+.-....                    |++ ..++..
T Consensus         8 ~~~~~~l~~~i~~~~-----~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~   81 (334)
T 1a5t_A            8 RPDFEKLVASYQAGR-----GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLAP   81 (334)
T ss_dssp             HHHHHHHHHHHHTTC-----CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEECC
T ss_pred             HHHHHHHHHHHHcCC-----cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEec
Confidence            455667777775433     245799999999999999998876421110                    111 122222


Q ss_pred             C---CCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEE
Q 043252          255 S---DDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIV  331 (337)
Q Consensus       255 ~---~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iiv  331 (337)
                      .   ....+.. .+++.+.+....                 ..+++-++|+|++........+.|...+.....++.+|+
T Consensus        82 ~~~~~~~~i~~-ir~l~~~~~~~~-----------------~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il  143 (334)
T 1a5t_A           82 EKGKNTLGVDA-VREVTEKLNEHA-----------------RLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFL  143 (334)
T ss_dssp             CTTCSSBCHHH-HHHHHHHTTSCC-----------------TTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEE
T ss_pred             cccCCCCCHHH-HHHHHHHHhhcc-----------------ccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEE
Confidence            1   1111111 122222221110                 125677999999987665666777777766556677777


Q ss_pred             EecC
Q 043252          332 TTRN  335 (337)
Q Consensus       332 TTR~  335 (337)
                      +|.+
T Consensus       144 ~t~~  147 (334)
T 1a5t_A          144 ATRE  147 (334)
T ss_dssp             EESC
T ss_pred             EeCC
Confidence            7754

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.80  E-value=0.00043  Score=61.98  Aligned_cols=52  Identities=25%  Similarity=0.285  Sum_probs=37.8

Q ss_pred             ccccccchhHHHHHHHHHhc----CCC--CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLK----DDS--RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~----~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|.+..++.|.+.+..    +..  ......+.|.|+|++|+|||+||+.+++.
T Consensus        11 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~   68 (322)
T 1xwi_A           11 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE   68 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHH
Confidence            35689999888888776632    110  01123468899999999999999999975

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.79  E-value=3.1e-05  Score=67.30  Aligned_cols=47  Identities=21%  Similarity=0.175  Sum_probs=33.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..+..+.+.+..-..    ....+.|+|..|+|||+||+.+++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~----~~~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAP----LDKPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTT----SCSCEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeCCHHHHHHHHHHHHHhC----CCCCEEEECCCCCcHHHHHHHHHHh
Confidence            3578999988888777654221    1236789999999999999999874

>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=97.79  E-value=7.7e-05  Score=66.80  Aligned_cols=115  Identities=19%  Similarity=0.199  Sum_probs=60.2

Q ss_pred             HHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC
Q 043252          198 KKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV  277 (337)
Q Consensus       198 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~  277 (337)
                      ...+..++..+.    .....+.|+|++|+||||||+.+++..... .+ ..+++++      ..+...+...+...   
T Consensus        23 ~~~~~~~~~~~~----~~~~~lll~G~~GtGKT~la~~i~~~~~~~-~~-~~~~i~~------~~~~~~~~~~~~~~---   87 (324)
T 1l8q_A           23 YEVVKEALENLG----SLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-GY-RVIYSSA------DDFAQAMVEHLKKG---   87 (324)
T ss_dssp             HHHHHHHHHTTT----TSCSSEEEECSSSSSHHHHHHHHHHHHHHT-TC-CEEEEEH------HHHHHHHHHHHHHT---
T ss_pred             HHHHHHHHhCcC----CCCCeEEEECCCCCcHHHHHHHHHHHHHHC-CC-EEEEEEH------HHHHHHHHHHHHcC---
Confidence            344555554332    134578999999999999999998752111 11 2344443      33344444444221   


Q ss_pred             CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCCh--hcHHHhhccCCC-CCCCcEEEEEecC
Q 043252          278 DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENY--TDWVHLSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       278 ~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~--~~~~~l~~~l~~-~~~gs~iivTTR~  335 (337)
                         .....    ...+ .+.-+|+|||+.....  .....+...+.. ...|..||+||.+
T Consensus        88 ---~~~~~----~~~~-~~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~  140 (324)
T 1l8q_A           88 ---TINEF----RNMY-KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDR  140 (324)
T ss_dssp             ---CHHHH----HHHH-HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             ---cHHHH----HHHh-cCCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecC
Confidence               12222    2222 2356999999965422  122333333321 1235678888753

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.77  E-value=1.4e-05  Score=63.32  Aligned_cols=23  Identities=30%  Similarity=0.348  Sum_probs=21.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.|+|+.|+|||||++.++..
T Consensus        37 ~~~~l~G~~G~GKTtL~~~i~~~   59 (149)
T 2kjq_A           37 QFIYVWGEEGAGKSHLLQAWVAQ   59 (149)
T ss_dssp             SEEEEESSSTTTTCHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999999999875

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.73  E-value=6.9e-05  Score=66.60  Aligned_cols=47  Identities=15%  Similarity=0.199  Sum_probs=36.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|+...+..+.+.+..-..    ....|.|+|.+|+|||++|+.+++.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~----~~~~vLi~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAP----SDATVLIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCS----TTSCEEEESCTTSCHHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhC----CCCcEEEECCCCchHHHHHHHHHHh
Confidence            4588999999988888764321    1235789999999999999999874

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.69  E-value=0.00037  Score=69.81  Aligned_cols=45  Identities=24%  Similarity=0.369  Sum_probs=37.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+.+++.+++.|....      ..-+.|+|++|+|||++|+.+...
T Consensus       186 d~~iGr~~~i~~l~~~l~~~~------~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRRR------KNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS------SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhccC------CCCeEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999996542      345789999999999999999864

>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=97.64  E-value=0.00034  Score=65.57  Aligned_cols=52  Identities=25%  Similarity=0.285  Sum_probs=38.3

Q ss_pred             ccccccchhHHHHHHHHHhc----CCC--CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLK----DDS--RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~----~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|.+..++.|.+.+..    +..  ......+.|.|+|++|+|||+||+.+++.
T Consensus       133 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~  190 (444)
T 2zan_A          133 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE  190 (444)
T ss_dssp             GGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999988887631    110  00123468899999999999999999975

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.64  E-value=0.00015  Score=68.54  Aligned_cols=45  Identities=29%  Similarity=0.434  Sum_probs=37.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+.+++.++..|....      ..-+.|+|++|+|||+||+.++..
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~------~~~~LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRT------KNNPVLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS------SCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccC------CCCeEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999997533      235679999999999999999874

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.61  E-value=0.00012  Score=74.38  Aligned_cols=45  Identities=27%  Similarity=0.473  Sum_probs=37.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+.++..++..|....      ...+.++|++|+||||||+.+.+.
T Consensus       170 d~viGr~~~i~~l~~~l~~~~------~~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          170 DPVIGRDEEIRRVIQILLRRT------KNNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSS------CCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHhcCC------CCceEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999997543      234689999999999999999874

>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=97.61  E-value=0.00013  Score=66.25  Aligned_cols=51  Identities=29%  Similarity=0.312  Sum_probs=37.4

Q ss_pred             cccccchhHHHHHHHHHhcC----C--CCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKD----D--SRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~----~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.|.+.+..+    .  .......+-|.|+|++|+|||+||+.+++.
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~  107 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE  107 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            56899999999888876321    0  001122346889999999999999999985

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=97.58  E-value=5.5e-05  Score=67.15  Aligned_cols=69  Identities=19%  Similarity=0.354  Sum_probs=46.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEe--CCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCV--SDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL  293 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v--~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L  293 (337)
                      .+++.|+|++|+||||||..+...     .-..++|+++  .+..+.                 ...+.+.....+.+.+
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-----~G~~VlyIs~~~eE~v~~-----------------~~~~le~~l~~i~~~l  180 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-----LGGKDKYATVRFGEPLSG-----------------YNTDFNVFVDDIARAM  180 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-----HHTTSCCEEEEBSCSSTT-----------------CBCCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-----CCCCEEEEEecchhhhhh-----------------hhcCHHHHHHHHHHHH
Confidence            357789999999999999998764     1123456766  332110                 0134566666666666


Q ss_pred             CCCeEEEEEeCCCC
Q 043252          294 FGKKFLLVLDDVWN  307 (337)
Q Consensus       294 ~~kr~LlVlDdv~~  307 (337)
                      ...+ +||||++..
T Consensus       181 ~~~~-LLVIDsI~a  193 (331)
T 2vhj_A          181 LQHR-VIVIDSLKN  193 (331)
T ss_dssp             HHCS-EEEEECCTT
T ss_pred             hhCC-EEEEecccc
Confidence            5555 999999964

>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=97.56  E-value=0.00013  Score=66.45  Aligned_cols=51  Identities=25%  Similarity=0.297  Sum_probs=37.8

Q ss_pred             cccccchhHHHHHHHHHhc----CCC--CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLK----DDS--RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~----~~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.|.+.+..    +..  ......+.+.|+|++|+|||+||+.+++.
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~  140 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQ  140 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            5689999999988887642    110  00123457899999999999999999874

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.56  E-value=0.00028  Score=62.12  Aligned_cols=51  Identities=22%  Similarity=0.317  Sum_probs=37.8

Q ss_pred             cccccchhHHHHHHHHHhcCCC------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.|.+++..+..      .-......+.|+|++|+||||||+.+++.
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~   77 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE   77 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            5689999999998887743100      00112457899999999999999999874

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.50  E-value=0.00026  Score=71.00  Aligned_cols=45  Identities=29%  Similarity=0.434  Sum_probs=37.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++||+.+++.+...|....      ..-+.++|++|+|||++|+.+.+.
T Consensus       180 d~iiG~~~~i~~l~~~l~~~~------~~~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRRT------KNNPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS------SCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCccCchHHHHHHHHHHhCCC------CCCeEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999997543      234789999999999999999864

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.49  E-value=0.00033  Score=60.35  Aligned_cols=52  Identities=29%  Similarity=0.324  Sum_probs=34.6

Q ss_pred             ccccccchhHHHHHHHH---HhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVEL---LLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~---L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|.+..++.+.+.   +..+..   -+.....-+.|+|++|+||||||+.+.+.
T Consensus        11 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   68 (257)
T 1lv7_A           11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE   68 (257)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            35689998777766554   332210   00112335889999999999999999874

>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=97.47  E-value=0.00059  Score=60.40  Aligned_cols=51  Identities=27%  Similarity=0.251  Sum_probs=37.4

Q ss_pred             cccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+..++.|.+++..+-.       -+-.....+.|+|++|+|||+||+.+++.
T Consensus        15 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           15 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHH
Confidence            4689999888888877643100       00123457899999999999999999975

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.45  E-value=0.0001  Score=65.57  Aligned_cols=42  Identities=17%  Similarity=0.190  Sum_probs=29.9

Q ss_pred             hhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       195 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...++.+.+++.....   .....+.|+|+.|+|||+||+.+++.
T Consensus       134 ~~~~~~~~~~i~~~~~---~~~~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          134 MEAFSAILDFVEQYPS---AEQKGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             HHHHHHHHHHHHHCSC---SSCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccc---cCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3445556667654321   12357889999999999999999875

>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=97.40  E-value=0.00022  Score=67.59  Aligned_cols=51  Identities=24%  Similarity=0.177  Sum_probs=37.6

Q ss_pred             cccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..+++|.+++...-.       -+.....-+.|+|++|+|||+||+.+.+.
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~  261 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE  261 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHH
Confidence            4689999999998887753200       00112346899999999999999999874

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.38  E-value=0.00016  Score=72.38  Aligned_cols=124  Identities=15%  Similarity=0.201  Sum_probs=72.0

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+...+.....   ........+.++|++|+|||+||+.+.+..  ...-...+.++++.-.+..    
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l--~~~~~~~i~i~~s~~~~~~----  564 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESI--FGDEESMIRIDMSEYMEKH----  564 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHH--HSCTTCEEEEEGGGGCSSC----
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh--cCCCcceEEEechhccccc----
Confidence            4689999999888888764321   112334579999999999999999998742  1111223445544322100    


Q ss_pred             HHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCC-----------CCCcEEEEEec
Q 043252          266 SILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAG-----------AQGSKIIVTTR  334 (337)
Q Consensus       266 ~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~-----------~~gs~iivTTR  334 (337)
                                   ......+...++.   ....+|+||++..........|...+..+           ....+||.||.
T Consensus       565 -------------~~~~~~l~~~~~~---~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn  628 (758)
T 3pxi_A          565 -------------STSGGQLTEKVRR---KPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSN  628 (758)
T ss_dssp             -------------CCC---CHHHHHH---CSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEES
T ss_pred             -------------ccccchhhHHHHh---CCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCC
Confidence                         0001111222222   23348999999877666666666555331           12457888875

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.34  E-value=0.00073  Score=62.07  Aligned_cols=52  Identities=21%  Similarity=0.276  Sum_probs=38.4

Q ss_pred             ccccccchhHHHHHHHHHhcC----CC--CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKD----DS--RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~----~~--~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -..++|.+..++.|..++...    ..  ........+.|+|++|+|||+||+.+++.
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~  171 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE  171 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHH
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            457999999999998887321    10  00112457899999999999999999874

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.30  E-value=0.00049  Score=60.69  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=22.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....+.++|++|+|||+||+.+++.
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~   59 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRK   59 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4568889999999999999999985

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.27  E-value=0.0003  Score=71.45  Aligned_cols=136  Identities=14%  Similarity=0.221  Sum_probs=72.3

Q ss_pred             cccccchhHHHHHHHHHhcCC---CCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDD---SRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+...+....   ...+.....+.|+|+.|+|||++|+.+.+...  ..-...+.++++...... .  
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~--~~~~~~i~i~~~~~~~~~-~--  632 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF--DTEEAMIRIDMTEYMEKH-A--  632 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHH--SSGGGEEEECTTTCCSSG-G--
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc--CCCCcEEEEechhccchh-H--
Confidence            357999998888887775421   00122346899999999999999999987421  101123344444322210 0  


Q ss_pred             HHHHHhhCCCC--CCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCC-----------CCcEEEEE
Q 043252          266 SILLSIASDQN--VDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGA-----------QGSKIIVT  332 (337)
Q Consensus       266 ~il~~~~~~~~--~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~-----------~gs~iivT  332 (337)
                        ...+.+..+  ........+...++.   ...-+|+||++...+......|...+..+.           .+..||+|
T Consensus       633 --~s~l~g~~~~~~G~~~~g~l~~~~~~---~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~t  707 (854)
T 1qvr_A          633 --VSRLIGAPPGYVGYEEGGQLTEAVRR---RPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILT  707 (854)
T ss_dssp             --GGGC--------------CHHHHHHH---CSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEE
T ss_pred             --HHHHcCCCCCCcCccccchHHHHHHh---CCCeEEEEecccccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEe
Confidence              011111000  000111223333332   224589999998776666667766665331           23447777


Q ss_pred             ec
Q 043252          333 TR  334 (337)
Q Consensus       333 TR  334 (337)
                      |.
T Consensus       708 sn  709 (854)
T 1qvr_A          708 SN  709 (854)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.18  E-value=0.00076  Score=62.63  Aligned_cols=53  Identities=21%  Similarity=0.143  Sum_probs=38.0

Q ss_pred             cccccccchhHHHHHHHHHhc----CCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          187 EEAKVYGRETEKKEIVELLLK----DDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~----~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-.++.|.++.+++|.+.+.-    ++.   -+-...+-|.++|++|.|||+||+.+.+.
T Consensus       179 ~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e  238 (437)
T 4b4t_L          179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT  238 (437)
T ss_dssp             CSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             ChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            345688998888877665532    110   01234578999999999999999999985

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.18  E-value=0.0015  Score=58.89  Aligned_cols=92  Identities=17%  Similarity=0.187  Sum_probs=56.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccc----cccceEEEEeCCCCCHHHHHHHHHHHhhCCC-----------CCCC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVED----HFDLKAWTCVSDDFDVIRLTKSILLSIASDQ-----------NVDN  279 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~-----------~~~~  279 (337)
                      .-.++.|+|++|+||||||..+........    .-..++|++....++...+.. ++..++...           ....
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g~~~~~~l~~l~~~~~~~~  199 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFNVDHDAVLDNVLYARAYTS  199 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCST
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcCCCHHHHHhceeEeecCCH
Confidence            456999999999999999988876422211    123678999888888776543 334433211           1012


Q ss_pred             CCHHHHHHHHHHHcC---CCeEEEEEeCCCC
Q 043252          280 HDLNKLQEELKKQLF---GKKFLLVLDDVWN  307 (337)
Q Consensus       280 ~~~~~~~~~l~~~L~---~kr~LlVlDdv~~  307 (337)
                      .....+...+...+.   .+--|||+|.+..
T Consensus       200 e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          200 EHQMELLDYVAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             THHHHHHHHHHHHHHHSCSSEEEEEEETSGG
T ss_pred             HHHHHHHHHHHHHHHhcCCCccEEEEechHH
Confidence            222234444455543   4566999999843

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=97.16  E-value=0.0011  Score=63.56  Aligned_cols=51  Identities=25%  Similarity=0.303  Sum_probs=35.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.++-.+.+.+.+.-...........+.++|++|+||||||+.+...
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~  131 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKS  131 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            457888877777655443111001113568999999999999999999874

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.16  E-value=0.00049  Score=63.04  Aligned_cols=53  Identities=26%  Similarity=0.185  Sum_probs=37.5

Q ss_pred             cccccccchhHHHHHHHHHhc----CCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          187 EEAKVYGRETEKKEIVELLLK----DDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~----~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-.++.|.++.+++|.+.+.-    ++.   -+-...+-|.++|++|.|||.||+.+.+.
T Consensus       146 ~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e  205 (405)
T 4b4t_J          146 TYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHH  205 (405)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHh
Confidence            345688998888877665432    110   01223567899999999999999999985

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=97.14  E-value=0.0015  Score=59.31  Aligned_cols=85  Identities=18%  Similarity=0.119  Sum_probs=55.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEELKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l~~  291 (337)
                      -.++.|.|.+|+||||||..+.....  ..=..++|++....++...     ...++.+..    ....+.+++.+.+..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~--~~g~~vlyi~~E~s~~~~~-----a~~~g~d~~~l~i~~~~~~e~~l~~l~~  146 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQ--KAGGTCAFIDAEHALDPVY-----ARALGVNTDELLVSQPDNGEQALEIMEL  146 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHH--HCCCeEEEEECCCChhHHH-----HHHcCCCHHHceeecCCcHHHHHHHHHH
Confidence            35889999999999999988765421  1123688999888776541     334432211    023456777777776


Q ss_pred             HcCC-CeEEEEEeCCCC
Q 043252          292 QLFG-KKFLLVLDDVWN  307 (337)
Q Consensus       292 ~L~~-kr~LlVlDdv~~  307 (337)
                      .++. .--+||+|.+-.
T Consensus       147 l~~~~~~~lVVIDsl~~  163 (366)
T 1xp8_A          147 LVRSGAIDVVVVDSVAA  163 (366)
T ss_dssp             HHTTTCCSEEEEECTTT
T ss_pred             HHhcCCCCEEEEeChHH
Confidence            6653 344999999843

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.14  E-value=0.00077  Score=62.47  Aligned_cols=53  Identities=30%  Similarity=0.251  Sum_probs=38.5

Q ss_pred             cccccccchhHHHHHHHHHhc----CC---CCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          187 EEAKVYGRETEKKEIVELLLK----DD---SRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~----~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-.++.|.++.++.|.+.+.-    ++   .-+-...+-|.++|++|+|||+||+.+.+.
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~  229 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANS  229 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHH
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            345788999888888776532    10   001234567999999999999999999985

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.11  E-value=0.0015  Score=59.01  Aligned_cols=86  Identities=21%  Similarity=0.188  Sum_probs=55.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l~  290 (337)
                      .-.++.|+|++|+|||||+..+......  .=..++|++....++..     .++.++....    ....+.++....+.
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~~~--~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~  132 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEAQK--MGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVD  132 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHHHH--TTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHH
Confidence            3469999999999999999988764221  11246788877777654     3344433211    13345666666666


Q ss_pred             HHcC-CCeEEEEEeCCCC
Q 043252          291 KQLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       291 ~~L~-~kr~LlVlDdv~~  307 (337)
                      ..+. .+.-++|+|.+-.
T Consensus       133 ~l~~~~~~dlvVIDSi~~  150 (356)
T 3hr8_A          133 ELVRSGVVDLIVVDSVAA  150 (356)
T ss_dssp             HHHHTSCCSEEEEECTTT
T ss_pred             HHhhhcCCCeEEehHhhh
Confidence            5553 4455899999854

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=97.10  E-value=0.0016  Score=58.87  Aligned_cols=85  Identities=20%  Similarity=0.127  Sum_probs=54.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEELKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l~~  291 (337)
                      -.++.|+|++|+||||||..+.....  ..=..++|++....++..     ..+.++....    ....+.++....+..
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~--~~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~~  133 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQ--AAGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIADM  133 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH--hCCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            45999999999999999988875421  111357889888777653     2333432211    023356666666655


Q ss_pred             HcCC-CeEEEEEeCCCC
Q 043252          292 QLFG-KKFLLVLDDVWN  307 (337)
Q Consensus       292 ~L~~-kr~LlVlDdv~~  307 (337)
                      .... +--+||+|.+-.
T Consensus       134 l~~~~~~~lIVIDsl~~  150 (349)
T 2zr9_A          134 LVRSGALDIIVIDSVAA  150 (349)
T ss_dssp             HHTTTCCSEEEEECGGG
T ss_pred             HHhcCCCCEEEEcChHh
Confidence            5543 455999999854

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.10  E-value=0.0021  Score=53.98  Aligned_cols=114  Identities=16%  Similarity=0.056  Sum_probs=60.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------------------
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------------------  276 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------------------  276 (337)
                      .++.|+|++|+|||||++.+......  .=..+.|+....  ....+...+. .+.....                    
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~~~--~~~~v~~~~~~~--~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKGLR--DGDPCIYVTTEE--SRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEKEDQ   98 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHH--HTCCEEEEESSS--CHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC----CT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHH--CCCeEEEEEccc--CHHHHHHHHH-HhcchHHHHhhCCEEEEeccccccCce
Confidence            58999999999999999998753211  112355555433  3444443332 2221100                    


Q ss_pred             --CCCCCHHHHHHHHHHHc---CCCeEEEEEeCCCCC---ChhcHHHhhccCCC--CCCCcEEEEEecC
Q 043252          277 --VDNHDLNKLQEELKKQL---FGKKFLLVLDDVWNE---NYTDWVHLSLPFQA--GAQGSKIIVTTRN  335 (337)
Q Consensus       277 --~~~~~~~~~~~~l~~~L---~~kr~LlVlDdv~~~---~~~~~~~l~~~l~~--~~~gs~iivTTR~  335 (337)
                        ....+..++...+...+   .-+..+||||.+...   +......+...|..  ...|..||+||..
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~  167 (235)
T 2w0m_A           99 WSLVNLTPEELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQY  167 (235)
T ss_dssp             TBCSSCCHHHHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC-
T ss_pred             eeecCCCHHHHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEecc
Confidence              01114555555555544   223459999998632   22223333332221  1346788888865

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.08  E-value=0.00087  Score=62.98  Aligned_cols=47  Identities=19%  Similarity=0.273  Sum_probs=35.0

Q ss_pred             cccccchhHHHHHHHH---HhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVEL---LLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~---L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.+..+   +....    ...+-+.++|++|+|||+||+.+.+.
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~----~~~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKK----MAGRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTC----CTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCC----CCCCeEEEECCCcCCHHHHHHHHHHH
Confidence            6789999887765444   33322    12356889999999999999999875

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=97.06  E-value=0.0012  Score=58.87  Aligned_cols=90  Identities=17%  Similarity=0.174  Sum_probs=56.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccc---------cc-----cceEEEEeCCCCCHHHHHHHHHHHhhCCCC-----
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVED---------HF-----DLKAWTCVSDDFDVIRLTKSILLSIASDQN-----  276 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---------~F-----~~~~wv~v~~~~~~~~~~~~il~~~~~~~~-----  276 (337)
                      -.++.|+|.+|+||||||..+........         ..     ..++|++....++...+.. ++..++.+..     
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~  176 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLDN  176 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhcC
Confidence            46999999999999999988875421111         11     3678999888887776654 3444432210     


Q ss_pred             ---CCCCCHH---HHHHHHHHHcC--CCeEEEEEeCCC
Q 043252          277 ---VDNHDLN---KLQEELKKQLF--GKKFLLVLDDVW  306 (337)
Q Consensus       277 ---~~~~~~~---~~~~~l~~~L~--~kr~LlVlDdv~  306 (337)
                         ....+.+   .+...+...+.  .+--|||+|.+-
T Consensus       177 l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          177 TFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             EEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             EEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence               0122333   34445555554  345599999984

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.03  E-value=0.0014  Score=65.32  Aligned_cols=99  Identities=17%  Similarity=0.163  Sum_probs=59.2

Q ss_pred             ccccccchhHHHHHHHHH----hcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCH
Q 043252          188 EAKVYGRETEKKEIVELL----LKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDV  260 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L----~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~  260 (337)
                      -.++.|.++.+++|.+++    ..++.   -+-...+-|.++|++|.|||+||+.+++.  ...+|   +.|+.+.    
T Consensus       203 ~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~e--lg~~~---~~v~~~~----  273 (806)
T 3cf2_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE--TGAFF---FLINGPE----  273 (806)
T ss_dssp             GGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTT--TTCEE---EEEEHHH----
T ss_pred             hhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH--hCCeE---EEEEhHH----
Confidence            346788888887776654    22221   12234678999999999999999999985  33333   2333221    


Q ss_pred             HHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          261 IRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       261 ~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                                +....  .......+...+........++|+||++..
T Consensus       274 ----------l~sk~--~gese~~lr~lF~~A~~~~PsIIfIDEiDa  308 (806)
T 3cf2_A          274 ----------IMSKL--AGESESNLRKAFEEAEKNAPAIIFIDELDA  308 (806)
T ss_dssp             ----------HHSSC--TTHHHHHHHHHHHHHTTSCSEEEEEESGGG
T ss_pred             ----------hhccc--chHHHHHHHHHHHHHHHcCCeEEEEehhcc
Confidence                      11111  112223334444444556789999999954

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.01  E-value=0.00052  Score=68.76  Aligned_cols=119  Identities=13%  Similarity=0.123  Sum_probs=65.4

Q ss_pred             cccccchhHHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+...+.....   ..+.....+.++|++|+|||++|+.+.+..  .   ...+.++++.-.....   
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l--~---~~~~~i~~s~~~~~~~---  529 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL--G---IELLRFDMSEYMERHT---  529 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH--T---CEEEEEEGGGCSSSSC---
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh--c---CCEEEEechhhcchhh---
Confidence            3578999888888777653210   012335579999999999999999998742  1   1233444443221100   


Q ss_pred             HHHHHhhCCCCCCCCCH---HHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCC
Q 043252          266 SILLSIASDQNVDNHDL---NKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQ  321 (337)
Q Consensus       266 ~il~~~~~~~~~~~~~~---~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~  321 (337)
                        +..+.+..+ .....   ..+...++.   ....+|+||++.....+....|...+.
T Consensus       530 --~~~l~g~~~-g~~g~~~~~~l~~~~~~---~~~~vl~lDEi~~~~~~~~~~Ll~~le  582 (758)
T 1r6b_X          530 --VSRLIGAPP-GYVGFDQGGLLTDAVIK---HPHAVLLLDEIEKAHPDVFNILLQVMD  582 (758)
T ss_dssp             --CSSSCCCCS-CSHHHHHTTHHHHHHHH---CSSEEEEEETGGGSCHHHHHHHHHHHH
T ss_pred             --HhhhcCCCC-CCcCccccchHHHHHHh---CCCcEEEEeCccccCHHHHHHHHHHhc
Confidence              000111110 11000   112223322   345799999998776666666665554

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=97.01  E-value=0.0014  Score=55.61  Aligned_cols=91  Identities=14%  Similarity=0.096  Sum_probs=53.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccc----cccceEEEEeCCCCCHHHHHHHHHHHhhCCC--------CCCCCCHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVED----HFDLKAWTCVSDDFDVIRLTKSILLSIASDQ--------NVDNHDLN  283 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~--------~~~~~~~~  283 (337)
                      -.++.|+|++|+|||||++.+........    .-...+|+.....++...+. .++..+....        .....+..
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~  102 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNTD  102 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCHH
Confidence            35999999999999999999876321211    12467888877766655443 3333333211        00112222


Q ss_pred             H---HHHHHHHHcC-CCeEEEEEeCCCC
Q 043252          284 K---LQEELKKQLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       284 ~---~~~~l~~~L~-~kr~LlVlDdv~~  307 (337)
                      .   +...+.+.+. .+.-+||||++..
T Consensus       103 ~~~~~~~~~~~~~~~~~~~lliiD~~~~  130 (243)
T 1n0w_A          103 HQTQLLYQASAMMVESRYALLIVDSATA  130 (243)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETSSG
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEeCchH
Confidence            2   2333444443 4567999999864

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=97.01  E-value=0.0055  Score=52.14  Aligned_cols=23  Identities=22%  Similarity=0.561  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999999763

>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=96.99  E-value=0.0014  Score=61.73  Aligned_cols=98  Identities=18%  Similarity=0.170  Sum_probs=54.6

Q ss_pred             cccccchhHHHHHHHHHh---cCC---CCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHH
Q 043252          189 AKVYGRETEKKEIVELLL---KDD---SRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~---~~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~  262 (337)
                      .+++|.++.++++.+.+.   .+.   .-+....+-+.|+|++|+|||+||+.+.+..  ...|   +.++++.....  
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~--~~~f---~~is~~~~~~~--   88 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEA--NVPF---FHISGSDFVEL--   88 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHH--TCCE---EEEEGGGTTTC--
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHc--CCCe---eeCCHHHHHHH--
Confidence            568999887766655532   210   0001122358899999999999999998742  2222   23333322110  


Q ss_pred             HHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          263 LTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       263 ~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                                   . .......+...+.....+...+|+||++..
T Consensus        89 -------------~-~g~~~~~~r~lf~~A~~~~p~ILfIDEid~  119 (476)
T 2ce7_A           89 -------------F-VGVGAARVRDLFAQAKAHAPCIVFIDEIDA  119 (476)
T ss_dssp             -------------C-TTHHHHHHHHHHHHHHHTCSEEEEEETGGG
T ss_pred             -------------H-hcccHHHHHHHHHHHHhcCCCEEEEechhh
Confidence                         0 001112223334444456788999999954

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.98  E-value=0.0053  Score=53.93  Aligned_cols=26  Identities=27%  Similarity=0.241  Sum_probs=22.6

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....+|+|+|..|+||||||+.+...
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~   54 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNH   54 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999988754

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=96.98  E-value=0.0015  Score=59.20  Aligned_cols=85  Identities=21%  Similarity=0.122  Sum_probs=52.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~~  291 (337)
                      -.++.|.|.+|+||||||..+......  .=..++|++....++...     +..++.....    ...+.+++.+.+..
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~~~~--~g~~vlyid~E~s~~~~~-----a~~~g~~~~~l~i~~~~~~e~~~~~~~~  135 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAAAQR--EGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDA  135 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHH--TTCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH--CCCeEEEEeCCCCccHHH-----HHHcCCChhheeeeCCCCHHHHHHHHHH
Confidence            359999999999999999888754221  123578999888777442     3334322110    22345555555554


Q ss_pred             HcC-CCeEEEEEeCCCC
Q 043252          292 QLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       292 ~L~-~kr~LlVlDdv~~  307 (337)
                      ..+ .+--+||+|.+-.
T Consensus       136 l~~~~~~~lVVIDsl~~  152 (356)
T 1u94_A          136 LARSGAVDVIVVDSVAA  152 (356)
T ss_dssp             HHHHTCCSEEEEECGGG
T ss_pred             HHhccCCCEEEEcCHHH
Confidence            432 3445999999843

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.95  E-value=0.00056  Score=63.50  Aligned_cols=53  Identities=25%  Similarity=0.255  Sum_probs=38.6

Q ss_pred             cccccccchhHHHHHHHHHh----cCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          187 EEAKVYGRETEKKEIVELLL----KDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~----~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-.++.|.++.+++|.+.+.    .++.   .+-...+-|.++|++|.|||.||+.+.+.
T Consensus       179 t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e  238 (434)
T 4b4t_M          179 TYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQ  238 (434)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             ChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHH
Confidence            34578899988888876543    2210   01234578999999999999999999985

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.95  E-value=0.0032  Score=55.67  Aligned_cols=86  Identities=13%  Similarity=0.094  Sum_probs=53.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHH-HHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKL-QEELKKQ  292 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~-~~~l~~~  292 (337)
                      ++.|.|++|+|||||+.++.........=..++||+..+.++...     +++++.+...    ...+.++. ...+...
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~r-----a~~lGvd~d~llv~~~~~~E~~~l~i~~~l  104 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAY-----LRSMGVDPERVIHTPVQSLEQLRIDMVNQL  104 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHH-----HHHTTCCGGGEEEEECSBHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHH-----HHHhCCCHHHeEEEcCCCHHHHHHHHHHHH
Confidence            789999999999999977765422110023578999888887642     5555543211    23455555 3333332


Q ss_pred             --c-CCCeEEEEEeCCCCC
Q 043252          293 --L-FGKKFLLVLDDVWNE  308 (337)
Q Consensus       293 --L-~~kr~LlVlDdv~~~  308 (337)
                        + .++.-|||+|.|-..
T Consensus       105 ~~i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          105 DAIERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             HTCCTTCCEEEEEECSTTC
T ss_pred             HHhhccCceEEEEeccccc
Confidence              3 456679999999543

>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=96.90  E-value=0.00057  Score=57.64  Aligned_cols=112  Identities=11%  Similarity=-0.037  Sum_probs=59.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC-CCCCHHHHHHHHHHHcC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV-DNHDLNKLQEELKKQLF  294 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~-~~~~~~~~~~~l~~~L~  294 (337)
                      -.++.|.|..|+||||++..+....... .. .++.+....  +.. ....+++.++..... .......+.+.+.+.+.
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~-g~-kVli~~~~~--d~r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~   86 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYA-DV-KYLVFKPKI--DTR-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSF   86 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT-TC-CEEEEEECC--CGG-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTS
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhc-CC-EEEEEEecc--Cch-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhh
Confidence            4689999999999999997666532111 12 223332221  111 111233333221110 12234556666666665


Q ss_pred             CCeE-EEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          295 GKKF-LLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~-LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      +.++ +||+|.+..-..+..+.+. .+.+  .|-.||+|-+.
T Consensus        87 ~~~~dvViIDEaQ~l~~~~ve~l~-~L~~--~gi~Vil~Gl~  125 (223)
T 2b8t_A           87 NDETKVIGIDEVQFFDDRICEVAN-ILAE--NGFVVIISGLD  125 (223)
T ss_dssp             CTTCCEEEECSGGGSCTHHHHHHH-HHHH--TTCEEEEECCS
T ss_pred             CCCCCEEEEecCccCcHHHHHHHH-HHHh--CCCeEEEEecc
Confidence            5556 9999999654333333332 2332  26788888764

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.88  E-value=0.00081  Score=62.55  Aligned_cols=51  Identities=24%  Similarity=0.199  Sum_probs=36.9

Q ss_pred             cccccchhHHHHHHHHHh----cCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLL----KDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~----~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|.++.+++|.+.+.    .++.   -+-...+-|.++|++|.|||+||+.+.+.
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e  266 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANR  266 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhc
Confidence            468899888888876542    1110   01234578899999999999999999985

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=96.87  E-value=0.0028  Score=56.65  Aligned_cols=90  Identities=17%  Similarity=0.219  Sum_probs=56.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhccccccc----ccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDH----FDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDLN  283 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~~  283 (337)
                      -.++.|+|++|+||||||..+.........    -..++|++....++...+.. ++..++....        ....+.+
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~l~~~~~~~~~  185 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIEN-MAKALGLDIDNVMNNIYYIRAINTD  185 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHhCCCHHHHhccEEEEeCCCHH
Confidence            359999999999999999888764221111    23578999888887776553 3444432210        0122333


Q ss_pred             ---HHHHHHHHHcC--CCeEEEEEeCCC
Q 043252          284 ---KLQEELKKQLF--GKKFLLVLDDVW  306 (337)
Q Consensus       284 ---~~~~~l~~~L~--~kr~LlVlDdv~  306 (337)
                         .+...+...+.  .+--+||+|.+.
T Consensus       186 ~~~~~l~~l~~~~~~~~~~~lvVIDsl~  213 (324)
T 2z43_A          186 HQIAIVDDLQELVSKDPSIKLIVVDSVT  213 (324)
T ss_dssp             HHHHHHHHHHHHHHHCTTEEEEEETTTT
T ss_pred             HHHHHHHHHHHHHHhccCCCEEEEeCcH
Confidence               34445555553  456699999984

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.86  E-value=0.0015  Score=54.07  Aligned_cols=42  Identities=26%  Similarity=0.264  Sum_probs=33.2

Q ss_pred             chhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          194 RETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       194 r~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      |++.++.|.+.+....   .....+|+|.|+.|+|||||++.+..
T Consensus         3 ~~~~~~~l~~~~~~~~---~~~~~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIK---TAGRLVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             HHHHHHHHHHHHHTSC---CSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhc---cCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            5567788888887542   23457999999999999999998875

>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=96.79  E-value=0.00048  Score=61.96  Aligned_cols=50  Identities=28%  Similarity=0.389  Sum_probs=35.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.+...+..... .+.....+.|+|++|+||||||+.+.+.
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~-~~~~~~~~ll~Gp~G~GKTTLa~~ia~~   74 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKM-RGEVLDHVLLAGPPGLGKTTLAHIIASE   74 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHH-HTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHh-cCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            4578888777777666643200 0123457899999999999999999874

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.78  E-value=0.0019  Score=59.54  Aligned_cols=53  Identities=26%  Similarity=0.216  Sum_probs=38.0

Q ss_pred             cccccccchhHHHHHHHHHhc----CCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          187 EEAKVYGRETEKKEIVELLLK----DDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~----~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-.++.|.++.+++|.+.+.-    ++.   .+-...+-|.++|++|.|||.||+.+.+.
T Consensus       180 ~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e  239 (437)
T 4b4t_I          180 SYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQ  239 (437)
T ss_dssp             CGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHH
T ss_pred             cceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHH
Confidence            345688998888877665432    110   01234578999999999999999999985

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=96.75  E-value=0.013  Score=49.41  Aligned_cols=23  Identities=26%  Similarity=0.599  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999763

>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=96.70  E-value=0.0013  Score=57.98  Aligned_cols=51  Identities=22%  Similarity=0.269  Sum_probs=37.1

Q ss_pred             cccccchhHHHHHHHHHhcC--CC-C-----CCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKD--DS-R-----NDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~--~~-~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.+...+...  .. .     .......+.|+|++|+|||++|+.+.+.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   73 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999988877541  00 0     0012346789999999999999999874

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.67  E-value=0.005  Score=58.26  Aligned_cols=52  Identities=29%  Similarity=0.330  Sum_probs=34.1

Q ss_pred             ccccccchhHHHHHHHH---HhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVEL---LLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~---L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|.++.+.++.+.   +.....   -+-.-.+-+.|+|++|+||||||+.++..
T Consensus        30 f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~   87 (499)
T 2dhr_A           30 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   87 (499)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            35688988776665544   332210   00011234899999999999999999875

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.64  E-value=0.0018  Score=53.84  Aligned_cols=39  Identities=23%  Similarity=0.298  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.++|.+.+...    .+...+|+|+|+.|+|||||++.+..-
T Consensus         7 ~~~~~~~~~~~~----~~~g~~v~I~G~sGsGKSTl~~~l~~~   45 (208)
T 3c8u_A            7 LCQGVLERLDPR----QPGRQLVALSGAPGSGKSTLSNPLAAA   45 (208)
T ss_dssp             HHHHHHHHSCTT----CCSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc----CCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            345555655432    234579999999999999999998763

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=96.56  E-value=0.0088  Score=52.68  Aligned_cols=24  Identities=29%  Similarity=0.241  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+++|+|++|+||||++..+...
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~  128 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAI  128 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999999888653

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=96.56  E-value=0.0048  Score=55.72  Aligned_cols=93  Identities=18%  Similarity=0.214  Sum_probs=52.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccc----cceEEEEeCCCCCHHHHHHHHHHHhhCCC-----------CCCC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHF----DLKAWTCVSDDFDVIRLTKSILLSIASDQ-----------NVDN  279 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~wv~v~~~~~~~~~~~~il~~~~~~~-----------~~~~  279 (337)
                      .-.++.|+|+.|+|||||+..++.........    ..++|++....+....+ ..+........           ....
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~  208 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNS  208 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCCh
Confidence            45799999999999999999988642111111    23488887666544433 22333322110           0001


Q ss_pred             CCHHHHHHHHHHHcC------CCeEEEEEeCCCCC
Q 043252          280 HDLNKLQEELKKQLF------GKKFLLVLDDVWNE  308 (337)
Q Consensus       280 ~~~~~~~~~l~~~L~------~kr~LlVlDdv~~~  308 (337)
                      .....+...+...+.      .+.=|||||.+-..
T Consensus       209 ~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          209 NHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             HHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence            112233444444443      35669999999653

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.55  E-value=0.0038  Score=57.38  Aligned_cols=91  Identities=19%  Similarity=0.186  Sum_probs=51.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccc----cccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--------CCCCCHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVED----HFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--------VDNHDLN  283 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--------~~~~~~~  283 (337)
                      -.++.|+|++|+|||||+..++-......    .-..++|++....++...+. .+.+.++....        ....+..
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~-~~a~~~gl~~~~vleni~~~~~~~~~  256 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLV-SIAQRFGLDPDDALNNVAYARAYNAD  256 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHHH-HHHHHcCCChHhHhhcEEEeccCChH
Confidence            45999999999999999997653211111    22357888877766665533 34444432110        0112222


Q ss_pred             ---HHHHHHHHHcC-CCeEEEEEeCCCC
Q 043252          284 ---KLQEELKKQLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       284 ---~~~~~l~~~L~-~kr~LlVlDdv~~  307 (337)
                         .+...+...+. .+--+||+|.+-.
T Consensus       257 ~~~~~l~~~~~~l~~~~~~llVIDs~t~  284 (400)
T 3lda_A          257 HQLRLLDAAAQMMSESRFSLIVVDSVMA  284 (400)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETGGG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEecchhh
Confidence               22333333332 3566999999843

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.54  E-value=0.0015  Score=58.44  Aligned_cols=43  Identities=19%  Similarity=0.184  Sum_probs=36.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|++..++.+...+....        -+.++|++|+|||+||+.+.+.
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~--------~vll~G~pGtGKT~la~~la~~   69 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG--------HILLEGVPGLAKTLSVNTLAKT   69 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC--------CEEEESCCCHHHHHHHHHHHHH
T ss_pred             cceeCcHHHHHHHHHHHHcCC--------eEEEECCCCCcHHHHHHHHHHH
Confidence            458899999998888886532        5889999999999999999874

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.53  E-value=0.0012  Score=52.68  Aligned_cols=20  Identities=50%  Similarity=0.755  Sum_probs=18.8

Q ss_pred             EEEEEEccCCCchHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLV  236 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v  236 (337)
                      .+|.|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            37999999999999999998

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.51  E-value=0.0025  Score=60.36  Aligned_cols=43  Identities=16%  Similarity=0.255  Sum_probs=36.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.+...+....        -|.|+|++|+|||+||+.+.+.
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~--------~VLL~GpPGtGKT~LAraLa~~   64 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE--------SVFLLGPPGIAKSLIARRLKFA   64 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC--------EEEEECCSSSSHHHHHHHGGGG
T ss_pred             hhhHHHHHHHHHHHHHHhcCC--------eeEeecCchHHHHHHHHHHHHH
Confidence            347899999988888876543        6889999999999999999875

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.48  E-value=0.013  Score=52.05  Aligned_cols=45  Identities=16%  Similarity=0.132  Sum_probs=31.4

Q ss_pred             ccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       192 vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +|-...+..+...+....  ......+|+|.|+.|+|||||++.+..
T Consensus        70 ~~~~~~l~~~~~~~l~~~--~~~~p~iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           70 VTARQTLQQATYQFLGKP--EPKVPYIIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             HHHHHHHHHHHHHHHTCC--CCCCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             hcchHHHHHHHHHHhccC--CCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            344444555554554433  234577999999999999999998865

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.48  E-value=0.0018  Score=52.74  Aligned_cols=24  Identities=29%  Similarity=0.382  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++.|+|+.|+|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999764

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.47  E-value=0.0039  Score=54.71  Aligned_cols=42  Identities=19%  Similarity=0.305  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++++..++.... ......+|.|.|++|+||||+|+.+...
T Consensus        15 ~~~~~~~~~l~~~~-~~~~~~livl~G~sGsGKSTla~~L~~~   56 (287)
T 1gvn_B           15 RLNDNLEELIQGKK-AVESPTAFLLGGQPGSGKTSLRSAIFEE   56 (287)
T ss_dssp             HHHHHHHHHHTTCC-CCSSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccc-CCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34444444443332 2345679999999999999999999763

>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=96.43  E-value=0.0016  Score=53.57  Aligned_cols=52  Identities=19%  Similarity=0.239  Sum_probs=32.4

Q ss_pred             HHHHHHHHcCCCeE-EEEEeCCCC---CChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          285 LQEELKKQLFGKKF-LLVLDDVWN---ENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       285 ~~~~l~~~L~~kr~-LlVlDdv~~---~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      .....++.+.+.+| |||||++-.   ......+.+...+........||+|+|..
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            34556666766666 999999932   11223344555554445566799999963

>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=96.42  E-value=0.0019  Score=55.89  Aligned_cols=51  Identities=27%  Similarity=0.322  Sum_probs=34.4

Q ss_pred             cccccchhHHHHHHHHHhc---CCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLK---DDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~---~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.+.+.+..   +..   -+.....-+.|+|++|+|||+||+.+++.
T Consensus        11 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A           11 KDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             TTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            5689998888777765531   000   00011224779999999999999999875

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.40  E-value=0.019  Score=51.03  Aligned_cols=50  Identities=16%  Similarity=0.184  Sum_probs=33.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      -.++.|.|.+|+||||||..+..+.-...  ..++|++..  .+..++...++.
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~  117 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIV  117 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHH
Confidence            35999999999999999988875422222  456777655  345555555543

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=96.39  E-value=0.0018  Score=52.16  Aligned_cols=23  Identities=17%  Similarity=0.244  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|++|+||||+|+.+...
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~   26 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47999999999999999999763

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=96.38  E-value=0.0018  Score=51.69  Aligned_cols=23  Identities=22%  Similarity=0.189  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+++.+...
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999998653

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.36  E-value=0.0019  Score=52.39  Aligned_cols=23  Identities=13%  Similarity=0.469  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.+...
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            58999999999999999999764

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.35  E-value=0.002  Score=53.10  Aligned_cols=23  Identities=35%  Similarity=0.394  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|.|+|+.|+||||+++.+..
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            35899999999999999999975

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.34  E-value=0.0022  Score=51.56  Aligned_cols=22  Identities=36%  Similarity=0.459  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5899999999999999999976

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.33  E-value=0.004  Score=53.47  Aligned_cols=43  Identities=19%  Similarity=0.214  Sum_probs=30.5

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+.++..+..... ......+|.|+|++|+||||+|+.+...
T Consensus        13 ~~~~~~~~~~~~~~~-~~~~~~~i~l~G~~GsGKSTla~~L~~~   55 (253)
T 2p5t_B           13 HALARNLRSLTRGKK-SSKQPIAILLGGQSGAGKTTIHRIKQKE   55 (253)
T ss_dssp             HHHHHHHHHHHTTCC-CCSSCEEEEEESCGGGTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCC-cccCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            334455555554433 3445689999999999999999998763

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.32  E-value=0.0027  Score=52.38  Aligned_cols=24  Identities=38%  Similarity=0.401  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|+|+.|+|||||++.+...
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~   48 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQM   48 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999999998764

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.30  E-value=0.016  Score=53.80  Aligned_cols=24  Identities=25%  Similarity=0.412  Sum_probs=21.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|.++|.+|+||||++..+..
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHH
Confidence            468999999999999999987764

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.23  E-value=0.002  Score=51.62  Aligned_cols=23  Identities=26%  Similarity=0.407  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|+|+.|+|||||++.+...
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~   27 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999999999763

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=96.22  E-value=0.0043  Score=56.25  Aligned_cols=50  Identities=34%  Similarity=0.357  Sum_probs=36.0

Q ss_pred             ccccchhHHHHHHHHHhcC-------C--CCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVELLLKD-------D--SRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~-------~--~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|.+..++.+...+...       .  .........+.++|++|+|||++|+.+++.
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~   74 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARL   74 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4789998888888777310       0  001113457899999999999999999874

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.18  E-value=0.0026  Score=51.11  Aligned_cols=23  Identities=35%  Similarity=0.663  Sum_probs=20.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+++|+|+.|+|||||++.++.
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CEEEEEECCCCCCHHHHHHHHcc
Confidence            46999999999999999997553

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.18  E-value=0.0039  Score=50.06  Aligned_cols=23  Identities=26%  Similarity=0.502  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|.|+|+.|+||||+++.+..
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999875

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.17  E-value=0.003  Score=52.01  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.+...
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHhh
Confidence            48999999999999999999763

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=96.16  E-value=0.0033  Score=52.17  Aligned_cols=25  Identities=44%  Similarity=0.325  Sum_probs=21.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|+|+|+.|+|||||++.+..-
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~   29 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALART   29 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHH
Confidence            3469999999999999999998763

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.16  E-value=0.006  Score=56.91  Aligned_cols=87  Identities=21%  Similarity=0.213  Sum_probs=48.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhC-------CCCCCCCCHHH----H
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIAS-------DQNVDNHDLNK----L  285 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~-------~~~~~~~~~~~----~  285 (337)
                      .++|+|..|+|||||++.+..+.... +-+.++++.+.+.. ...+++.++...-..       ....+......    .
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~~~~-~~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~~~  231 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNIAQE-HGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVALT  231 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHHHHH-TCCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhhhhhc-cCcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHHHH
Confidence            68999999999999999988753222 22345666666543 233444444332000       00001111111    0


Q ss_pred             HHHHHHHc---CCCeEEEEEeCC
Q 043252          286 QEELKKQL---FGKKFLLVLDDV  305 (337)
Q Consensus       286 ~~~l~~~L---~~kr~LlVlDdv  305 (337)
                      .-.+.+++   ++++.||++||+
T Consensus       232 ~ltiAEyFrd~~G~~VLl~~D~i  254 (473)
T 1sky_E          232 GLTMAEYFRDEQGQDGLLFIDNI  254 (473)
T ss_dssp             HHHHHHHHHHHSCCEEEEEEECT
T ss_pred             HHHHHHHHHHhcCCcEEEEeccH
Confidence            11233333   589999999999

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.15  E-value=0.035  Score=51.44  Aligned_cols=24  Identities=33%  Similarity=0.311  Sum_probs=21.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|.++|++|+||||++..+..
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~  119 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAY  119 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999988864

>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=96.15  E-value=0.024  Score=53.07  Aligned_cols=38  Identities=18%  Similarity=0.340  Sum_probs=27.3

Q ss_pred             hhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       195 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.++.+...+....       ..+.|.|.+|.||||++..+...
T Consensus        31 ~~av~~~~~~i~~~~-------~~~li~G~aGTGKT~ll~~~~~~   68 (459)
T 3upu_A           31 KNAFNIVMKAIKEKK-------HHVTINGPAGTGATTLTKFIIEA   68 (459)
T ss_dssp             HHHHHHHHHHHHSSS-------CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCC-------CEEEEEeCCCCCHHHHHHHHHHH
Confidence            344455555554322       28999999999999999888764

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=96.15  E-value=0.0032  Score=52.38  Aligned_cols=24  Identities=33%  Similarity=0.523  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|+|+|+.|+|||||++.+...
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhh
Confidence            458999999999999999999764

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=96.14  E-value=0.0036  Score=50.97  Aligned_cols=24  Identities=33%  Similarity=0.383  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|++|+||||+++.+...
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~   28 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATG   28 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998753

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.14  E-value=0.0033  Score=51.14  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+++.+...
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~   24 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999764

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.13  E-value=0.0069  Score=54.46  Aligned_cols=46  Identities=20%  Similarity=0.255  Sum_probs=31.6

Q ss_pred             ccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          192 YGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       192 vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++.+.-.+.+++.|...-  ..+....|.|+|+.|+||||+++.+...
T Consensus         2 ~~~~~L~~~il~~l~~~i--~~g~~~~i~l~G~~G~GKTTl~~~la~~   47 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRI--EDNYRVCVILVGSPGSGKSTIAEELCQI   47 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTT--TTCSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHh--ccCCeeEEEEECCCCCcHHHHHHHHHHH
Confidence            344555666666664322  1234567999999999999999988653

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.12  E-value=0.0031  Score=51.98  Aligned_cols=24  Identities=33%  Similarity=0.535  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|+|+|+.|+|||||++.+...
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~   52 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADE   52 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHh
Confidence            459999999999999999999763

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.10  E-value=0.0031  Score=51.12  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=20.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+.|.|+|+.|+||||+|+.+..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999999865

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=96.09  E-value=0.0032  Score=51.11  Aligned_cols=22  Identities=41%  Similarity=0.537  Sum_probs=19.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|+|+.|+|||||++.++..
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999764

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=96.08  E-value=0.0036  Score=50.94  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++.|+|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999975

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.07  E-value=0.0029  Score=52.14  Aligned_cols=24  Identities=21%  Similarity=0.468  Sum_probs=21.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~   41 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEA   41 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999998764

>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=96.07  E-value=0.0053  Score=52.57  Aligned_cols=51  Identities=27%  Similarity=0.307  Sum_probs=32.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCC------CCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSR------NDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~------~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+..+.++.+....-...      +-.-.+-+.|+|++|+|||||++.++..
T Consensus        16 ~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~   72 (254)
T 1ixz_A           16 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   72 (254)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            56888876665554433210000      0001123899999999999999999875

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.05  E-value=0.0011  Score=54.24  Aligned_cols=22  Identities=27%  Similarity=0.070  Sum_probs=18.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++.|+|+.|+||||++..+..
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~   25 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVE   25 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4788999999999999955543

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=96.05  E-value=0.0032  Score=51.44  Aligned_cols=22  Identities=36%  Similarity=0.573  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|+|+.|+|||||++.+...
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~~   24 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            5789999999999999998753

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.03  E-value=0.0039  Score=51.38  Aligned_cols=24  Identities=29%  Similarity=0.504  Sum_probs=21.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|+|+|+.|+|||||++.+...
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999998763

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.01  E-value=0.058  Score=50.05  Aligned_cols=42  Identities=21%  Similarity=0.278  Sum_probs=29.0

Q ss_pred             HHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          197 EKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       197 ~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.++|.++|.....   ......++|.++|.+|+||||++..+..
T Consensus        78 ~~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~  122 (433)
T 2xxa_A           78 VRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGK  122 (433)
T ss_dssp             HHHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            34566666653221   0123578999999999999999987764

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=96.00  E-value=0.0036  Score=50.81  Aligned_cols=23  Identities=35%  Similarity=0.638  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+++.+...
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~   26 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDN   26 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999999999763

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.99  E-value=0.0056  Score=50.66  Aligned_cols=25  Identities=36%  Similarity=0.375  Sum_probs=22.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|+|+|+.|+|||||++.+...
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            4579999999999999999998763

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.97  E-value=0.0049  Score=50.59  Aligned_cols=24  Identities=38%  Similarity=0.404  Sum_probs=21.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|+|.|+.|+||||+++.+..
T Consensus         7 ~~~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            7 HPIIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999876

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.95  E-value=0.0032  Score=51.94  Aligned_cols=22  Identities=27%  Similarity=0.514  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++++|+|+.|+|||||++.+..
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            4789999999999999999875

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.93  E-value=0.004  Score=51.10  Aligned_cols=22  Identities=32%  Similarity=0.499  Sum_probs=20.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|+.|+||||+++.+...
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~   23 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKK   23 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHh
Confidence            6899999999999999999764

>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=95.93  E-value=0.014  Score=52.70  Aligned_cols=108  Identities=12%  Similarity=0.143  Sum_probs=56.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      .+++|+|+.|+|||||.+.+....  .......+ +.+.++....  .......+. ... ...........+...|...
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~~--~~~~~~~i-~t~ed~~e~~--~~~~~~~v~-q~~-~~~~~~~~~~~La~aL~~~  196 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDYL--NNTKYHHI-LTIEDPIEFV--HESKKCLVN-QRE-VHRDTLGFSEALRSALRED  196 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHH--HHHCCCEE-EEEESSCCSC--CCCSSSEEE-EEE-BTTTBSCHHHHHHHHTTSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcc--cCCCCcEE-EEccCcHHhh--hhcccccee-eee-eccccCCHHHHHHHHhhhC
Confidence            499999999999999999886531  11111111 2222221100  000000000 000 0011123445788888888


Q ss_pred             eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecCC
Q 043252          297 KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQ  336 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~~  336 (337)
                      .=+|++|++.+  .+.+..+....   ..|..||+||...
T Consensus       197 PdvillDEp~d--~e~~~~~~~~~---~~G~~vl~t~H~~  231 (356)
T 3jvv_A          197 PDIILVGEMRD--LETIRLALTAA---ETGHLVFGTLHTT  231 (356)
T ss_dssp             CSEEEESCCCS--HHHHHHHHHHH---HTTCEEEEEESCS
T ss_pred             cCEEecCCCCC--HHHHHHHHHHH---hcCCEEEEEEccC
Confidence            88999999964  35555543332   2355688888654

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.92  E-value=0.0063  Score=49.38  Aligned_cols=25  Identities=32%  Similarity=0.315  Sum_probs=22.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|.|++|+||||+++.+...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4578999999999999999998764

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.91  E-value=0.0046  Score=53.16  Aligned_cols=23  Identities=26%  Similarity=0.231  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||||+.+...
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhc
Confidence            47899999999999999998764

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.89  E-value=0.0037  Score=51.68  Aligned_cols=24  Identities=29%  Similarity=0.506  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|+|+.|+|||||++.+...
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~   35 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSE   35 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            458999999999999999998764

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=95.87  E-value=0.0039  Score=50.32  Aligned_cols=24  Identities=33%  Similarity=0.499  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|++|+||||+++.+...
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~   34 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASK   34 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHH
Confidence            457889999999999999998753

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.87  E-value=0.0063  Score=50.10  Aligned_cols=25  Identities=36%  Similarity=0.449  Sum_probs=22.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|.|+.|+||||+++.+...
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999999998763

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=95.86  E-value=0.0046  Score=51.82  Aligned_cols=22  Identities=41%  Similarity=0.522  Sum_probs=20.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|+|+|+.|+||||+++.+..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4899999999999999998865

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.85  E-value=0.0054  Score=49.90  Aligned_cols=23  Identities=26%  Similarity=0.356  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~   26 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEK   26 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999988753

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.84  E-value=0.0052  Score=50.12  Aligned_cols=24  Identities=25%  Similarity=0.378  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~   32 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQK   32 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999998763

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=95.84  E-value=0.0049  Score=50.81  Aligned_cols=22  Identities=36%  Similarity=0.462  Sum_probs=20.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|+|.|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3799999999999999999875

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=95.83  E-value=0.0049  Score=52.60  Aligned_cols=23  Identities=30%  Similarity=0.361  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|+|+|+.|+|||||++.+..
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            35999999999999999999984

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.83  E-value=0.0039  Score=50.10  Aligned_cols=22  Identities=45%  Similarity=0.604  Sum_probs=19.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+|+.+...
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            6899999999999999999763

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.82  E-value=0.0058  Score=54.29  Aligned_cols=25  Identities=24%  Similarity=0.216  Sum_probs=22.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|+|+|+.|+|||||++.+..-
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~gl  113 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQAL  113 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHhh
Confidence            4579999999999999999998763

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.81  E-value=0.0052  Score=50.96  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|+|||||++.+..
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~g   42 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRE   42 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35999999999999999999875

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=95.80  E-value=0.0058  Score=52.71  Aligned_cols=24  Identities=25%  Similarity=0.462  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|++|+||||+|+.+...
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~   27 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKI   27 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999998763

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=95.80  E-value=0.0054  Score=54.99  Aligned_cols=45  Identities=18%  Similarity=0.251  Sum_probs=32.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..+..+...+....      ..-+.|+|++|+|||+||+.+.+.
T Consensus        24 ~~i~G~~~~~~~l~~~~~~~~------~~~vLl~G~~GtGKT~la~~la~~   68 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAVDPG------IGGVLVFGDRGTGKSTAVRALAAL   68 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHCGG------GCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             hhccChHHHHHHHHHHhhCCC------CceEEEECCCCccHHHHHHHHHHh
Confidence            458999886665544443222      123889999999999999999874

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=95.79  E-value=0.0064  Score=49.38  Aligned_cols=23  Identities=35%  Similarity=0.431  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...|.|+|+.|+||||+++.+..
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999876

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=95.79  E-value=0.0066  Score=48.15  Aligned_cols=24  Identities=29%  Similarity=0.293  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|+|+.|.|||||++.++.-
T Consensus        33 Ge~v~L~G~nGaGKTTLlr~l~g~   56 (158)
T 1htw_A           33 AIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            359999999999999999999763

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=95.77  E-value=0.006  Score=53.95  Aligned_cols=24  Identities=29%  Similarity=0.409  Sum_probs=21.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+++|+|++|+|||||++.+..
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            346999999999999999998864

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=95.77  E-value=0.006  Score=50.38  Aligned_cols=22  Identities=36%  Similarity=0.502  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|+|.|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999965

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.76  E-value=0.0061  Score=49.34  Aligned_cols=23  Identities=26%  Similarity=0.258  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...|.|.|+.|+||||+++.+..
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999975

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.76  E-value=0.0057  Score=50.42  Aligned_cols=24  Identities=17%  Similarity=0.493  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|.|+|+.|+|||||++.+...
T Consensus        19 g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           19 RKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECcCCCCHHHHHHHHHhh
Confidence            468999999999999999998753

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=95.76  E-value=0.0088  Score=51.99  Aligned_cols=52  Identities=27%  Similarity=0.277  Sum_probs=33.1

Q ss_pred             ccccccchhHHHHHHHHHhcCCCC------CCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSR------NDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~------~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|.+..++++.+....-...      +-.-.+-+.|+|++|+|||||++.++..
T Consensus        39 ~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~   96 (278)
T 1iy2_A           39 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   96 (278)
T ss_dssp             GGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHH
Confidence            356889887766655443211000      0001123899999999999999999875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.76  E-value=0.0054  Score=48.83  Aligned_cols=25  Identities=32%  Similarity=0.388  Sum_probs=21.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|.|+.|+||||+++.+...
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~   30 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLA   30 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHH
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHH
Confidence            4669999999999999999998763

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.76  E-value=0.0062  Score=52.19  Aligned_cols=25  Identities=20%  Similarity=0.276  Sum_probs=21.7

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....+|+|.|+.|+||||+|+.+..
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3467999999999999999999876

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=95.76  E-value=0.0077  Score=48.84  Aligned_cols=24  Identities=29%  Similarity=0.357  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~   29 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998763

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.75  E-value=0.0058  Score=54.31  Aligned_cols=25  Identities=32%  Similarity=0.561  Sum_probs=20.9

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+.+||+|.|-|||||||.+-.+.-
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~   70 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSA   70 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHHH
Confidence            3578999999999999999977643

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=95.73  E-value=0.0059  Score=49.00  Aligned_cols=25  Identities=28%  Similarity=0.345  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...++.|+|+.|+|||||+..+...
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~   27 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAA   27 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            3569999999999999999988764

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.73  E-value=0.0079  Score=50.27  Aligned_cols=25  Identities=28%  Similarity=0.465  Sum_probs=21.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|+|.+|+|||||+..+...
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            3578999999999999999888764

>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=95.73  E-value=0.0078  Score=54.67  Aligned_cols=35  Identities=20%  Similarity=0.071  Sum_probs=26.1

Q ss_pred             HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          200 EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       200 ~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.++.+..-.     .-..++|+|+.|+|||||++.+.+.
T Consensus       163 raID~~~pi~-----rGQr~~IvG~sG~GKTtLl~~Iar~  197 (422)
T 3ice_A          163 RVLDLASPIG-----RGQRGLIVAPPKAGKTMLLQNIAQS  197 (422)
T ss_dssp             HHHHHHSCCB-----TTCEEEEECCSSSSHHHHHHHHHHH
T ss_pred             eeeeeeeeec-----CCcEEEEecCCCCChhHHHHHHHHH
Confidence            4556665332     2348999999999999999988764

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.73  E-value=0.0069  Score=51.67  Aligned_cols=23  Identities=22%  Similarity=0.274  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|+|.|+.|+|||||++.+..
T Consensus        25 g~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           25 PFLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999876

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=95.72  E-value=0.0097  Score=54.15  Aligned_cols=23  Identities=43%  Similarity=0.501  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.++|++|+|||++|+.+.+.
T Consensus        73 ~~ill~Gp~GtGKT~la~~la~~   95 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQTLAKH   95 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999999874

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.72  E-value=0.007  Score=50.72  Aligned_cols=26  Identities=27%  Similarity=0.313  Sum_probs=23.0

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.++|.|.|++|+||||.|+.+...
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999998764

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=95.70  E-value=0.0071  Score=49.73  Aligned_cols=24  Identities=25%  Similarity=0.284  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~   43 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEK   43 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999998763

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.70  E-value=0.0069  Score=49.98  Aligned_cols=23  Identities=30%  Similarity=0.456  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~   27 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDW   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH
Confidence            58999999999999999999764

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.69  E-value=0.005  Score=51.61  Aligned_cols=23  Identities=35%  Similarity=0.512  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.+...
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            48999999999999999998763

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=95.66  E-value=0.0045  Score=50.08  Aligned_cols=21  Identities=24%  Similarity=0.488  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +|.|.|++|+||||+|+.+..
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999865

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.65  E-value=0.0061  Score=49.83  Aligned_cols=23  Identities=35%  Similarity=0.424  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+|+.+...
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~   35 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEK   35 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999999999763

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=95.61  E-value=0.0068  Score=50.88  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|+|+.|+|||||.+.+...
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcc
Confidence            459999999999999999999864

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.61  E-value=0.04  Score=49.35  Aligned_cols=86  Identities=15%  Similarity=0.062  Sum_probs=52.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCC----------------------
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASD----------------------  274 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~----------------------  274 (337)
                      .++.|.|.+|+||||||..+......  .=..++|++.  ..+...+...++.....-                      
T Consensus        47 ~LiiIaG~pG~GKTt~al~ia~~~a~--~g~~Vl~fSl--Ems~~ql~~Rlls~~~~v~~~~l~~g~Ls~~e~~~l~~a~  122 (338)
T 4a1f_A           47 SLVIIGARPSMGKTSLMMNMVLSALN--DDRGVAVFSL--EMSAEQLALRALSDLTSINMHDLESGRLDDDQWENLAKCF  122 (338)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHH--TTCEEEEEES--SSCHHHHHHHHHHHHHCCCHHHHHHTCCCHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEeC--CCCHHHHHHHHHHHhhCCCHHHHhcCCCCHHHHHHHHHHH
Confidence            48999999999999999888764222  1124556554  345566666654432110                      


Q ss_pred             ----------CCCCCCCHHHHHHHHHHHcCC--CeEEEEEeCCC
Q 043252          275 ----------QNVDNHDLNKLQEELKKQLFG--KKFLLVLDDVW  306 (337)
Q Consensus       275 ----------~~~~~~~~~~~~~~l~~~L~~--kr~LlVlDdv~  306 (337)
                                ......+...+...+++..+.  ..-|||+|-+.
T Consensus       123 ~~l~~~~l~I~d~~~~si~~i~~~ir~l~~~~gg~~lIVIDyLq  166 (338)
T 4a1f_A          123 DHLSQKKLFFYDKSYVRIEQIRLQLRKLKSQHKELGIAFIDYLQ  166 (338)
T ss_dssp             HHHHHSCEEEECCTTCCHHHHHHHHHHHHHHCTTEEEEEEEEEE
T ss_pred             HHHhcCCeEEeCCCCCcHHHHHHHHHHHHHhcCCCCEEEEechH
Confidence                      001233566676666665432  46688888774

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=95.59  E-value=0.0055  Score=48.93  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~   25 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARA   25 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            37899999999999999998763

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=95.59  E-value=0.0084  Score=48.29  Aligned_cols=23  Identities=26%  Similarity=0.377  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|.|.|+.|+||||+++.+..
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=95.57  E-value=0.018  Score=51.00  Aligned_cols=24  Identities=29%  Similarity=0.317  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|+|+|+.|+|||||++.+..
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999876

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=95.56  E-value=0.0073  Score=50.47  Aligned_cols=24  Identities=29%  Similarity=0.257  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|+.|+||||+|+.+...
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~   27 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQER   27 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999998763

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.56  E-value=0.051  Score=50.80  Aligned_cols=89  Identities=11%  Similarity=0.097  Sum_probs=52.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHh------------------------
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSI------------------------  271 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~------------------------  271 (337)
                      -.++.|.|.+|+|||||+..+....... .=..++|++...  +...+...++...                        
T Consensus       203 G~liiI~G~pG~GKTtl~l~ia~~~~~~-~g~~Vl~~s~E~--s~~~l~~r~~~~~~~~~~~~l~~g~l~~~~~~~~~~a  279 (454)
T 2r6a_A          203 SDLIIVAARPSVGKTAFALNIAQNVATK-TNENVAIFSLEM--SAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMA  279 (454)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHHHHH-SSCCEEEEESSS--CHHHHHHHHHHHHHTCCHHHHHTSCCCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHh-CCCcEEEEECCC--CHHHHHHHHHHHHcCCCHHHHhcCCCCHHHHHHHHHH
Confidence            3599999999999999998887652211 112466766543  3444444443211                        


Q ss_pred             ----hCCC----CCCCCCHHHHHHHHHHHcC-CCeEEEEEeCCCC
Q 043252          272 ----ASDQ----NVDNHDLNKLQEELKKQLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       272 ----~~~~----~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~~  307 (337)
                          ....    .....+..++...++.... .+--+||+|.+..
T Consensus       280 ~~~l~~~~l~i~d~~~~s~~~i~~~~~~l~~~~~~~livID~l~~  324 (454)
T 2r6a_A          280 MGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQL  324 (454)
T ss_dssp             HHHHHSSCEEEECCTTCCHHHHHHHHHHHHTTTCCCEEEEECGGG
T ss_pred             HHHHhcCCEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEccHHH
Confidence                0000    0022356777777776653 3445999998843

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.56  E-value=0.0074  Score=51.77  Aligned_cols=23  Identities=35%  Similarity=0.456  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|+|+|+.|+|||||++.+..
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            35999999999999999999973

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.55  E-value=0.0073  Score=47.96  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=19.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRS   23 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999998763

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.54  E-value=0.0051  Score=49.61  Aligned_cols=24  Identities=33%  Similarity=0.300  Sum_probs=17.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~   28 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHER   28 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999998753

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.53  E-value=0.0066  Score=52.82  Aligned_cols=51  Identities=25%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             cccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|.++.++.|.+.+..+-.       -+-.-.+-+.|+|++|+||||||+.+...
T Consensus        10 ~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A           10 ADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             --CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            4567777777666654321000       00001122999999999999999999874

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.52  E-value=0.0074  Score=49.05  Aligned_cols=22  Identities=41%  Similarity=0.619  Sum_probs=20.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|.|.|+.|+||||+++.+...
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~   23 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEY   23 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999763

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=95.51  E-value=0.0082  Score=50.24  Aligned_cols=46  Identities=22%  Similarity=0.215  Sum_probs=31.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhccccc---c-cccceEEEEeCCCCCHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVE---D-HFDLKAWTCVSDDFDVI  261 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~-~F~~~~wv~v~~~~~~~  261 (337)
                      -.+++|+|+.|+|||||++.+.......   . .-...+|+.-...+...
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~   74 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPE   74 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHH
Confidence            4699999999999999999997531111   0 12346777765544443

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=95.47  E-value=0.014  Score=47.33  Aligned_cols=25  Identities=36%  Similarity=0.329  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4567899999999999999998764

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.46  E-value=0.011  Score=57.55  Aligned_cols=43  Identities=26%  Similarity=0.299  Sum_probs=36.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.+...+...        ..+.|+|++|+||||||+.+...
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g--------~~vll~Gp~GtGKTtlar~ia~~   83 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK--------RHVLLIGEPGTGKSMLGQAMAEL   83 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT--------CCEEEECCTTSSHHHHHHHHHHT
T ss_pred             ceEECchhhHhhccccccCC--------CEEEEEeCCCCCHHHHHHHHhcc
Confidence            56899988888887777543        37899999999999999999874

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=95.45  E-value=0.0089  Score=49.48  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+++.+...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~   32 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEA   32 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999999764

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.44  E-value=0.019  Score=51.95  Aligned_cols=24  Identities=38%  Similarity=0.394  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+++|+|+.|+|||||++.+..
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag  179 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAH  179 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHh
Confidence            467999999999999999998865

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.43  E-value=0.027  Score=61.34  Aligned_cols=85  Identities=21%  Similarity=0.110  Sum_probs=54.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~  290 (337)
                      ..+.+.|+|++|+|||+||.++......  .=..++|+.+.+.++...     ++.++.+...    ...+.+.....+.
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~--~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~ 1498 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQR--EGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD 1498 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT--TTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH--cCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHH
Confidence            3469999999999999999888764222  112467888888777655     3344321110    2334455555555


Q ss_pred             HHcC-CCeEEEEEeCCC
Q 043252          291 KQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       291 ~~L~-~kr~LlVlDdv~  306 (337)
                      ...+ .+--+||+|.+.
T Consensus      1499 ~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1499 ALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHTCCSEEEESCGG
T ss_pred             HHHhcCCCCEEEEcChh
Confidence            5543 456699999994

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=95.41  E-value=0.0085  Score=51.04  Aligned_cols=22  Identities=23%  Similarity=0.451  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        25 e~~~liG~nGsGKSTLl~~l~G   46 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            5899999999999999999974

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.40  E-value=0.0083  Score=49.97  Aligned_cols=41  Identities=24%  Similarity=0.265  Sum_probs=29.6

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +..+..+.+...+..      ....+|.|+|.+|+|||||+..+...
T Consensus        13 ~~~~~~~~~~~~~~~------~~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           13 ENKRLAEKNREALRE------SGTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             HHHHHHHHHHHHHHH------HTCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             hcHHHHHHHHHhhcc------cCceEEEEEcCCCCCHHHHHHHHHHH
Confidence            344455555555532      24679999999999999999888764

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=95.40  E-value=0.015  Score=48.33  Aligned_cols=22  Identities=32%  Similarity=0.294  Sum_probs=20.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +++|+|+.|+|||||.+.+..-
T Consensus        24 ~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           24 IVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             EEEEECCTTSSTTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            8999999999999999998753

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.40  E-value=0.06  Score=50.17  Aligned_cols=51  Identities=16%  Similarity=0.084  Sum_probs=33.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILL  269 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~  269 (337)
                      -.++.|.|.+|+||||||..+....... .=..++|++..  .+...+...++.
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~-~g~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALK-EGVGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEESS--SCHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHh-CCCeEEEEECC--CCHHHHHHHHHH
Confidence            3589999999999999998887642211 11246676654  345555555543

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.39  E-value=0.0085  Score=50.36  Aligned_cols=24  Identities=25%  Similarity=0.346  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|+.|+||||+|+.+...
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~   30 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTH   30 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999999763

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=95.39  E-value=0.0044  Score=51.42  Aligned_cols=22  Identities=36%  Similarity=0.560  Sum_probs=19.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +|+|.|+.|+||||+++.+...
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~   23 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGA   23 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            7899999999999999998754

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=95.39  E-value=0.059  Score=51.02  Aligned_cols=89  Identities=11%  Similarity=0.039  Sum_probs=52.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCC---------------------
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASD---------------------  274 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~---------------------  274 (337)
                      -.++.|.|.+|+||||||..+..+.... +=..++|++...  +..++...++.....-                     
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~~a~~-~g~~vl~~s~E~--s~~~l~~r~~~~~~~~~~~~~~~~~~g~l~~~~~~~~  318 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQWGTA-MGKKVGLAMLEE--SVEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQW  318 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHHHTTT-SCCCEEEEESSS--CHHHHHHHHHHHHTTSCCTTCHHHHHHHHHTSHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHHHHHh-cCCcEEEEeccC--CHHHHHHHHHHHHcCCChhhccccccCCCCHHHHHHH
Confidence            4589999999999999998887643221 112466776544  4555555544322110                     


Q ss_pred             -------C------CCCCCCHHHHHHHHHHHcCC-CeEEEEEeCCCC
Q 043252          275 -------Q------NVDNHDLNKLQEELKKQLFG-KKFLLVLDDVWN  307 (337)
Q Consensus       275 -------~------~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~  307 (337)
                             .      .....+.+.+...+++.... +-=+||+|.+..
T Consensus       319 ~~~~~~~~~l~i~~~~~~~~~~~i~~~i~~~~~~~~~~lvVID~l~~  365 (503)
T 1q57_A          319 FDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISI  365 (503)
T ss_dssp             HHHHHTTTCEEEECCC---CHHHHHHHHHHHHHTTCCSEEEEECTTC
T ss_pred             HHHHhccCCEEEECCCCCCCHHHHHHHHHHHHHhcCCCEEEEccchh
Confidence                   0      00124566777777665432 344999999854

>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=95.39  E-value=0.029  Score=47.30  Aligned_cols=89  Identities=16%  Similarity=0.192  Sum_probs=45.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc-ccccccc-cceEEEEeCCCCCHHHHHHHHHHHhhCCCCC------------------
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND-KQVEDHF-DLKAWTCVSDDFDVIRLTKSILLSIASDQNV------------------  277 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~-~~~~~~F-~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~------------------  277 (337)
                      .+.|+|+.|+||||+.....-+ ....... .+.+.+..........+...+...+......                  
T Consensus        78 ~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  157 (235)
T 3llm_A           78 VVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHAS  157 (235)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEECCCSSSE
T ss_pred             EEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEEeechhhccCCCCCe
Confidence            8899999999999877554322 1111122 2233333333222333444444333221100                  


Q ss_pred             -CCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          278 -DNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       278 -~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                       ...+.+.+...+...+.+- =+||||+++.
T Consensus       158 Ivv~Tpg~l~~~l~~~l~~~-~~lVlDEah~  187 (235)
T 3llm_A          158 IMFCTVGVLLRKLEAGIRGI-SHVIVDEIHE  187 (235)
T ss_dssp             EEEEEHHHHHHHHHHCCTTC-CEEEECCTTS
T ss_pred             EEEECHHHHHHHHHhhhcCC-cEEEEECCcc
Confidence             0123456666666544333 3789999976

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.39  E-value=0.0099  Score=52.48  Aligned_cols=24  Identities=38%  Similarity=0.394  Sum_probs=21.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+++|+|+.|+||||+++.+..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag  122 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAH  122 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            356999999999999999998865

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=95.38  E-value=0.0082  Score=50.97  Aligned_cols=22  Identities=27%  Similarity=0.540  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        32 e~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            4899999999999999999964

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.38  E-value=0.0092  Score=49.32  Aligned_cols=24  Identities=25%  Similarity=0.272  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+++.+...
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~   33 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEY   33 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999999999764

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=95.37  E-value=0.048  Score=50.38  Aligned_cols=24  Identities=29%  Similarity=0.281  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++.|+|.+|+||||++..+...
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~  121 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALY  121 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999888653

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.36  E-value=0.0076  Score=49.34  Aligned_cols=22  Identities=32%  Similarity=0.362  Sum_probs=19.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +++|+|+.|+|||||++.+...
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~   24 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhh
Confidence            6899999999999999988764

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=95.35  E-value=0.011  Score=49.04  Aligned_cols=24  Identities=29%  Similarity=0.268  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|.|+.|+||||+++.+...
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~~   48 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEHQ   48 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998763

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=95.35  E-value=0.0085  Score=50.45  Aligned_cols=22  Identities=36%  Similarity=0.533  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~G   52 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGL   52 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999964

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=95.29  E-value=0.014  Score=50.85  Aligned_cols=22  Identities=41%  Similarity=0.551  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            4899999999999999999964

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.28  E-value=0.0054  Score=49.36  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|..|+|||||++.+..-
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~   25 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPI   25 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999999998764

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=95.28  E-value=0.018  Score=49.09  Aligned_cols=25  Identities=20%  Similarity=0.118  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|.|++|+||||+|+.+...
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~   52 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKS   52 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999998753

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.26  E-value=0.009  Score=49.99  Aligned_cols=24  Identities=25%  Similarity=0.221  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|+.|+||||+++.+...
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~   28 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTK   28 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999999764

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=95.25  E-value=0.086  Score=50.90  Aligned_cols=23  Identities=30%  Similarity=0.525  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|.|||||++.+..
T Consensus       369 G~~~~ivG~sGsGKSTll~~l~g  391 (582)
T 3b5x_A          369 GKTVALVGRSGSGKSTIANLFTR  391 (582)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999964

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=95.25  E-value=0.013  Score=48.00  Aligned_cols=25  Identities=32%  Similarity=0.456  Sum_probs=22.3

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....+|+|.|+.|+||||+++.+..
T Consensus        10 ~~~~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHH
Confidence            3568999999999999999999875

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=95.25  E-value=0.013  Score=52.43  Aligned_cols=25  Identities=36%  Similarity=0.321  Sum_probs=21.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+++|+|+.|+||||+++.+...
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~  152 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANW  152 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999988753

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=95.23  E-value=0.012  Score=48.33  Aligned_cols=23  Identities=26%  Similarity=0.345  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|.|+.|+||||+++.+...
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHT
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH
Confidence            58999999999999999999764

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=95.23  E-value=0.012  Score=51.29  Aligned_cols=23  Identities=35%  Similarity=0.648  Sum_probs=21.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      ...+|+|.|+.|+||||+|+.+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            45799999999999999999987

>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=95.22  E-value=0.063  Score=53.64  Aligned_cols=100  Identities=20%  Similarity=0.194  Sum_probs=58.7

Q ss_pred             cccccccchhHHHHHHHHHhcCCC-------CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCC
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDS-------RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFD  259 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~-------~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~  259 (337)
                      .-..+.|.++.++.|.+.+.-+-.       -+-...+-|.++|++|.|||.||+.+.+.  ....|     +.++.   
T Consensus       475 ~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e--~~~~f-----~~v~~---  544 (806)
T 3cf2_A          475 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--CQANF-----ISIKG---  544 (806)
T ss_dssp             CSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHT--TTCEE-----EECCH---
T ss_pred             CHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHH--hCCce-----EEecc---
Confidence            345677888888887776543211       01223456889999999999999999985  22222     22221   


Q ss_pred             HHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          260 VIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       260 ~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                       .+    ++    ...  ...+...+...+...-+...++|+||++..
T Consensus       545 -~~----l~----s~~--vGese~~vr~lF~~Ar~~~P~IifiDEiDs  581 (806)
T 3cf2_A          545 -PE----LL----TMW--FGESEANVREIFDKARQAAPCVLFFDELDS  581 (806)
T ss_dssp             -HH----HH----TTT--CSSCHHHHHHHHHHHHTTCSEEEECSCGGG
T ss_pred             -ch----hh----ccc--cchHHHHHHHHHHHHHHcCCceeechhhhH
Confidence             11    11    111  222333344444444456789999999953

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.21  E-value=0.0065  Score=51.22  Aligned_cols=21  Identities=29%  Similarity=0.430  Sum_probs=15.9

Q ss_pred             EEEEEEccCCCchHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .+++|+|+.|+|||||++.+.
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~   48 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLL   48 (231)
T ss_dssp             CEEEEECSCC----CHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            589999999999999999998

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=95.18  E-value=0.022  Score=52.88  Aligned_cols=51  Identities=24%  Similarity=0.307  Sum_probs=35.7

Q ss_pred             cccccchhHHHHHHHHHhcC--------CCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKD--------DSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~--------~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+..++.|...+...        ........+-|.++|++|+||||+|+.+...
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~   73 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            45889888888876666321        0001112456889999999999999999864

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.18  E-value=0.011  Score=49.00  Aligned_cols=22  Identities=32%  Similarity=0.522  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999998653

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=95.17  E-value=0.014  Score=48.59  Aligned_cols=23  Identities=26%  Similarity=0.353  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999864

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=95.16  E-value=0.01  Score=51.22  Aligned_cols=22  Identities=41%  Similarity=0.601  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        33 e~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           33 DVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999964

>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=95.16  E-value=0.092  Score=50.60  Aligned_cols=102  Identities=16%  Similarity=0.145  Sum_probs=51.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHH-HHcC-
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELK-KQLF-  294 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~-~~L~-  294 (337)
                      .++.|.|.+|.||||++..+.......   ...+.+..........    +.+.+..    ...+...+..... .... 
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~---g~~Vl~~ApT~~Aa~~----L~e~~~~----~a~Tih~ll~~~~~~~~~~  273 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESL---GLEVGLCAPTGKAARR----LGEVTGR----TASTVHRLLGYGPQGFRHN  273 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHH----HHHHHTS----CEEEHHHHTTEETTEESCS
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhc---CCeEEEecCcHHHHHH----hHhhhcc----cHHHHHHHHcCCcchhhhh
Confidence            488999999999999998887642211   1234444433222222    2222211    1111111100000 0000 


Q ss_pred             ----CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          295 ----GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       295 ----~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                          .+-=+||+|++...+...+..+...++   .+.++|++
T Consensus       274 ~~~~~~~dvlIIDEasml~~~~~~~Ll~~~~---~~~~lilv  312 (574)
T 3e1s_A          274 HLEPAPYDLLIVDEVSMMGDALMLSLLAAVP---PGARVLLV  312 (574)
T ss_dssp             SSSCCSCSEEEECCGGGCCHHHHHHHHTTSC---TTCEEEEE
T ss_pred             hcccccCCEEEEcCccCCCHHHHHHHHHhCc---CCCEEEEE
Confidence                012389999987666666677766665   45666664

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.16  E-value=0.037  Score=60.33  Aligned_cols=85  Identities=22%  Similarity=0.135  Sum_probs=56.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~~  291 (337)
                      -.++.|+|++|+||||||.++.......  =..++|++....++...     ++.++.+...    +..+.+++.+.++.
T Consensus       383 G~lilI~G~pGsGKTtLaLqia~~~a~~--G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~I~~~~~~e~il~~~~~  455 (2050)
T 3cmu_A          383 GRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDA  455 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHHHTT--TCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEEcCCCHHHHH-----HHHcCCCHHHeEEeCCCCHHHHHHHHHH
Confidence            4599999999999999998887653221  23578888888776542     4444432211    33566777766665


Q ss_pred             HcC-CCeEEEEEeCCCC
Q 043252          292 QLF-GKKFLLVLDDVWN  307 (337)
Q Consensus       292 ~L~-~kr~LlVlDdv~~  307 (337)
                      ..+ .+--|||+|.+..
T Consensus       456 lv~~~~~~lIVIDSL~a  472 (2050)
T 3cmu_A          456 LARSGAVDVIVVDSVAA  472 (2050)
T ss_dssp             HHHHTCCSEEEESCGGG
T ss_pred             HHHhcCCcEEEECCHHH
Confidence            542 3455999999854

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=95.14  E-value=0.026  Score=53.00  Aligned_cols=42  Identities=33%  Similarity=0.381  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          197 EKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       197 ~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+.|.+.|.....   -.-....+++|+|..|+|||||++.+..
T Consensus       271 l~~~l~~~l~~~~~~Isl~i~~GeVI~LVGpNGSGKTTLl~~LAg  315 (503)
T 2yhs_A          271 LKEEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLAR  315 (503)
T ss_dssp             HHHHHHHHHHTTBCCCCCCSCTTEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCceeeccCCeEEEEECCCcccHHHHHHHHHH
Confidence            34455555543211   0123467999999999999999998875

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.14  E-value=0.0099  Score=49.62  Aligned_cols=23  Identities=26%  Similarity=0.460  Sum_probs=20.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|.|+.|+||||+|+.+...
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~   28 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKE   28 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999764

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=95.10  E-value=0.011  Score=50.28  Aligned_cols=22  Identities=32%  Similarity=0.570  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999964

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.10  E-value=0.13  Score=47.92  Aligned_cols=49  Identities=16%  Similarity=0.144  Sum_probs=31.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      -.++.|.|.+|+||||||..+..+.-..+  ..++|++...  +..++...++
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~g--~~vl~fSlEm--s~~ql~~R~~  245 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLEM--GKKENIKRLI  245 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHTT--CEEEEECSSS--CTTHHHHHHH
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHcC--CEEEEEECCC--CHHHHHHHHH
Confidence            35899999999999999988876532221  2456665443  3334444433

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.08  E-value=0.019  Score=47.46  Aligned_cols=38  Identities=11%  Similarity=0.016  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -+..+..++..-     +....+.|+|++|.||||+|..+.+.
T Consensus        44 f~~~l~~~~~~i-----Pkkn~ili~GPPGtGKTt~a~ala~~   81 (212)
T 1tue_A           44 FLGALKSFLKGT-----PKKNCLVFCGPANTGKSYFGMSFIHF   81 (212)
T ss_dssp             HHHHHHHHHHTC-----TTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-----CcccEEEEECCCCCCHHHHHHHHHHH
Confidence            355666666431     22347999999999999999888774

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=95.07  E-value=0.013  Score=48.73  Aligned_cols=22  Identities=23%  Similarity=0.460  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998653

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=95.07  E-value=0.012  Score=50.77  Aligned_cols=22  Identities=41%  Similarity=0.594  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        34 e~~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999964

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=95.07  E-value=0.013  Score=50.31  Aligned_cols=22  Identities=32%  Similarity=0.600  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999987

>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=95.06  E-value=0.15  Score=47.62  Aligned_cols=65  Identities=23%  Similarity=0.275  Sum_probs=42.9

Q ss_pred             HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHH
Q 043252          200 EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLS  270 (337)
Q Consensus       200 ~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~  270 (337)
                      +.++.|..-.     +-.-++|+|..|+|||+|++.+.++. .+.+-+.++++-+.+.. .+.+++.++...
T Consensus       142 r~ID~l~pig-----kGQr~~Ifgg~G~GKT~L~~~i~~~~-~~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          142 KVVDLLAPYA-----KGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             HHHHHHSCEE-----TTCEEEEEECTTSSHHHHHHHHHHHT-TTTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EEEecccccc-----cCCeeeeecCCCCChHHHHHHHHHhh-HhhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            4566665322     23478999999999999999887752 22333556777777654 345666666654

>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=95.06  E-value=0.016  Score=51.27  Aligned_cols=25  Identities=32%  Similarity=0.327  Sum_probs=22.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|+|++|+||||++..+...
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~  127 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKM  127 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHH
Confidence            4679999999999999999888754

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=95.06  E-value=0.013  Score=47.20  Aligned_cols=24  Identities=25%  Similarity=0.398  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++.|+|+.|+|||||+..+...
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHh
Confidence            569999999999999999988764

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=95.05  E-value=0.014  Score=49.71  Aligned_cols=23  Identities=35%  Similarity=0.456  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|+|||||.+.++.
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35999999999999999999964

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=95.04  E-value=0.012  Score=50.89  Aligned_cols=22  Identities=32%  Similarity=0.502  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        51 ei~~liG~NGsGKSTLlk~l~G   72 (263)
T 2olj_A           51 EVVVVIGPSGSGKSTFLRCLNL   72 (263)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEEcCCCCcHHHHHHHHHc
Confidence            4899999999999999999964

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=95.04  E-value=0.012  Score=50.99  Aligned_cols=22  Identities=41%  Similarity=0.691  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||++.+..
T Consensus        38 e~~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             CEEEEECCTTSCHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            4899999999999999999964

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.01  E-value=0.037  Score=49.22  Aligned_cols=25  Identities=28%  Similarity=0.484  Sum_probs=21.9

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....+|.|+|.+|+||||++..+..
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~LA~  127 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKMAN  127 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999988865

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=95.00  E-value=0.013  Score=50.67  Aligned_cols=23  Identities=35%  Similarity=0.499  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        47 e~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999873

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.98  E-value=0.01  Score=49.54  Aligned_cols=22  Identities=36%  Similarity=0.588  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~G   57 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTIST   57 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3899999999999999999975

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.98  E-value=0.013  Score=50.19  Aligned_cols=22  Identities=45%  Similarity=0.735  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999965

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.97  E-value=0.011  Score=50.71  Aligned_cols=22  Identities=32%  Similarity=0.563  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|.|+|+.|+||||+++.+..
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            3899999999999999999975

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=94.95  E-value=0.015  Score=47.34  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=21.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|..|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            457899999999999999998764

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.94  E-value=0.013  Score=50.37  Aligned_cols=22  Identities=32%  Similarity=0.573  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        42 ei~~l~G~NGsGKSTLlk~l~G   63 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLRIIST   63 (256)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4999999999999999999975

>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=94.94  E-value=0.093  Score=49.12  Aligned_cols=99  Identities=19%  Similarity=0.197  Sum_probs=59.9

Q ss_pred             HHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCC-----
Q 043252          201 IVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASD-----  274 (337)
Q Consensus       201 l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~-----  274 (337)
                      .++.|..-.     +-.-++|.|..|+|||+|++.+.++. .+.+-+.++++-+.+.. ...+++.++...=...     
T Consensus       155 vID~l~pig-----kGqr~gIfgg~GvGKT~L~~~l~~~~-a~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~  228 (498)
T 1fx0_B          155 VVNLLAPYR-----RGGKIGLFGGAGVGKTVLIMELINNI-AKAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIA  228 (498)
T ss_dssp             THHHHSCCC-----TTCCEEEEECSSSSHHHHHHHHHHHT-TTTCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTC
T ss_pred             Eeeeecccc-----cCCeEEeecCCCCCchHHHHHHHHHH-HhhCCCEEEEEEcccCcHHHHHHHHhhhccccccccccc
Confidence            456665332     23478999999999999999888752 22344677888887655 3456676666531111     


Q ss_pred             --CCC-----CCCC------HHHHHHHHHHHc---CCCeEEEEEeCC
Q 043252          275 --QNV-----DNHD------LNKLQEELKKQL---FGKKFLLVLDDV  305 (337)
Q Consensus       275 --~~~-----~~~~------~~~~~~~l~~~L---~~kr~LlVlDdv  305 (337)
                        ...     ....      .....-.+.+++   +++..||++||+
T Consensus       229 ~~rtvvV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~Dsi  275 (498)
T 1fx0_B          229 ESKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNI  275 (498)
T ss_dssp             CCCEEEEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECS
T ss_pred             ccceEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccH
Confidence              100     1111      112223344555   368999999998

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=94.90  E-value=0.015  Score=47.72  Aligned_cols=21  Identities=29%  Similarity=0.425  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +|+|.|+.|+||||+++.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            899999999999999999865

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.88  E-value=0.015  Score=50.52  Aligned_cols=22  Identities=41%  Similarity=0.665  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        46 e~~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           46 KVTALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999964

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=94.88  E-value=0.026  Score=48.30  Aligned_cols=26  Identities=27%  Similarity=0.314  Sum_probs=22.2

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .....++.+.|.||+|||||+..+..
T Consensus        11 ~~~~~i~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           11 GMASMIVVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             TCCCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CcceEEEEEeCCCCCCHHHHHHHHHH
Confidence            34567899999999999999998874

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=94.88  E-value=0.038  Score=59.37  Aligned_cols=86  Identities=21%  Similarity=0.115  Sum_probs=56.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC----CCCCCHHHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN----VDNHDLNKLQEELKK  291 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~----~~~~~~~~~~~~l~~  291 (337)
                      -+++.|+|++|+||||||.++......  .=..++|++....++...     ++.++.+..    ....+.+++.+.+..
T Consensus       383 G~lilI~G~pGsGKTtLaLq~a~~~~~--~G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~i~~~~~~e~~l~~l~~  455 (1706)
T 3cmw_A          383 GRIVEIYGPESSGKTTLTLQVIAAAQR--EGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDA  455 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHH--TTCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHH--hCCCeEEEEccCchHHHH-----HHHcCCCHHHeEEcCCCCHHHHHHHHHH
Confidence            459999999999999999888764222  223688898888777542     344433211    023456666666665


Q ss_pred             HcC-CCeEEEEEeCCCCC
Q 043252          292 QLF-GKKFLLVLDDVWNE  308 (337)
Q Consensus       292 ~L~-~kr~LlVlDdv~~~  308 (337)
                      ... .+--+||+|.+...
T Consensus       456 lv~~~~~~lVVIDSL~al  473 (1706)
T 3cmw_A          456 LARSGAVDVIVVDSVAAL  473 (1706)
T ss_dssp             HHHHTCCSEEEESCSTTC
T ss_pred             HHHhcCCCEEEECCHHHh
Confidence            442 34559999999543

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.86  E-value=0.015  Score=50.10  Aligned_cols=22  Identities=36%  Similarity=0.753  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999975

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=94.86  E-value=0.014  Score=49.92  Aligned_cols=22  Identities=27%  Similarity=0.530  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        27 e~~~liG~NGsGKSTLlk~l~G   48 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAG   48 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4899999999999999999875

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=94.85  E-value=0.016  Score=49.04  Aligned_cols=23  Identities=22%  Similarity=0.348  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|.|.|+.|+||||+++.+..
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999875

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.84  E-value=0.019  Score=49.54  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g   47 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMID   47 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHH
Confidence            35999999999999999998875

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.83  E-value=0.034  Score=50.21  Aligned_cols=37  Identities=27%  Similarity=0.409  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          198 KKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       198 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+...+....    ....+|+|+|.+|+|||||+..+..
T Consensus        65 ~~~~~~~~~~~~----~~~~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           65 AQQLLLRLLPDS----GNAHRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             HHHHHHHHGGGC----CCSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhHhhc----CCceEEEEECCCCCCHHHHHHHHHH
Confidence            444555554322    3567999999999999999988764

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=94.82  E-value=0.015  Score=50.38  Aligned_cols=22  Identities=36%  Similarity=0.524  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        34 e~~~liG~nGsGKSTLl~~i~G   55 (266)
T 2yz2_A           34 ECLLVAGNTGSGKSTLLQIVAG   55 (266)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4899999999999999999965

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.81  E-value=0.015  Score=50.76  Aligned_cols=22  Identities=32%  Similarity=0.499  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        48 e~~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4899999999999999999975

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=94.81  E-value=0.014  Score=47.05  Aligned_cols=21  Identities=43%  Similarity=0.551  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|+|+|.+|+|||||.+.+..
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999999876

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.80  E-value=0.017  Score=51.63  Aligned_cols=23  Identities=35%  Similarity=0.362  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||||+.+...
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~   30 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKK   30 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHHH
Confidence            58999999999999999998764

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=94.80  E-value=0.017  Score=47.90  Aligned_cols=73  Identities=10%  Similarity=0.092  Sum_probs=42.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHH-----------hhCCCCCCCCCHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLS-----------IASDQNVDNHDLNKLQ  286 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~-----------~~~~~~~~~~~~~~~~  286 (337)
                      +|.|.|++|+||+|.|+.+...      |. ...++      ..+++++-+..           +...   ..-+.+...
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~------~g-~~~is------tGdllR~~i~~~t~lg~~~~~~~~~G---~lvpd~iv~   65 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKE------KG-FVHIS------TGDILREAVQKGTPLGKKAKEYMERG---ELVPDDLII   65 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH------HC-CEEEE------HHHHHHHHHHHTCHHHHHHHHHHHHT---CCCCHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH------HC-CeEEc------HHHHHHHHHHhcChhhhhHHHHHhcC---CcCCHHHHH
Confidence            6889999999999999998764      32 12232      23444332221           1111   223344556


Q ss_pred             HHHHHHcCCCeEEEEEeCCCC
Q 043252          287 EELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       287 ~~l~~~L~~kr~LlVlDdv~~  307 (337)
                      ..+.+.+..... +|||++=.
T Consensus        66 ~lv~~~l~~~~~-~ilDGfPR   85 (206)
T 3sr0_A           66 ALIEEVFPKHGN-VIFDGFPR   85 (206)
T ss_dssp             HHHHHHCCSSSC-EEEESCCC
T ss_pred             HHHHHhhccCCc-eEecCCch
Confidence            667777755443 67898843

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=94.78  E-value=0.015  Score=49.92  Aligned_cols=23  Identities=30%  Similarity=0.632  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl   54 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGI   54 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999753

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.77  E-value=0.017  Score=48.40  Aligned_cols=22  Identities=41%  Similarity=0.492  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|+.|+||||+++.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~   23 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDK   23 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999998763

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=94.76  E-value=0.017  Score=47.93  Aligned_cols=22  Identities=32%  Similarity=0.392  Sum_probs=19.5

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEK   23 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998763

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.76  E-value=0.016  Score=47.34  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            357899999999999999999764

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=94.74  E-value=0.016  Score=48.79  Aligned_cols=26  Identities=27%  Similarity=0.074  Sum_probs=22.4

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....+|+|.|+.|+|||||++.+...
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc
Confidence            34579999999999999999998763

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=94.73  E-value=0.017  Score=50.96  Aligned_cols=23  Identities=22%  Similarity=0.342  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|.|||||++.+..
T Consensus       126 Ge~vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          126 KNCLAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHhh
Confidence            35999999999999999999875

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=94.73  E-value=0.019  Score=48.42  Aligned_cols=24  Identities=25%  Similarity=0.212  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|+.|+||||+|+.+...
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~   39 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKN   39 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357999999999999999999764

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.72  E-value=0.021  Score=44.41  Aligned_cols=23  Identities=22%  Similarity=0.408  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|.+|+|||||...+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999988764

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=94.71  E-value=0.021  Score=45.14  Aligned_cols=23  Identities=26%  Similarity=0.423  Sum_probs=20.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|+|+|.+|+|||||.+.+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47899999999999999998763

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=94.69  E-value=0.019  Score=50.36  Aligned_cols=22  Identities=36%  Similarity=0.459  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999876

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=94.66  E-value=0.018  Score=49.93  Aligned_cols=21  Identities=38%  Similarity=0.749  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++|+|+.|+|||||.+.++.
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g   24 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFK   24 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            689999999999999999975

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.61  E-value=0.024  Score=50.63  Aligned_cols=24  Identities=21%  Similarity=0.340  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.|+|+.|+|||||+..+...
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999999999863

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.60  E-value=0.021  Score=50.76  Aligned_cols=23  Identities=30%  Similarity=0.384  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|+|+.|+||||||+.+...
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~   28 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADA   28 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998763

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=94.53  E-value=0.029  Score=52.08  Aligned_cols=43  Identities=33%  Similarity=0.364  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.+++.....   .......+|.|+|.+|+||||++..+...
T Consensus        77 ~~~~l~~ll~~~~~~~~~~~~~~~vI~ivG~~GvGKTTla~~La~~  122 (432)
T 2v3c_C           77 VYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARY  122 (432)
T ss_dssp             HHHHHHHHHCCSCCCCCCCSSSCCCEEEECCSSSSTTHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcCccccCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34556666643311   01133579999999999999999887653

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=94.50  E-value=0.053  Score=49.25  Aligned_cols=36  Identities=19%  Similarity=0.148  Sum_probs=27.3

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++.|..-.     .-.-++|+|.+|+|||+|++.+.+.
T Consensus       163 iraID~l~Pig-----rGQR~lIfg~~g~GKT~Ll~~Ia~~  198 (427)
T 3l0o_A          163 TRLIDLFAPIG-----KGQRGMIVAPPKAGKTTILKEIANG  198 (427)
T ss_dssp             HHHHHHHSCCB-----TTCEEEEEECTTCCHHHHHHHHHHH
T ss_pred             chhhhhccccc-----CCceEEEecCCCCChhHHHHHHHHH
Confidence            35677776432     2347899999999999999988874

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.50  E-value=0.013  Score=51.49  Aligned_cols=23  Identities=22%  Similarity=0.455  Sum_probs=17.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|+|.|..|+||||+|+.+..
T Consensus         5 ~~iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            5 HPIISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             SCEEEEESCC---CCTHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999998875

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=94.50  E-value=0.021  Score=44.47  Aligned_cols=22  Identities=27%  Similarity=0.658  Sum_probs=19.5

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||...+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5789999999999999998754

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=94.49  E-value=0.025  Score=49.96  Aligned_cols=22  Identities=23%  Similarity=0.481  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|.|+|+.|+||||||..+..
T Consensus         4 ~~i~i~GptgsGKt~la~~La~   25 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAK   25 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHHHHHH
Confidence            5899999999999999999875

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=94.48  E-value=0.02  Score=49.43  Aligned_cols=22  Identities=36%  Similarity=0.522  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            3899999999999999999975

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=94.42  E-value=0.022  Score=49.45  Aligned_cols=22  Identities=32%  Similarity=0.452  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++.|+|++|+|||||+..+..
T Consensus        31 ~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           31 TVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            4999999999999999988875

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=94.42  E-value=0.023  Score=52.51  Aligned_cols=25  Identities=28%  Similarity=0.361  Sum_probs=22.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|+|++|+||||+|+.+...
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            4579999999999999999998764

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=94.40  E-value=0.029  Score=45.07  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=21.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|.+|+|||||.+.+...
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999999863

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=94.35  E-value=0.023  Score=49.73  Aligned_cols=23  Identities=26%  Similarity=0.355  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|+|++|+|||||++.+...
T Consensus        36 ~~~~i~G~~G~GKTTl~~~ia~~   58 (296)
T 1cr0_A           36 EVIMVTSGSGMGKSTFVRQQALQ   58 (296)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH
Confidence            49999999999999999988764

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=94.35  E-value=0.024  Score=50.34  Aligned_cols=25  Identities=36%  Similarity=0.523  Sum_probs=22.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.++.|+|+.|.|||||.+.+...
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhh
Confidence            4789999999999999999999854

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=94.34  E-value=0.13  Score=49.83  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|.|||||++.+..
T Consensus       369 Ge~~~ivG~sGsGKSTll~~l~g  391 (587)
T 3qf4_A          369 GSLVAVLGETGSGKSTLMNLIPR  391 (587)
T ss_dssp             TCEEEEECSSSSSHHHHHHTTTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999998864

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=94.34  E-value=0.031  Score=49.21  Aligned_cols=25  Identities=28%  Similarity=0.143  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|+|+.|+||||||..+...
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~   33 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKI   33 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHh
Confidence            3568999999999999999998763

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.33  E-value=0.048  Score=51.09  Aligned_cols=97  Identities=21%  Similarity=0.212  Sum_probs=53.2

Q ss_pred             HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHH-HHHHhccccccccc-ceEEEEeCCCC-CHHHHHHHHHHHhhCCCC
Q 043252          200 EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLA-QLVYNDKQVEDHFD-LKAWTCVSDDF-DVIRLTKSILLSIASDQN  276 (337)
Q Consensus       200 ~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~-~~~wv~v~~~~-~~~~~~~~il~~~~~~~~  276 (337)
                      +.++.|..-.     .-.-++|+|..|+|||+|| ..+.+..    .-+ .++++-+.+.. .+.++..++...=.....
T Consensus       151 raID~l~Pig-----rGQR~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~t  221 (502)
T 2qe7_A          151 KAIDSMIPIG-----RGQRELIIGDRQTGKTTIAIDTIINQK----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYT  221 (502)
T ss_dssp             HHHHHSSCCB-----TTCBCEEEECSSSCHHHHHHHHHHGGG----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTE
T ss_pred             eecccccccc-----cCCEEEEECCCCCCchHHHHHHHHHhh----cCCcEEEEEECCCcchHHHHHHHHHhhCCCccee
Confidence            3555655322     2336899999999999995 5776642    234 24666666643 344555555542111110


Q ss_pred             C----CC-CC-HHH-----HHHHHHHHc--CCCeEEEEEeCC
Q 043252          277 V----DN-HD-LNK-----LQEELKKQL--FGKKFLLVLDDV  305 (337)
Q Consensus       277 ~----~~-~~-~~~-----~~~~l~~~L--~~kr~LlVlDdv  305 (337)
                      .    .. .. ...     ..-.+.+++  +++..||++||+
T Consensus       222 vvV~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLl~~Dsl  263 (502)
T 2qe7_A          222 IVVTASASEPAPLLYLAPYAGCAMGEYFMYKGKHALVVYDDL  263 (502)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEECH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEecH
Confidence            0    11 11 111     111233333  589999999999

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.32  E-value=0.054  Score=51.22  Aligned_cols=41  Identities=32%  Similarity=0.374  Sum_probs=27.4

Q ss_pred             HHHHHHHHhcCCCC---CCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          198 KKEIVELLLKDDSR---NDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       198 ~~~l~~~L~~~~~~---~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++|.++|......   ......+|+|+|.+|+||||++..+..
T Consensus        80 ~~eL~~ll~~~~~~~~~~~~~~~vI~ivG~~GvGKTTl~~kLA~  123 (504)
T 2j37_W           80 FKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSKLAY  123 (504)
T ss_dssp             HHHHHHHHCCCCCCCCCCSS--EEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhccccchhccccCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            45566666542211   124578999999999999999988863

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=94.30  E-value=0.031  Score=47.08  Aligned_cols=25  Identities=36%  Similarity=0.414  Sum_probs=22.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|.|+.|+||||+++.+...
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999875

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=94.28  E-value=0.026  Score=51.39  Aligned_cols=24  Identities=29%  Similarity=0.091  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+++|+|+.|+|||||++.+...
T Consensus       169 ~~~i~l~G~~GsGKSTl~~~l~~~  192 (377)
T 1svm_A          169 KRYWLFKGPIDSGKTTLAAALLEL  192 (377)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            459999999999999999999863

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=94.26  E-value=0.025  Score=49.58  Aligned_cols=23  Identities=26%  Similarity=0.599  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        65 e~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           65 QLLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            48999999999999999999763

>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=94.26  E-value=0.028  Score=49.36  Aligned_cols=24  Identities=29%  Similarity=0.281  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+++|+|.+|+||||++..++..
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~  121 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALY  121 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            459999999999999999988753

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=94.24  E-value=0.025  Score=51.04  Aligned_cols=22  Identities=41%  Similarity=0.596  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        31 e~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCchHHHHHHHHhc
Confidence            4899999999999999999975

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=94.24  E-value=0.033  Score=43.57  Aligned_cols=24  Identities=21%  Similarity=0.404  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            446789999999999999998764

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=94.22  E-value=0.018  Score=50.82  Aligned_cols=23  Identities=26%  Similarity=0.610  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|+|||||++.+..
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCchHHHHHHHHHc
Confidence            35899999999999999999965

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.20  E-value=0.03  Score=47.32  Aligned_cols=24  Identities=29%  Similarity=0.347  Sum_probs=21.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|+|.|+.|+||||+++.+..
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999998875

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=94.19  E-value=0.066  Score=50.23  Aligned_cols=85  Identities=19%  Similarity=0.204  Sum_probs=48.1

Q ss_pred             EEEEEEccCCCchHHHH-HHHHhccccccccc-ceEEEEeCCCC-CHHHHHHHHHHHhhCCCC-----CCCCC-HHH---
Q 043252          217 SVIPIIGMGGLGKTTLA-QLVYNDKQVEDHFD-LKAWTCVSDDF-DVIRLTKSILLSIASDQN-----VDNHD-LNK---  284 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~-~~~wv~v~~~~-~~~~~~~~il~~~~~~~~-----~~~~~-~~~---  284 (337)
                      .-++|+|..|+|||+|| ..+.+..    .-+ .++++-+.+.. .+.++..++...=.....     ..... ...   
T Consensus       176 QR~~I~g~~g~GKT~Lal~~I~~~~----~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a  251 (515)
T 2r9v_A          176 QRELIIGDRQTGKTAIAIDTIINQK----GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIA  251 (515)
T ss_dssp             CBEEEEEETTSSHHHHHHHHHHTTT----TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHH
T ss_pred             CEEEEEcCCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHH
Confidence            36899999999999996 5777642    234 24666666643 344555555542111100     01111 111   


Q ss_pred             --HHHHHHHHc--CCCeEEEEEeCC
Q 043252          285 --LQEELKKQL--FGKKFLLVLDDV  305 (337)
Q Consensus       285 --~~~~l~~~L--~~kr~LlVlDdv  305 (337)
                        ..-.+.+++  +++..||++||+
T Consensus       252 ~~~a~tiAEyfrd~G~dVLli~Dsl  276 (515)
T 2r9v_A          252 PYAGCAMGEYFAYSGRDALVVYDDL  276 (515)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEEETH
T ss_pred             HHHHHHHHHHHHHcCCcEEEEeccH
Confidence              111233333  589999999999

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=94.18  E-value=0.12  Score=47.95  Aligned_cols=26  Identities=27%  Similarity=0.216  Sum_probs=23.1

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....++..|.|.+|.||||+.+...+
T Consensus       158 ~~~~~v~~I~G~aGsGKTt~I~~~~~  183 (446)
T 3vkw_A          158 VSSAKVVLVDGVPGCGKTKEILSRVN  183 (446)
T ss_dssp             CCCSEEEEEEECTTSCHHHHHHHHCC
T ss_pred             cccccEEEEEcCCCCCHHHHHHHHhc
Confidence            45688999999999999999998875

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=94.17  E-value=0.027  Score=45.40  Aligned_cols=23  Identities=26%  Similarity=0.602  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|.+|+|||||+..+...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999998754

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=94.14  E-value=0.044  Score=50.78  Aligned_cols=88  Identities=17%  Similarity=0.271  Sum_probs=49.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhccccc-cccc-ceEEEEeCCCC-CHHHHHHHHHHHhhCCCC-----CCCCC-HHH----
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVE-DHFD-LKAWTCVSDDF-DVIRLTKSILLSIASDQN-----VDNHD-LNK----  284 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~-~~~wv~v~~~~-~~~~~~~~il~~~~~~~~-----~~~~~-~~~----  284 (337)
                      -++|.|..|+|||+|+..+.+..... ++=+ .++++-+.+.. .+.+++.++...=.....     ..... ...    
T Consensus       153 r~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~~a~  232 (465)
T 3vr4_D          153 KLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATP  232 (465)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHHHHH
T ss_pred             EEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHHHHH
Confidence            57899999999999999998864331 1111 45566666543 445666665543101000     01111 111    


Q ss_pred             -HHHHHHHHc---CCCeEEEEEeCC
Q 043252          285 -LQEELKKQL---FGKKFLLVLDDV  305 (337)
Q Consensus       285 -~~~~l~~~L---~~kr~LlVlDdv  305 (337)
                       ..-.+.+++   +++..||++||+
T Consensus       233 ~~a~tiAEyfrd~~G~~VLl~~Dsl  257 (465)
T 3vr4_D          233 RMALTAAEYLAYEKGMHVLVIMTDM  257 (465)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEECH
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEcCh
Confidence             122344444   389999999999

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=94.13  E-value=0.037  Score=43.68  Aligned_cols=24  Identities=33%  Similarity=0.537  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||.+.+...
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            456899999999999999998764

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=94.12  E-value=0.028  Score=43.86  Aligned_cols=23  Identities=30%  Similarity=0.593  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|.+|+|||||...+...
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999998754

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=94.11  E-value=0.043  Score=43.45  Aligned_cols=25  Identities=32%  Similarity=0.391  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|+|.+|+|||||...+...
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999998764

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=94.10  E-value=0.03  Score=44.96  Aligned_cols=21  Identities=24%  Similarity=0.517  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +..|+|+.|.|||||+..++-
T Consensus        28 ~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHH
Confidence            889999999999999998853

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.06  E-value=0.035  Score=47.01  Aligned_cols=24  Identities=25%  Similarity=0.318  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|..|+||||+++.+...
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~   25 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH
Confidence            358999999999999999999864

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=94.06  E-value=0.03  Score=43.98  Aligned_cols=23  Identities=26%  Similarity=0.544  Sum_probs=20.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998763

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=94.06  E-value=0.029  Score=50.75  Aligned_cols=22  Identities=36%  Similarity=0.543  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        55 ei~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           55 QIYGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEEcCCCchHHHHHHHHhc
Confidence            4999999999999999999964

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=94.03  E-value=0.031  Score=43.74  Aligned_cols=22  Identities=27%  Similarity=0.585  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||.+.+.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5789999999999999998764

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.03  E-value=0.07  Score=43.78  Aligned_cols=85  Identities=22%  Similarity=0.176  Sum_probs=43.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHHHHc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELKKQL  293 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~~~L  293 (337)
                      .|+|=|.-|+||||.++.+++.-  ...-..++...-+......+.+..++..-......    -..+..+....+...|
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L--~~~g~~v~~treP~~t~~~~~ir~~l~~~~~~~~~~~ll~~a~r~~~~~~I~~~L   79 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYL--EKRGKKVILKREPGGTETGEKIRKILLEEEVTPKAELFLFLASRNLLVTEIKQYL   79 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCSSHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH--HHCCCcEEEEECCCCCcHHHHHHHHhhcccCChHHHHHHHHHHHHHHHHHHHHHH
Confidence            47888999999999999998752  22222233333333223334444444321100000    0011233445566666


Q ss_pred             CCCeEEEEEeCC
Q 043252          294 FGKKFLLVLDDV  305 (337)
Q Consensus       294 ~~kr~LlVlDdv  305 (337)
                      ... ..||.|-.
T Consensus        80 ~~g-~~Vi~DRy   90 (197)
T 3hjn_A           80 SEG-YAVLLDRY   90 (197)
T ss_dssp             TTT-CEEEEESC
T ss_pred             HCC-CeEEeccc
Confidence            544 35677765

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=94.03  E-value=0.03  Score=43.96  Aligned_cols=24  Identities=25%  Similarity=0.365  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            456899999999999999988754

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=94.02  E-value=0.03  Score=50.52  Aligned_cols=22  Identities=32%  Similarity=0.625  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        42 e~~~llGpnGsGKSTLLr~iaG   63 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAG   63 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4899999999999999999974

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=94.01  E-value=0.072  Score=54.21  Aligned_cols=21  Identities=24%  Similarity=0.071  Sum_probs=19.5

Q ss_pred             cEEEEEEccCCCchHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLV  236 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v  236 (337)
                      -.+++|.|+.|.||||+.+.+
T Consensus       662 g~i~~ItGpNGsGKSTlLr~i  682 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQT  682 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            469999999999999999988

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=93.97  E-value=0.032  Score=43.52  Aligned_cols=23  Identities=26%  Similarity=0.534  Sum_probs=19.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|..|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999888754

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.96  E-value=0.032  Score=43.73  Aligned_cols=22  Identities=14%  Similarity=0.400  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|..|+|||||...+.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5789999999999999888754

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=93.96  E-value=0.041  Score=44.47  Aligned_cols=25  Identities=24%  Similarity=0.509  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|+|..|+|||||...+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3457899999999999999998764

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=93.96  E-value=0.031  Score=44.88  Aligned_cols=24  Identities=29%  Similarity=0.378  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+...
T Consensus         7 ~~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            7 KCKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcC
Confidence            456789999999999999988764

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=93.96  E-value=0.031  Score=45.11  Aligned_cols=23  Identities=35%  Similarity=0.301  Sum_probs=19.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .--|.|+|.+|+|||||.+.+.+
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~   36 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYS   36 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            45688999999999999987764

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=93.96  E-value=0.077  Score=46.23  Aligned_cols=42  Identities=12%  Similarity=0.181  Sum_probs=29.8

Q ss_pred             HHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          198 KKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       198 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++.+.|.............|+|+|.+|+|||||...+...
T Consensus         8 ~~~l~~~l~~~~~~~~~~~~~i~vvG~~~~GKSSLln~l~g~   49 (299)
T 2aka_B            8 VNRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVGR   49 (299)
T ss_dssp             HHHHHHHHTTSCCCTTCCCCEEEEEEBTTSCHHHHHHHHHTS
T ss_pred             HHHHHHHHHhcCCCCCCCCCeEEEEeCCCCCHHHHHHHHHCC
Confidence            455566665433212335678999999999999999999765

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.95  E-value=0.032  Score=43.77  Aligned_cols=23  Identities=22%  Similarity=0.397  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|..|+|||||.+.+...
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999988764

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.91  E-value=0.037  Score=45.73  Aligned_cols=25  Identities=36%  Similarity=0.329  Sum_probs=21.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|+|.+|+|||||...+...
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4567899999999999999998764

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=93.91  E-value=0.04  Score=43.86  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=20.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|+|+|.+|+|||||.+.+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999864

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=93.90  E-value=0.033  Score=44.95  Aligned_cols=24  Identities=21%  Similarity=0.192  Sum_probs=20.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            446889999999999999877654

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=93.89  E-value=0.032  Score=50.74  Aligned_cols=22  Identities=27%  Similarity=0.570  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~llGpsGsGKSTLLr~iaG   51 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLRMIAG   51 (381)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEEcCCCchHHHHHHHHHc
Confidence            4899999999999999999975

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=93.89  E-value=0.032  Score=50.36  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~llGpnGsGKSTLLr~iaG   51 (359)
T 2yyz_A           30 EFVALLGPSGCGKTTTLLMLAG   51 (359)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEEcCCCchHHHHHHHHHC
Confidence            4899999999999999999974

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=93.87  E-value=0.033  Score=43.49  Aligned_cols=21  Identities=29%  Similarity=0.406  Sum_probs=18.8

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|.+|+|||||...+...
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            789999999999999988753

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.87  E-value=0.032  Score=43.69  Aligned_cols=21  Identities=29%  Similarity=0.580  Sum_probs=18.9

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|.|+|.+|+|||||.+.+.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            578999999999999998864

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.84  E-value=0.1  Score=43.70  Aligned_cols=25  Identities=36%  Similarity=0.478  Sum_probs=22.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|.|+.|+||||+++.+.+.
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~   44 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEY   44 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999999999875

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.84  E-value=0.033  Score=50.34  Aligned_cols=22  Identities=27%  Similarity=0.496  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~llGpnGsGKSTLLr~iaG   51 (362)
T 2it1_A           30 EFMALLGPSGSGKSTLLYTIAG   51 (362)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCchHHHHHHHHhc
Confidence            4899999999999999999975

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.83  E-value=0.045  Score=44.07  Aligned_cols=25  Identities=20%  Similarity=0.418  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|+|..|+|||||...+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           22 LKGEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             TTCEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHcC
Confidence            3457889999999999999998765

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=93.82  E-value=0.09  Score=56.59  Aligned_cols=84  Identities=20%  Similarity=0.130  Sum_probs=57.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~  290 (337)
                      .-++|-|+|+.|+||||||.++...  .+..=...+|+...+.++..-     ++.++.+...    .+..-++....+.
T Consensus      1430 rg~~iei~g~~~sGkttl~~~~~a~--~~~~g~~~~~i~~e~~~~~~~-----~~~~Gv~~~~l~~~~p~~~e~~l~~~~ 1502 (1706)
T 3cmw_A         1430 MGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD 1502 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH--HHhcCCeEEEEecCCCCCHHH-----HHHcCCCHHHeEEeCCCcHHHHHHHHH
Confidence            3479999999999999999888754  333335688999888887664     5555544321    3344455555566


Q ss_pred             HHcC-CCeEEEEEeCC
Q 043252          291 KQLF-GKKFLLVLDDV  305 (337)
Q Consensus       291 ~~L~-~kr~LlVlDdv  305 (337)
                      ..++ +.--+||+|-|
T Consensus      1503 ~~~~s~~~~~vvvDsv 1518 (1706)
T 3cmw_A         1503 ALARSGAVDVIVVDSV 1518 (1706)
T ss_dssp             HHHHHTCCSEEEESCS
T ss_pred             HHHHcCCCCEEEEccH
Confidence            6664 44559999988

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=93.82  E-value=0.035  Score=43.99  Aligned_cols=24  Identities=25%  Similarity=0.519  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus         7 ~~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            7 LFKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            456899999999999999998754

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=93.82  E-value=0.04  Score=45.25  Aligned_cols=23  Identities=26%  Similarity=0.294  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|.|+.|+||||||..+...
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            47899999999999999998753

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=93.81  E-value=0.034  Score=46.89  Aligned_cols=39  Identities=18%  Similarity=0.202  Sum_probs=26.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSD  256 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~  256 (337)
                      -.++.|.|++|+|||||+..+.....  ..=..++|++...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~--~~~~~v~~~~~e~   61 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGL--KMGEPGIYVALEE   61 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHH--HTTCCEEEEESSS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEEccC
Confidence            35899999999999999877754321  1112466776544

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=93.79  E-value=0.036  Score=43.48  Aligned_cols=23  Identities=35%  Similarity=0.469  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|..|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            46899999999999999988754

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.78  E-value=0.061  Score=42.57  Aligned_cols=25  Identities=28%  Similarity=0.368  Sum_probs=21.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..--|.|+|.+|+|||||...+...
T Consensus         5 ~~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            5 RQLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             ceEEEEEECcCCCCHHHHHHHHHhC
Confidence            3456889999999999999988754

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=93.78  E-value=0.041  Score=44.13  Aligned_cols=25  Identities=28%  Similarity=0.385  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|.+|+|||||...+...
T Consensus        15 ~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           15 QEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhcC
Confidence            3567899999999999999998764

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=93.77  E-value=0.035  Score=50.45  Aligned_cols=22  Identities=27%  Similarity=0.507  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~llGpnGsGKSTLLr~iaG   51 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAG   51 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCcHHHHHHHHHHc
Confidence            4899999999999999999974

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=93.77  E-value=0.035  Score=44.56  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||...+...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            5789999999999999998764

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=93.76  E-value=0.036  Score=44.77  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHhC
Confidence            456889999999999999888754

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.75  E-value=0.046  Score=43.38  Aligned_cols=25  Identities=36%  Similarity=0.530  Sum_probs=21.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|.+|+|||||...+...
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            3567899999999999999888764

>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=93.75  E-value=0.089  Score=48.75  Aligned_cols=87  Identities=13%  Similarity=0.226  Sum_probs=49.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhccccc--------cccc-ceEEEEeCCCC-CHHHHHHHHHHHh--hC-----CCCCCCC
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVE--------DHFD-LKAWTCVSDDF-DVIRLTKSILLSI--AS-----DQNVDNH  280 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~--------~~F~-~~~wv~v~~~~-~~~~~~~~il~~~--~~-----~~~~~~~  280 (337)
                      -++|.|..|+|||+|+..+.+.....        ++=+ .++++-+.+.. .+.+++.++...=  ..     ... +..
T Consensus       149 r~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~rtvvv~~t~-d~p  227 (464)
T 3gqb_B          149 KLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKA-DDP  227 (464)
T ss_dssp             BCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGGEEEEEEET-TSC
T ss_pred             EEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccceEEEEECC-CCC
Confidence            67899999999999999998764431        1111 45566666543 3455555544321  00     001 111


Q ss_pred             CHHH-----HHHHHHHHc---CCCeEEEEEeCC
Q 043252          281 DLNK-----LQEELKKQL---FGKKFLLVLDDV  305 (337)
Q Consensus       281 ~~~~-----~~~~l~~~L---~~kr~LlVlDdv  305 (337)
                      ....     ..-.+.+++   +++..||++||+
T Consensus       228 ~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~Ddl  260 (464)
T 3gqb_B          228 TIERILTPRMALTVAEYLAFEHDYHVLVILTDM  260 (464)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTCCEEEEEEETH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcCh
Confidence            2221     122334444   389999999999

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=93.75  E-value=0.053  Score=47.76  Aligned_cols=32  Identities=22%  Similarity=0.314  Sum_probs=25.6

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHH
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .+++|.+.+.         -.+++|+|+.|+|||||.+.+.
T Consensus       155 gi~~L~~~l~---------G~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          155 GIDELVDYLE---------GFICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             THHHHHHHTT---------TCEEEEECSTTSSHHHHHHHHH
T ss_pred             CHHHHHhhcc---------CcEEEEECCCCCCHHHHHHHHH
Confidence            3566666663         2389999999999999999997

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=93.75  E-value=0.037  Score=43.34  Aligned_cols=23  Identities=17%  Similarity=0.326  Sum_probs=20.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|..|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999988753

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.74  E-value=0.046  Score=42.88  Aligned_cols=22  Identities=32%  Similarity=0.454  Sum_probs=19.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      --|.|+|.+|+|||||...+..
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4588999999999999998853

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=93.72  E-value=0.036  Score=50.32  Aligned_cols=22  Identities=27%  Similarity=0.523  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        38 e~~~llGpnGsGKSTLLr~iaG   59 (372)
T 1v43_A           38 EFLVLLGPSGCGKTTTLRMIAG   59 (372)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHHc
Confidence            4899999999999999999974

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=93.71  E-value=0.05  Score=43.09  Aligned_cols=25  Identities=24%  Similarity=0.454  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|..|+|||||...+...
T Consensus         8 ~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            8 ETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            4567899999999999999998764

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.70  E-value=0.041  Score=47.29  Aligned_cols=23  Identities=35%  Similarity=0.579  Sum_probs=19.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|+|.|-||+||||+|..+...
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~   24 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSG   24 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH
T ss_pred             cEEEEecCCCCcHHHHHHHHHHH
Confidence            57888999999999999877653

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=93.67  E-value=0.035  Score=50.26  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...++|+|+.|+|||||++.+..
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~g  192 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAA  192 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999998865

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=93.66  E-value=0.038  Score=44.77  Aligned_cols=23  Identities=35%  Similarity=0.602  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|+|.+|+|||||...+.+.
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            36799999999999999988763

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=93.65  E-value=0.046  Score=48.98  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=21.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+++|+|++|+|||||.+.+..
T Consensus        54 ~g~~v~i~G~~GaGKSTLl~~l~g   77 (337)
T 2qm8_A           54 RAIRVGITGVPGVGKSTTIDALGS   77 (337)
T ss_dssp             CSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999874

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.64  E-value=0.045  Score=49.26  Aligned_cols=24  Identities=21%  Similarity=0.177  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|+|+|++|+|||||...+..
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~   96 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGK   96 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHH
Confidence            467999999999999999998875

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.64  E-value=0.033  Score=44.19  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|..|+|||||...+...
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcC
Confidence            4567899999999999999998754

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=93.62  E-value=0.04  Score=43.64  Aligned_cols=25  Identities=28%  Similarity=0.248  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|..|+|||||...+...
T Consensus        14 ~~~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           14 YIFKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECCCCCCHHHHHHHHHcC
Confidence            3457899999999999999998764

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=93.62  E-value=0.03  Score=45.74  Aligned_cols=22  Identities=27%  Similarity=0.542  Sum_probs=19.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .-|.|+|.+|+|||||.+.+..
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3578999999999999999875

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=93.61  E-value=0.045  Score=47.65  Aligned_cols=23  Identities=35%  Similarity=0.534  Sum_probs=19.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++|+|.|-||+||||+|..+..
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~   24 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVA   24 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHH
Confidence            36888899999999999987765

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=93.59  E-value=0.024  Score=46.54  Aligned_cols=24  Identities=17%  Similarity=0.191  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|..|+|||||.+.+...
T Consensus        26 ~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           26 GIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999888653

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=93.58  E-value=0.028  Score=48.36  Aligned_cols=25  Identities=24%  Similarity=0.256  Sum_probs=21.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|.|..|+||||+++.+...
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~   47 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQL   47 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHh
Confidence            3579999999999999999988764

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=93.58  E-value=0.04  Score=44.10  Aligned_cols=23  Identities=22%  Similarity=0.508  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|..|+|||||...+.+.
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999998764

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=93.58  E-value=0.04  Score=44.07  Aligned_cols=24  Identities=25%  Similarity=0.383  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+.+.
T Consensus        10 ~~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           10 LFKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            457889999999999999988754

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=93.56  E-value=0.034  Score=48.96  Aligned_cols=21  Identities=33%  Similarity=0.662  Sum_probs=18.6

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|+|+|..|+|||||.+.++.
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            349999999999999999775

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=93.56  E-value=0.041  Score=43.55  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=19.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|..|+|||||...+...
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999988753

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=93.54  E-value=0.23  Score=41.86  Aligned_cols=100  Identities=16%  Similarity=0.134  Sum_probs=53.3

Q ss_pred             EEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhC---C--------CC----CCCCCHH
Q 043252          219 IPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIAS---D--------QN----VDNHDLN  283 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~---~--------~~----~~~~~~~  283 (337)
                      +.|+|+.|.|||.+|..+....    . ...+++ ++.    ..+..++.+.+..   .        ..    ....+.+
T Consensus       111 ~ll~~~tG~GKT~~a~~~~~~~----~-~~~liv-~P~----~~L~~q~~~~~~~~~~~~v~~~~g~~~~~~~i~v~T~~  180 (237)
T 2fz4_A          111 GCIVLPTGSGKTHVAMAAINEL----S-TPTLIV-VPT----LALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYD  180 (237)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS----C-SCEEEE-ESS----HHHHHHHHHHHGGGCGGGEEEESSSCBCCCSEEEEEHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHc----C-CCEEEE-eCC----HHHHHHHHHHHHhCCCCeEEEEeCCCCCcCCEEEEeHH
Confidence            7789999999999998776542    1 123333 222    1233334333322   1        00    0001223


Q ss_pred             HHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          284 KLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       284 ~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                      .+..... .+..+--+||+|++.......+..+...++   ...++++|
T Consensus       181 ~l~~~~~-~~~~~~~llIiDEaH~l~~~~~~~i~~~~~---~~~~l~LS  225 (237)
T 2fz4_A          181 SAYVNAE-KLGNRFMLLIFDEVHHLPAESYVQIAQMSI---APFRLGLT  225 (237)
T ss_dssp             HHHHTHH-HHTTTCSEEEEECSSCCCTTTHHHHHHTCC---CSEEEEEE
T ss_pred             HHHhhHH-HhcccCCEEEEECCccCCChHHHHHHHhcc---CCEEEEEe
Confidence            3433333 333445599999998765566777766554   23345555

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=93.53  E-value=0.03  Score=50.41  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        27 e~~~llGpnGsGKSTLLr~iaG   48 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAG   48 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHT
T ss_pred             CEEEEECCCCccHHHHHHHHHc
Confidence            4899999999999999999975

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=93.51  E-value=0.042  Score=44.13  Aligned_cols=25  Identities=20%  Similarity=0.242  Sum_probs=21.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|..|+|||||...+...
T Consensus        10 ~~~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           10 YLIKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEEECCCCCCHHHHHHHHhcC
Confidence            3457889999999999999998764

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=93.51  E-value=0.077  Score=49.38  Aligned_cols=89  Identities=15%  Similarity=0.218  Sum_probs=50.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhccccccc--ccceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC-----CCCC-HH----
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDH--FDLKAWTCVSDDF-DVIRLTKSILLSIASDQNV-----DNHD-LN----  283 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~-----~~~~-~~----  283 (337)
                      .-++|.|..|+|||+|+..+.++......  =+.++++-+.+.. .+.+++.++...=......     .... ..    
T Consensus       153 Qr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~r~~~  232 (469)
T 2c61_A          153 QKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVT  232 (469)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHHHHHH
Confidence            36778899999999999999876443111  0245566665543 3456666665431111000     1111 11    


Q ss_pred             -HHHHHHHHHc---CCCeEEEEEeCC
Q 043252          284 -KLQEELKKQL---FGKKFLLVLDDV  305 (337)
Q Consensus       284 -~~~~~l~~~L---~~kr~LlVlDdv  305 (337)
                       ...-.+.+++   +++..||++||+
T Consensus       233 ~~~a~tiAEyfrdd~G~dVLl~~Dsl  258 (469)
T 2c61_A          233 PRMALTAAEYLAYEHGMHVLVILTDI  258 (469)
T ss_dssp             HHHHHHHHHHHHHHHCCEEEEEEECH
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeCH
Confidence             1122233343   379999999998

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=93.49  E-value=0.042  Score=43.81  Aligned_cols=23  Identities=26%  Similarity=0.329  Sum_probs=19.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|.+|+|||||...+.+.
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999888754

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=93.48  E-value=0.031  Score=44.41  Aligned_cols=24  Identities=17%  Similarity=0.221  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            7 ELRLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEEEECCGGGCHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346789999999999999988764

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=93.47  E-value=0.048  Score=49.55  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|+|||||++.+..
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~  158 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMID  158 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            45899999999999999998875

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=93.47  E-value=0.043  Score=44.34  Aligned_cols=24  Identities=29%  Similarity=0.437  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+...
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           25 VFKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            457899999999999999988764

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=93.46  E-value=0.043  Score=43.74  Aligned_cols=24  Identities=29%  Similarity=0.596  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+...
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhC
Confidence            456889999999999999998754

>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=93.44  E-value=0.04  Score=48.43  Aligned_cols=23  Identities=39%  Similarity=0.417  Sum_probs=20.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++.++|.+|+||||++..+..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~  120 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAY  120 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56999999999999999988864

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=93.44  E-value=0.046  Score=50.00  Aligned_cols=22  Identities=36%  Similarity=0.537  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|.|.|+.|+||||||..+..
T Consensus         3 ~~i~i~GptgsGKttla~~La~   24 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQ   24 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHH
Confidence            5899999999999999998875

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=93.43  E-value=0.044  Score=43.54  Aligned_cols=24  Identities=25%  Similarity=0.365  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            346889999999999999988764

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.43  E-value=0.057  Score=48.86  Aligned_cols=23  Identities=39%  Similarity=0.567  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.+...
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~  198 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQE  198 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            38999999999999999999863

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=93.43  E-value=0.044  Score=43.58  Aligned_cols=23  Identities=26%  Similarity=0.281  Sum_probs=20.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|.+|+|||||...+...
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            46789999999999999988764

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=93.43  E-value=0.044  Score=44.54  Aligned_cols=23  Identities=35%  Similarity=0.628  Sum_probs=19.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..-|.|+|.+|+|||||...+..
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            35689999999999999988864

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=93.43  E-value=0.05  Score=43.33  Aligned_cols=24  Identities=25%  Similarity=0.389  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            457889999999999999988753

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=93.40  E-value=0.24  Score=49.48  Aligned_cols=33  Identities=24%  Similarity=0.441  Sum_probs=23.3

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHH
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      ..+.+...+...        .++.|+|+.|.||||++..+.
T Consensus        98 q~~~i~~~l~~~--------~~vii~gpTGSGKTtllp~ll  130 (773)
T 2xau_A           98 QRDEFLKLYQNN--------QIMVFVGETGSGKTTQIPQFV  130 (773)
T ss_dssp             GHHHHHHHHHHC--------SEEEEECCTTSSHHHHHHHHH
T ss_pred             HHHHHHHHHhCC--------CeEEEECCCCCCHHHHHHHHH
Confidence            345556666432        389999999999999665553

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=93.39  E-value=0.06  Score=42.24  Aligned_cols=24  Identities=33%  Similarity=0.371  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998754

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=93.38  E-value=0.044  Score=44.55  Aligned_cols=23  Identities=22%  Similarity=0.520  Sum_probs=19.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..-|.|+|.+|+|||||.+.+.+
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l~~   42 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVVFH   42 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            34688999999999999987765

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=93.38  E-value=0.035  Score=45.27  Aligned_cols=23  Identities=35%  Similarity=0.538  Sum_probs=20.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      ...-|.|+|.+|+|||||.+.+.
T Consensus        22 ~~~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           22 GIFKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHTC
T ss_pred             cEEEEEEECCCCCCHHHHHHHHH
Confidence            35678999999999999999885

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=93.36  E-value=0.14  Score=42.49  Aligned_cols=24  Identities=21%  Similarity=0.227  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|+.|+||||+++.+...
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~   29 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAER   29 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999999764

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=93.35  E-value=0.046  Score=44.37  Aligned_cols=24  Identities=25%  Similarity=0.400  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346889999999999999988764

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=93.35  E-value=0.045  Score=50.02  Aligned_cols=22  Identities=27%  Similarity=0.449  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        48 e~~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           48 QRVGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHhC
Confidence            4899999999999999999975

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=93.32  E-value=0.086  Score=49.51  Aligned_cols=102  Identities=20%  Similarity=0.201  Sum_probs=54.3

Q ss_pred             HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHH-HHHHhcccc----ccccc-ceEEEEeCCCC-CHHHHHHHHHHHhh
Q 043252          200 EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLA-QLVYNDKQV----EDHFD-LKAWTCVSDDF-DVIRLTKSILLSIA  272 (337)
Q Consensus       200 ~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~----~~~F~-~~~wv~v~~~~-~~~~~~~~il~~~~  272 (337)
                      +.++.|..-.     .-.-++|+|..|+|||+|| ..+.+....    .++-+ .++++-+.+.. .+.++..++...=.
T Consensus       151 raID~l~Pig-----rGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~  225 (510)
T 2ck3_A          151 KAVDSLVPIG-----RGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADA  225 (510)
T ss_dssp             HHHHHHSCCB-----TTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTC
T ss_pred             eeeccccccc-----cCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCC
Confidence            3566665322     2236899999999999995 566664221    11234 35677777644 34455555554211


Q ss_pred             CCCC-----CCCCC-HHH-----HHHHHHHHc--CCCeEEEEEeCCC
Q 043252          273 SDQN-----VDNHD-LNK-----LQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       273 ~~~~-----~~~~~-~~~-----~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      ....     ..... ...     ..-.+.+++  +++..||++||+.
T Consensus       226 m~~tvvV~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dslt  272 (510)
T 2ck3_A          226 MKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLS  272 (510)
T ss_dssp             GGGEEEEEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             cccceEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHH
Confidence            0000     01111 111     111233333  5899999999993

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=93.30  E-value=0.048  Score=43.28  Aligned_cols=24  Identities=25%  Similarity=0.326  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+...
T Consensus        10 ~~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           10 AFKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456899999999999999988754

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=93.29  E-value=0.061  Score=44.93  Aligned_cols=25  Identities=20%  Similarity=0.313  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|+|.+|+|||||...+...
T Consensus        28 ~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           28 HKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3568899999999999999998764

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=93.29  E-value=0.072  Score=42.43  Aligned_cols=25  Identities=24%  Similarity=0.505  Sum_probs=21.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..--|.|+|.+|+|||||...+.+.
T Consensus        17 ~~~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           17 PTYKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3457899999999999999998754

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=93.28  E-value=0.047  Score=44.93  Aligned_cols=24  Identities=29%  Similarity=0.378  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||.+.+...
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            457889999999999999998764

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=93.27  E-value=0.048  Score=44.12  Aligned_cols=24  Identities=21%  Similarity=0.339  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+...
T Consensus        23 ~~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           23 ELKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            456899999999999999998754

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=93.26  E-value=0.048  Score=44.51  Aligned_cols=25  Identities=32%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|.+|+|||||...+...
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            3567899999999999999988764

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=93.26  E-value=0.052  Score=43.92  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=22.1

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .....|.|+|..|+|||||...+...
T Consensus        15 ~~~~ki~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           15 KTKLQVVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             -CEEEEEEECCTTSCHHHHHHHHSCC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            35678999999999999999998764

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=93.25  E-value=0.027  Score=50.77  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        32 e~~~llGpnGsGKSTLLr~iaG   53 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAG   53 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4899999999999999999974

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=93.24  E-value=0.1  Score=44.85  Aligned_cols=37  Identities=22%  Similarity=0.228  Sum_probs=27.7

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-+..||....    +....|.++|++|.|||.+|..+.+.
T Consensus        91 ~~l~~~l~~~~----~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           91 SVFLGWATKKF----GKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHHTTCS----TTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhCCC----CCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            44667775321    23457999999999999999999874

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=93.23  E-value=0.05  Score=44.33  Aligned_cols=24  Identities=33%  Similarity=0.379  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            8 MFKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999998764

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=93.22  E-value=0.049  Score=44.70  Aligned_cols=24  Identities=33%  Similarity=0.473  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        26 ~~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           26 LFKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            457899999999999999988754

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=93.22  E-value=0.048  Score=44.04  Aligned_cols=24  Identities=29%  Similarity=0.362  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+.+.
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcC
Confidence            346889999999999999998764

>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=93.21  E-value=0.33  Score=43.18  Aligned_cols=96  Identities=16%  Similarity=0.008  Sum_probs=57.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHH-HcC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKK-QLF  294 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~-~L~  294 (337)
                      .++..++|+.|.||++.++.+..... ...|+....+.+....+.                      ..+.+.+.. -+-
T Consensus        18 ~~~yl~~G~e~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~----------------------~~l~~~~~~~plf   74 (343)
T 1jr3_D           18 RAAYLLLGNDPLLLQESQDAVRQVAA-AQGFEEHHTFSIDPNTDW----------------------NAIFSLCQAMSLF   74 (343)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHHH-HHTCCEEEEEECCTTCCH----------------------HHHHHHHHHHHHC
T ss_pred             CcEEEEECCcHHHHHHHHHHHHHHHH-hCCCCeeEEEEecCCCCH----------------------HHHHHHhcCcCCc
Confidence            45899999999999999988866321 122322111222222333                      333332222 123


Q ss_pred             CCeEEEEEeCCCC-CChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          295 GKKFLLVLDDVWN-ENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       295 ~kr~LlVlDdv~~-~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      +++-++|+|++.. .....++.|...+.....++.+|++|-
T Consensus        75 ~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~  115 (343)
T 1jr3_D           75 ASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGN  115 (343)
T ss_dssp             CSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEES
T ss_pred             cCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcC
Confidence            5667888899866 444677778777765556777776663

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=93.21  E-value=0.081  Score=46.51  Aligned_cols=34  Identities=24%  Similarity=0.400  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++++..++.         -.+++|+|+.|+|||||.+.+...
T Consensus       159 gv~~lf~~l~---------geiv~l~G~sG~GKSTll~~l~g~  192 (301)
T 1u0l_A          159 GIEELKEYLK---------GKISTMAGLSGVGKSSLLNAINPG  192 (301)
T ss_dssp             THHHHHHHHS---------SSEEEEECSTTSSHHHHHHHHSTT
T ss_pred             CHHHHHHHhc---------CCeEEEECCCCCcHHHHHHHhccc
Confidence            3566666663         238999999999999999999763

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=93.19  E-value=0.059  Score=48.34  Aligned_cols=24  Identities=21%  Similarity=0.232  Sum_probs=21.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|+|+|.+|+|||||+..+..
T Consensus        55 ~~~~i~i~G~~g~GKSTl~~~l~~   78 (341)
T 2p67_A           55 NTLRLGVTGTPGAGKSTFLEAFGM   78 (341)
T ss_dssp             CSEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            467999999999999999988853

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=93.18  E-value=0.05  Score=44.37  Aligned_cols=24  Identities=29%  Similarity=0.505  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        24 ~~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           24 YRKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEEECCCCcCHHHHHHHHHhC
Confidence            457899999999999999998764

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=93.15  E-value=0.052  Score=43.71  Aligned_cols=24  Identities=25%  Similarity=0.346  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+...
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999998764

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=93.14  E-value=0.051  Score=48.87  Aligned_cols=23  Identities=35%  Similarity=0.527  Sum_probs=21.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.+.+.
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~   94 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNG   94 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            49999999999999999999875

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=93.13  E-value=0.049  Score=43.61  Aligned_cols=25  Identities=20%  Similarity=0.329  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      ..-|.|+|.+|+|||||...+....
T Consensus        18 ~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           18 ELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999999999997643

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=93.13  E-value=0.073  Score=43.28  Aligned_cols=25  Identities=28%  Similarity=0.579  Sum_probs=21.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...-|.|+|..|+|||||...+...
T Consensus        13 ~~~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           13 ALHKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            3567899999999999999988754

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=93.12  E-value=0.053  Score=43.71  Aligned_cols=24  Identities=21%  Similarity=0.351  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+.+.
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999998754

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=93.11  E-value=0.14  Score=43.35  Aligned_cols=24  Identities=38%  Similarity=0.486  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|+.|+||||+++.+...
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~   50 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVET   50 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999999875

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=93.11  E-value=0.053  Score=43.87  Aligned_cols=24  Identities=29%  Similarity=0.358  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           23 ALKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=93.08  E-value=0.053  Score=43.75  Aligned_cols=24  Identities=29%  Similarity=0.340  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+.+.
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           21 LFKYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            346889999999999999988754

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=93.07  E-value=0.13  Score=47.69  Aligned_cols=47  Identities=21%  Similarity=0.256  Sum_probs=33.6

Q ss_pred             cchhHHHHHHHHHhcCCCC-----CCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          193 GRETEKKEIVELLLKDDSR-----NDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~-----~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++-++.|.+.+......     .......|+|+|.+|+|||||.+.+...
T Consensus       152 gv~~L~~~i~~~l~~~~~~~~~~~~~~~~~kvaivG~~gvGKSTLln~l~g~  203 (439)
T 1mky_A          152 NLDTMLETIIKKLEEKGLDLESKPEITDAIKVAIVGRPNVGKSTLFNAILNK  203 (439)
T ss_dssp             SHHHHHHHHHHHHHHTTCCSSSCCCCCSCEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CHHHHHHHHHHhcccccccchhccccccCceEEEECCCCCCHHHHHHHHhCC
Confidence            5567777777777532210     1234568999999999999999999765

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=93.07  E-value=0.054  Score=43.71  Aligned_cols=25  Identities=28%  Similarity=0.372  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..--|.|+|..|+|||||...+...
T Consensus        15 ~~~ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           15 YLFKLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            3457899999999999999998764

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=93.04  E-value=0.053  Score=44.08  Aligned_cols=24  Identities=25%  Similarity=0.302  Sum_probs=20.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999888754

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=93.04  E-value=0.091  Score=48.49  Aligned_cols=23  Identities=26%  Similarity=0.306  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -.+++|+|+.|+|||||.+.+..
T Consensus       167 ggii~I~GpnGSGKTTlL~allg  189 (418)
T 1p9r_A          167 HGIILVTGPTGSGKSTTLYAGLQ  189 (418)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHh
Confidence            35999999999999999998875

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=93.02  E-value=0.053  Score=44.24  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=20.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+...
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            457889999999999999988754

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=93.02  E-value=0.056  Score=44.45  Aligned_cols=24  Identities=21%  Similarity=0.266  Sum_probs=20.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|+|.+|+|||||...+...
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            457889999999999999988764

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=93.00  E-value=0.061  Score=47.31  Aligned_cols=24  Identities=29%  Similarity=0.486  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|.+|+|||||...+...
T Consensus         8 ~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            8 CGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC
Confidence            458999999999999999998764

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=92.98  E-value=0.036  Score=44.23  Aligned_cols=24  Identities=33%  Similarity=0.353  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+...
T Consensus        18 ~~~i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A           18 ELRILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            457889999999999999988743

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=92.97  E-value=0.089  Score=48.40  Aligned_cols=23  Identities=17%  Similarity=0.342  Sum_probs=21.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+++|+|+.|+|||||.+.+..
T Consensus        69 ~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           69 VLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CeEEEEECCCCCcHHHHHHHHhC
Confidence            45999999999999999999986

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=92.96  E-value=0.065  Score=51.00  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.++|++|.||||+|+.+...
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~~   58 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTRY   58 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998653

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=92.96  E-value=0.057  Score=43.95  Aligned_cols=24  Identities=17%  Similarity=0.271  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+...
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhC
Confidence            457899999999999999988754

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=92.95  E-value=0.057  Score=43.44  Aligned_cols=24  Identities=29%  Similarity=0.322  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+...
T Consensus        20 ~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           20 IFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999988754

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=92.94  E-value=0.049  Score=45.15  Aligned_cols=22  Identities=32%  Similarity=0.360  Sum_probs=19.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|.|.|+.|+||||+++.+..
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~   25 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVAS   25 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999998865

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=92.92  E-value=0.057  Score=44.11  Aligned_cols=24  Identities=29%  Similarity=0.458  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            8 LFKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999998764

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=92.92  E-value=0.058  Score=43.40  Aligned_cols=23  Identities=39%  Similarity=0.525  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|.+|+|||||...+.+.
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999998764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.92  E-value=0.085  Score=42.56  Aligned_cols=24  Identities=17%  Similarity=0.297  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+...
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            446889999999999999999865

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=92.90  E-value=0.12  Score=43.48  Aligned_cols=49  Identities=18%  Similarity=0.232  Sum_probs=30.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      -.++.|.|.+|+|||+||..+..+. ....-..+++++...  +...+...+
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~-~~~~~~~v~~~s~E~--~~~~~~~~~   78 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKG-AEEYGEPGVFVTLEE--RARDLRREM   78 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHH-HHHHCCCEEEEESSS--CHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH-HHhcCCCceeecccC--CHHHHHHHH
Confidence            3589999999999999997765321 112223455555443  455555544

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=92.89  E-value=0.056  Score=44.65  Aligned_cols=24  Identities=29%  Similarity=0.481  Sum_probs=20.2

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC-
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            356889999999999999988753

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=92.88  E-value=0.05  Score=44.10  Aligned_cols=24  Identities=25%  Similarity=0.272  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhC
Confidence            346899999999999999998653

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=92.87  E-value=0.065  Score=47.28  Aligned_cols=27  Identities=22%  Similarity=0.347  Sum_probs=23.4

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+....|+|+|.+|+|||||...+...
T Consensus         7 ~~~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            7 HMKVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             CCEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            345789999999999999999998764

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=92.87  E-value=0.054  Score=50.01  Aligned_cols=20  Identities=45%  Similarity=0.753  Sum_probs=19.0

Q ss_pred             EEEEccCCCchHHHHHHHHh
Q 043252          219 IPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++|+|+.|+|||||.+.++.
T Consensus        45 vaLvG~nGaGKSTLln~L~G   64 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFN   64 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            99999999999999999975

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.87  E-value=0.16  Score=42.24  Aligned_cols=23  Identities=39%  Similarity=0.511  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|.|+.|+||||+++.+...
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~   26 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVET   26 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            48899999999999999999875

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=92.87  E-value=0.059  Score=44.94  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=18.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||+|...+.++
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4779999999999999887653

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=92.86  E-value=0.057  Score=43.16  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+...
T Consensus        21 ~~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           21 EHKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            347889999999999999998754

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=92.85  E-value=0.09  Score=49.31  Aligned_cols=83  Identities=18%  Similarity=0.194  Sum_probs=46.8

Q ss_pred             EEEEEEccCCCchHHHH-HHHHhccccccccc-ceEEEEeCCCC-CHHHHHHHHHHHhhCC-------CCCCCCC-----
Q 043252          217 SVIPIIGMGGLGKTTLA-QLVYNDKQVEDHFD-LKAWTCVSDDF-DVIRLTKSILLSIASD-------QNVDNHD-----  281 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~-~~~wv~v~~~~-~~~~~~~~il~~~~~~-------~~~~~~~-----  281 (337)
                      .-++|+|..|+|||+|| ..+.+..    .-+ .++++-+.+.. .+.++..++...=...       ...+...     
T Consensus       164 QR~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a  239 (507)
T 1fx0_A          164 QRELIIGDRQTGKTAVATDTILNQQ----GQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLA  239 (507)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCC----TTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHH
T ss_pred             CEEEEecCCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHH
Confidence            36789999999999995 5777642    134 34666666643 2334444443321000       0001000     


Q ss_pred             ---HHHHHHHHHHHcCCCeEEEEEeCC
Q 043252          282 ---LNKLQEELKKQLFGKKFLLVLDDV  305 (337)
Q Consensus       282 ---~~~~~~~l~~~L~~kr~LlVlDdv  305 (337)
                         .-...+.++.  +++..||++||+
T Consensus       240 ~~~a~tiAEyfrd--~G~dVLli~Dsl  264 (507)
T 1fx0_A          240 PYTGAALAEYFMY--RERHTLIIYDDL  264 (507)
T ss_dssp             HHHHHHHHHHHHH--TTCEEEEEEECH
T ss_pred             HHHHHHHHHHHHH--cCCcEEEEEecH
Confidence               1123344444  599999999998

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=92.84  E-value=0.059  Score=44.72  Aligned_cols=23  Identities=35%  Similarity=0.628  Sum_probs=20.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..-|.|+|.+|+|||||...+..
T Consensus        37 ~~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           37 YYRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            45689999999999999988864

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=92.82  E-value=0.052  Score=43.96  Aligned_cols=24  Identities=38%  Similarity=0.500  Sum_probs=20.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+...
T Consensus        26 ~~ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           26 KLQVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHCC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            346889999999999999998754

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.80  E-value=0.087  Score=42.54  Aligned_cols=24  Identities=25%  Similarity=0.430  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            8 DYRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCcHHHHHHHHHcC
Confidence            456899999999999999998753

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=92.74  E-value=0.063  Score=48.38  Aligned_cols=23  Identities=22%  Similarity=0.384  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.+...
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~  238 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGL  238 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CEEEEECCCCccHHHHHHHHhcc
Confidence            38999999999999999999864

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.73  E-value=0.063  Score=44.03  Aligned_cols=23  Identities=30%  Similarity=0.479  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|.+|+|||||...+...
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHhcC
Confidence            46899999999999999988764

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=92.72  E-value=0.051  Score=50.87  Aligned_cols=23  Identities=26%  Similarity=0.385  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.++.-
T Consensus       139 e~v~IvGpnGsGKSTLlr~L~Gl  161 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSRTLCSY  161 (460)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCc
Confidence            48999999999999999999763

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=92.72  E-value=0.064  Score=44.96  Aligned_cols=23  Identities=17%  Similarity=0.068  Sum_probs=19.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.|.+.|.||+||||+|-.+...
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~   29 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHA   29 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCcHHHHHHHHHHH
Confidence            35788999999999998777654

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=92.71  E-value=0.076  Score=45.79  Aligned_cols=24  Identities=21%  Similarity=0.383  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|.+|+|||||...+...
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999998764

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.70  E-value=0.092  Score=42.10  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+...
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999998853

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.68  E-value=0.065  Score=43.25  Aligned_cols=24  Identities=33%  Similarity=0.422  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           18 MLKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            347899999999999999998764

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=92.66  E-value=0.039  Score=53.46  Aligned_cols=22  Identities=32%  Similarity=0.381  Sum_probs=19.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|++|+|||+||+.+.+.
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~  350 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRV  350 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTT
T ss_pred             ceEEECCCchHHHHHHHHHHHh
Confidence            5889999999999999998764

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=92.65  E-value=0.081  Score=44.55  Aligned_cols=25  Identities=20%  Similarity=0.324  Sum_probs=21.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|+|+|..|+|||||...+...
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCC
Confidence            3567899999999999999998864

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=92.64  E-value=0.045  Score=48.85  Aligned_cols=103  Identities=13%  Similarity=0.013  Sum_probs=53.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      .+++|+|+.|+|||||++.+..-..   .-...+.+.-......... .   ..+..- . .  .-......+...|..+
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~---~~~g~i~i~~~~e~~~~~~-~---~~i~~~-~-g--gg~~~r~~la~aL~~~  240 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIP---KEERIISIEDTEEIVFKHH-K---NYTQLF-F-G--GNITSADCLKSCLRMR  240 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSC---TTSCEEEEESSCCCCCSSC-S---SEEEEE-C-B--TTBCHHHHHHHHTTSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCc---CCCcEEEECCeeccccccc-h---hEEEEE-e-C--CChhHHHHHHHHhhhC
Confidence            3899999999999999999986421   1223444432211110000 0   000000 0 0  1112334566677777


Q ss_pred             eEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          297 KFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       297 r~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      .=+|+||++...  +.++.+. .+..+  +.-+|+||..
T Consensus       241 p~ilildE~~~~--e~~~~l~-~~~~g--~~tvi~t~H~  274 (330)
T 2pt7_A          241 PDRIILGELRSS--EAYDFYN-VLCSG--HKGTLTTLHA  274 (330)
T ss_dssp             CSEEEECCCCST--HHHHHHH-HHHTT--CCCEEEEEEC
T ss_pred             CCEEEEcCCChH--HHHHHHH-HHhcC--CCEEEEEEcc
Confidence            778999999763  4454443 23221  2236777754

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=92.63  E-value=0.066  Score=43.72  Aligned_cols=24  Identities=21%  Similarity=0.328  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        29 ~~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           29 LFKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhhC
Confidence            457899999999999999988754

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=92.62  E-value=0.066  Score=43.83  Aligned_cols=24  Identities=25%  Similarity=0.284  Sum_probs=20.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+.++
T Consensus        30 ~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           30 AIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            346789999999999999888754

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=92.60  E-value=0.067  Score=43.92  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         9 ~~ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A            9 FIKCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999888754

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=92.60  E-value=0.067  Score=43.80  Aligned_cols=24  Identities=33%  Similarity=0.464  Sum_probs=20.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            457899999999999999988754

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=92.55  E-value=0.052  Score=51.99  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+|.|+|+.|+|||||++.+...
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~  392 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAAR  392 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHHh
Confidence            468999999999999999999864

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=92.55  E-value=0.069  Score=43.54  Aligned_cols=23  Identities=35%  Similarity=0.492  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|.+|+|||||...+...
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           26 KKLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999988764

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=92.53  E-value=0.054  Score=43.64  Aligned_cols=24  Identities=21%  Similarity=0.318  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      --|.|+|..|+|||||...+....
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            468899999999999999987653

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=92.52  E-value=0.07  Score=44.92  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...++|.|++|+||||+|+.+...
T Consensus         8 ~~~~~~~G~pGsGKsT~a~~L~~~   31 (230)
T 3gmt_A            8 HMRLILLGAPGAGKGTQANFIKEK   31 (230)
T ss_dssp             -CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ccceeeECCCCCCHHHHHHHHHHH
Confidence            457899999999999999988763

>1jwy_B Dynamin A GTPase domain; dynamin, GTPase, GDP, myosin, fusion-protein, hydrolase; HET: BGC ADP GDP; 2.30A {Dictyostelium discoideum} SCOP: c.37.1.8 PDB: 1jx2_B*

Probab=92.50  E-value=0.14  Score=44.99  Aligned_cols=41  Identities=12%  Similarity=0.216  Sum_probs=28.4

Q ss_pred             HHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          198 KKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       198 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +++|.+.+..-.. .......|+|+|..|+|||||...+...
T Consensus         7 ~~~l~~~~~~~~~-~~~~~~~I~vvG~~~~GKSTlln~l~g~   47 (315)
T 1jwy_B            7 INKLQDVFNTLGS-DPLDLPQIVVVGSQSSGKSSVLENIVGR   47 (315)
T ss_dssp             HHHHHHHTTTSSS-CTTCCCEEEEEECSSSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHcCC-CCCCCCeEEEEcCCCCCHHHHHHHHHCC
Confidence            3445555432221 1345778999999999999999998764

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=92.49  E-value=0.078  Score=43.65  Aligned_cols=23  Identities=22%  Similarity=0.144  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|+.|+||||+++.+...
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~   29 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEH   29 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHH
Confidence            48999999999999999999763

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=92.46  E-value=0.072  Score=44.06  Aligned_cols=24  Identities=25%  Similarity=0.335  Sum_probs=20.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|.+|+|||||...+...
T Consensus        27 ~~ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           27 RCKLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            346789999999999999988764

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=92.43  E-value=0.16  Score=48.92  Aligned_cols=26  Identities=19%  Similarity=0.096  Sum_probs=22.4

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +...+|.|.|+.|+||||+|+.+...
T Consensus       394 q~~~~I~l~GlsGSGKSTiA~~La~~  419 (573)
T 1m8p_A          394 TQGFTIFLTGYMNSGKDAIARALQVT  419 (573)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccceEEEeecCCCCCHHHHHHHHHHH
Confidence            34578999999999999999998764

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=92.42  E-value=0.093  Score=40.90  Aligned_cols=21  Identities=33%  Similarity=0.561  Sum_probs=18.9

Q ss_pred             EEEEEEccCCCchHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .+..|+|+.|.|||||...++
T Consensus        24 g~~~I~G~NGsGKStil~Ai~   44 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDAIL   44 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            488999999999999998875

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=92.39  E-value=0.082  Score=49.60  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+|.++|++|+||||+++.+...
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~   62 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRY   62 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999999998764

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=92.38  E-value=0.042  Score=43.84  Aligned_cols=24  Identities=29%  Similarity=0.398  Sum_probs=10.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|..|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            8 LFKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEEECCCCC------------
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            457899999999999999888653

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=92.35  E-value=0.21  Score=48.45  Aligned_cols=22  Identities=32%  Similarity=0.321  Sum_probs=19.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +++.|.|.+|.||||++..+..
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~  186 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLA  186 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHH
Confidence            4899999999999999877754

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=92.31  E-value=0.066  Score=49.39  Aligned_cols=21  Identities=33%  Similarity=0.662  Sum_probs=19.1

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |+|+|..|+|||||.+.++..
T Consensus        34 I~lvG~sGaGKSTLln~L~g~   54 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLT   54 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            499999999999999999864

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=92.29  E-value=0.076  Score=43.76  Aligned_cols=24  Identities=25%  Similarity=0.369  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .--|.|+|..|+|||||...+...
T Consensus        25 ~~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           25 LIKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEEESCTTSSHHHHHHHHHCS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            456899999999999999998764

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=92.28  E-value=0.095  Score=50.04  Aligned_cols=24  Identities=25%  Similarity=0.594  Sum_probs=21.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .-.+++|+|+.|+|||||.+.+..
T Consensus        24 ~Gei~gLiGpNGaGKSTLlkiL~G   47 (538)
T 3ozx_A           24 NNTILGVLGKNGVGKTTVLKILAG   47 (538)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            346999999999999999999975

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=92.25  E-value=0.077  Score=49.80  Aligned_cols=22  Identities=27%  Similarity=0.265  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~liG~nGsGKSTLl~~l~G   51 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVT   51 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHhc
Confidence            5999999999999999999875

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=92.24  E-value=0.07  Score=50.96  Aligned_cols=23  Identities=39%  Similarity=0.780  Sum_probs=20.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.++.-
T Consensus       295 ei~~i~G~nGsGKSTLl~~l~Gl  317 (538)
T 3ozx_A          295 EIIGILGPNGIGKTTFARILVGE  317 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999863

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=92.24  E-value=0.075  Score=50.78  Aligned_cols=23  Identities=39%  Similarity=0.658  Sum_probs=21.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||++.++.-
T Consensus       313 e~~~i~G~NGsGKSTLlk~l~Gl  335 (538)
T 1yqt_A          313 EVIGIVGPNGIGKTTFVKMLAGV  335 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999864

>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=92.23  E-value=0.12  Score=42.55  Aligned_cols=24  Identities=17%  Similarity=0.123  Sum_probs=21.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|+|+|+.|+||+|+|..+-+
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~   33 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQS   33 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHH
Confidence            457999999999999999988755

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=92.23  E-value=0.078  Score=49.27  Aligned_cols=24  Identities=17%  Similarity=0.228  Sum_probs=21.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+++|+|+.|+|||||.+.+...
T Consensus       157 Gq~~~IvG~sGsGKSTLl~~Iag~  180 (438)
T 2dpy_A          157 GQRMGLFAGSGVGKSVLLGMMARY  180 (438)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            359999999999999999999875

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=92.20  E-value=0.077  Score=50.73  Aligned_cols=22  Identities=32%  Similarity=0.569  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        48 e~~~LvG~NGaGKSTLlk~l~G   69 (538)
T 1yqt_A           48 MVVGIVGPNGTGKSTAVKILAG   69 (538)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4999999999999999999975

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=92.06  E-value=0.44  Score=53.76  Aligned_cols=80  Identities=15%  Similarity=0.068  Sum_probs=45.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCC
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLFGK  296 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~k  296 (337)
                      +-+.++|++|.|||++|+.+....   ..+ ..+.++.+...+...+...+-..+.........-.       .-.-.++
T Consensus      1268 ~~vLL~GPpGtGKT~la~~~l~~~---~~~-~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~-------~P~~~gk 1336 (2695)
T 4akg_A         1268 RGIILCGPPGSGKTMIMNNALRNS---SLY-DVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTL-------LPKSDIK 1336 (2695)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC---SSC-EEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEE-------EEBSSSS
T ss_pred             CeEEEECCCCCCHHHHHHHHHhcC---CCC-ceEEEEeecCCCHHHHHHHHHHHhhhccccCCccc-------cCCCCCc
Confidence            378899999999999997776532   122 23456777666666555444443321110000000       0001367


Q ss_pred             eEEEEEeCCCC
Q 043252          297 KFLLVLDDVWN  307 (337)
Q Consensus       297 r~LlVlDdv~~  307 (337)
                      +++|.+||+.-
T Consensus      1337 ~~VlFiDEinm 1347 (2695)
T 4akg_A         1337 NLVLFCDEINL 1347 (2695)
T ss_dssp             CEEEEEETTTC
T ss_pred             eEEEEeccccc
Confidence            88999999743

>1zcb_A G alpha I/13; GTP-binding, lipoprotein, membrane, transducer, signaling PR; HET: GDP; 2.00A {Mus musculus} SCOP: a.66.1.1 c.37.1.8 PDB: 3ab3_A* 3cx8_A* 3cx7_A* 3cx6_A* 1zca_A*

Probab=92.05  E-value=0.1  Score=47.23  Aligned_cols=23  Identities=26%  Similarity=0.462  Sum_probs=19.4

Q ss_pred             CCcEEEEEEccCCCchHHHHHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLV  236 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v  236 (337)
                      .+..-|.|.|.||+||||+++.+
T Consensus        31 ~~~~killlG~~~SGKST~~kq~   53 (362)
T 1zcb_A           31 ARLVKILLLGAGESGKSTFLKQM   53 (362)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHH
T ss_pred             cCccEEEEECCCCCcHHHHHHHH
Confidence            34567899999999999999875

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=92.01  E-value=0.09  Score=49.75  Aligned_cols=45  Identities=9%  Similarity=-0.103  Sum_probs=30.0

Q ss_pred             cccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          191 VYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       191 ~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.|.+-.+.+.+... +   ..+...+|.+.|+.|+||||+|+.+...
T Consensus       374 ~f~rpeV~~vLr~~~~-~---~~~~~~~I~l~GlsGsGKSTIa~~La~~  418 (511)
T 1g8f_A          374 WFSYPEVVKILRESNP-P---RPKQGFSIVLGNSLTVSREQLSIALLST  418 (511)
T ss_dssp             TTSCHHHHHHHHHHSC-C---GGGCCEEEEECTTCCSCHHHHHHHHHHH
T ss_pred             cccChhhHHHHHHhcc-c---ccccceEEEecccCCCCHHHHHHHHHHH
Confidence            3445444444544431 1   1124578999999999999999999875

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=92.00  E-value=0.075  Score=44.71  Aligned_cols=24  Identities=33%  Similarity=0.379  Sum_probs=18.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|.|.|+.|+||||+++.+.+.
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~   48 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDR   48 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999999875

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=91.99  E-value=0.11  Score=50.32  Aligned_cols=25  Identities=24%  Similarity=0.296  Sum_probs=22.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...+|.|.|+.|+||||+|+.+...
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~   75 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEY   75 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            4578999999999999999998763

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=91.96  E-value=0.21  Score=42.88  Aligned_cols=25  Identities=24%  Similarity=0.517  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.++|..|+|||||...+...
T Consensus        38 ~~~~I~vvG~~g~GKSSLin~l~~~   62 (270)
T 1h65_A           38 NSLTILVMGKGGVGKSSTVNSIIGE   62 (270)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHhCC
Confidence            3567899999999999999998764

>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=91.94  E-value=0.18  Score=41.84  Aligned_cols=109  Identities=11%  Similarity=-0.026  Sum_probs=49.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC-CCCCHHHHHHHHHHHcC
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV-DNHDLNKLQEELKKQLF  294 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~-~~~~~~~~~~~l~~~L~  294 (337)
                      -.+..++|..|.||||.+......... ....+.++ ....  +.+.-...+++.++..... ...+..    .+.+.+.
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~-~g~kVli~-k~~~--d~R~ge~~i~s~~g~~~~a~~~~~~~----~~~~~~~   99 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQF-AKQHAIVF-KPCI--DNRYSEEDVVSHNGLKVKAVPVSASK----DIFKHIT   99 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHH-TTCCEEEE-ECC-------------------CCEEECSSGG----GGGGGCC
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHH-CCCEEEEE-Eecc--CCcchHHHHHhhcCCeeEEeecCCHH----HHHHHHh
Confidence            468889999999999988655543222 22233332 2111  1111112233333221110 111111    2333333


Q ss_pred             CCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          295 GKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       295 ~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ++-=+|++|.+..-+.+..+.+. .+.+  .|-.||+|-++
T Consensus       100 ~~~dvViIDEaQF~~~~~V~~l~-~l~~--~~~~Vi~~Gl~  137 (214)
T 2j9r_A          100 EEMDVIAIDEVQFFDGDIVEVVQ-VLAN--RGYRVIVAGLD  137 (214)
T ss_dssp             SSCCEEEECCGGGSCTTHHHHHH-HHHH--TTCEEEEEECS
T ss_pred             cCCCEEEEECcccCCHHHHHHHH-HHhh--CCCEEEEEecc
Confidence            33339999999665434443333 2222  36689998774

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=91.85  E-value=0.22  Score=42.56  Aligned_cols=25  Identities=20%  Similarity=0.501  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|+|+|..|+|||||...+...
T Consensus        35 ~~~~I~lvG~~g~GKSSLin~l~~~   59 (262)
T 3def_A           35 NSMTVLVLGKGGVGKSSTVNSLIGE   59 (262)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHTS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3567899999999999999998764

>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=91.85  E-value=0.7  Score=43.28  Aligned_cols=94  Identities=17%  Similarity=0.202  Sum_probs=53.0

Q ss_pred             HHHHHhcCCCCCCCCcEEEEEEccCCCchHHHH-HHHHhccccccccc-ceEEEEeCCCC-CHHHHHHHHHHHhhCCCCC
Q 043252          201 IVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLA-QLVYNDKQVEDHFD-LKAWTCVSDDF-DVIRLTKSILLSIASDQNV  277 (337)
Q Consensus       201 l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~-~~~wv~v~~~~-~~~~~~~~il~~~~~~~~~  277 (337)
                      .++.|..-.     .-.-++|.|..|+|||+|+ ..+.+.    .+-+ .++++-+.+.. .+.++..++.+.=......
T Consensus       152 aID~l~Pig-----rGQR~~Ifg~~g~GKT~l~l~~I~n~----~~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tv  222 (513)
T 3oaa_A          152 AVDSMIPIG-----RGQRELIIGDRQTGKTALAIDAIINQ----RDSGIKCIYVAIGQKASTISNVVRKLEEHGALANTI  222 (513)
T ss_dssp             HHHHHSCCB-----TTCBCEEEESSSSSHHHHHHHHHHTT----SSSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEE
T ss_pred             eeccccccc-----cCCEEEeecCCCCCcchHHHHHHHhh----ccCCceEEEEEecCChHHHHHHHHHHhhcCcccceE
Confidence            555555322     2236789999999999996 566663    1233 35677777654 3445666554431111100


Q ss_pred             -----CCCCH-H---------HHHHHHHHHcCCCeEEEEEeCC
Q 043252          278 -----DNHDL-N---------KLQEELKKQLFGKKFLLVLDDV  305 (337)
Q Consensus       278 -----~~~~~-~---------~~~~~l~~~L~~kr~LlVlDdv  305 (337)
                           ..... .         ...+.++.  +++..||++||+
T Consensus       223 vV~atad~p~~~r~~a~~~a~tiAEyfrd--~G~dVLli~Dsl  263 (513)
T 3oaa_A          223 VVVATASESAALQYLAPYAGCAMGEYFRD--RGEDALIIYDDL  263 (513)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHH--TTCEEEEEEETH
T ss_pred             EEEECCCCChHHHHHHHHHHHHHHHHHHh--cCCCEEEEecCh
Confidence                 11111 1         12333443  689999999999

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=91.84  E-value=0.061  Score=43.22  Aligned_cols=24  Identities=17%  Similarity=0.223  Sum_probs=20.6

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        22 ~~~i~v~G~~~~GKssli~~l~~~   45 (189)
T 2x77_A           22 KIRVLMLGLDNAGKTSILYRLHLG   45 (189)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            456899999999999999998643

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=91.83  E-value=0.41  Score=43.60  Aligned_cols=46  Identities=26%  Similarity=0.314  Sum_probs=31.6

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|....+.++.+.+..-..   .... |.|.|..|+|||++|+.++..
T Consensus       138 ~~ig~s~~m~~l~~~i~~~a~---~~~~-vli~Ge~GtGK~~lAr~ih~~  183 (387)
T 1ny5_A          138 EYVFESPKMKEILEKIKKISC---AECP-VLITGESGVGKEVVARLIHKL  183 (387)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTT---CCSC-EEEECSTTSSHHHHHHHHHHH
T ss_pred             hhhhccHHhhHHHHHHHHhcC---CCCC-eEEecCCCcCHHHHHHHHHHh
Confidence            356666666666665543221   1233 489999999999999999864

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=91.81  E-value=0.09  Score=51.00  Aligned_cols=23  Identities=39%  Similarity=0.658  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|+|+.|+|||||.+.++.-
T Consensus       383 ei~~i~G~NGsGKSTLlk~l~Gl  405 (607)
T 3bk7_A          383 EVIGIVGPNGIGKTTFVKMLAGV  405 (607)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999999863

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=91.77  E-value=0.12  Score=44.11  Aligned_cols=25  Identities=20%  Similarity=0.306  Sum_probs=21.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|+|+|.+|+|||||...+...
T Consensus        21 ~~~~I~lvG~~g~GKStl~n~l~~~   45 (260)
T 2xtp_A           21 SELRIILVGKTGTGKSAAGNSILRK   45 (260)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhCC
Confidence            3467899999999999999988754

---

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	337
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	7e-30
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	4e-04

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score =  112 bits (282), Expect = 7e-30
 Identities = 24/176 (13%), Positives = 52/176 (29%), Gaps = 22/176 (12%)

Query: 173 SKKARQRRDTTSLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTL 232
            +   ++    ++ ++   Y RE     +++ L +     D     + + G  G GK+ +
Sbjct: 4   RQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMC---DLDSFFLFLHGRAGSGKSVI 60

Query: 233 AQLVYNDKQ--VEDHFDLKAWTCVSDDFDVIRLTKSILLSIAS---------DQNVDNHD 281
           A    +     +  ++D   W   S             + +                   
Sbjct: 61  ASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTS 120

Query: 282 LNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRNQD 337
           +   +      +     L V DDV  E    W              + +VTTR+ +
Sbjct: 121 VVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQ--------ELRLRCLVTTRDVE 168

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

 Score = 39.4 bits (90), Expect = 4e-04
 Identities = 19/108 (17%), Positives = 31/108 (28%), Gaps = 3/108 (2%)

Query: 190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPII---GMGGLGKTTLAQLVYNDKQVEDHF 246
           ++  R  E + +  + L       G   V  I    G  G+GKTTLA+            
Sbjct: 17  ELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAK 76

Query: 247 DLKAWTCVSDDFDVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQLF 294
           +         +        +IL  I                ++ K L 
Sbjct: 77  EGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALV 124

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	337
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.93
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.88
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.65
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.63
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.61
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.58
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.54
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.51
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.5
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.48
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.36
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.32
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.1
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.09
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.0
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.87
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.8
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.8
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.76
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.73
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.63
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.54
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.46
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.42
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.35
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.3
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.27
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.25
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.24
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.19
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.17
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.15
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.15
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.14
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.13
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.11
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.99
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.97
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.97
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.96
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.94
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.94
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	96.93
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.93
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.91
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.87
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.81
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.81
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.81
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.78
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.77
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.76
d1okkd2	207	GTPase domain of the signal recognition particle r	96.76
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.7
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.68
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.67
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.64
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.61
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.59
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	96.52
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.52
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.51
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.5
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.44
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.4
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.39
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.23
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.15
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.15
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.14
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.14
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.11
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.11
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.09
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.07
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.05
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.04
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.0
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.97
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.97
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.97
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.94
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.88
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.88
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.86
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.83
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.76
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.73
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.72
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.68
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.62
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.59
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.59
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	95.52
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	95.46
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	95.42
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.41
d1g2912	240	Maltose transport protein MalK, N-terminal domain	95.4
d1xpua3	289	Transcription termination factor Rho, ATPase domai	95.38
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	95.37
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.35
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.33
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.31
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.29
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	95.27
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.26
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	95.23
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	95.22
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	95.21
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.2
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	95.19
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.18
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.13
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.12
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	95.07
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.05
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	95.02
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.02
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.84
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.82
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.79
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	94.76
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.76
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.75
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	94.7
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.69
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	94.67
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	94.66
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.66
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.65
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.62
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	94.6
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	94.59
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.57
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.55
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	94.53
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	94.53
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.52
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.52
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	94.48
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.44
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.44
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	94.43
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.42
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.41
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.38
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.38
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	94.36
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.35
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.35
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	94.27
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.27
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.26
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.24
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.23
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	94.22
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.2
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	94.2
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.2
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	94.19
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.18
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.17
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	94.15
d1nrjb_	209	Signal recognition particle receptor beta-subunit	94.15
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.14
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	94.13
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.11
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	94.11
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	94.01
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	94.01
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.0
d2fh5b1	207	Signal recognition particle receptor beta-subunit	93.96
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.96
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	93.94
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	93.93
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.93
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.92
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.88
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	93.85
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.84
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	93.82
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	93.81
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.79
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.76
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	93.72
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.71
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.7
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	93.66
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.64
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.6
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	93.57
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	93.55
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	93.55
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.54
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.5
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	93.48
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	93.47
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	93.35
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.33
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.29
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	93.25
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.24
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	93.22
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.15
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	93.15
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	93.08
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	93.07
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.0
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	92.97
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.97
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	92.43
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	92.41
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	92.37
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.29
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	91.7
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	91.54
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	91.39
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.31
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	91.12
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	91.09
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	91.09
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.98
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	90.81
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	90.71
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.68
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	89.64
d1tuea_	205	Replication protein E1 helicase domain {Human papi	89.58
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	89.37
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	89.09
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	89.01
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	88.47
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	88.36
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.82
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	87.39
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	87.28
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	86.54
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	86.39
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	85.95
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	85.56
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	85.17
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	84.37
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	84.28
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	84.01
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	83.21
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	82.95
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	82.5
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	80.99
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	80.28

>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=99.93  E-value=8.2e-26  Score=198.39  Aligned_cols=142  Identities=17%  Similarity=0.142  Sum_probs=107.4

Q ss_pred             cCccccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc--ccccccceEEEEeCCCCCHH
Q 043252          184 SLVEEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ--VEDHFDLKAWTCVSDDFDVI  261 (337)
Q Consensus       184 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~v~~~~~~~  261 (337)
                      ..+..+.++||+.++++|+++|....   +....+|+|+||||+||||||+++|++..  ...+|++++|+++++.++..
T Consensus        15 ~~p~~~~~~gR~~~~~~i~~~L~~~~---~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~   91 (277)
T d2a5yb3          15 NVPKQMTCYIREYHVDRVIKKLDEMC---DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKS   91 (277)
T ss_dssp             TCBCCCCSCCCHHHHHHHHHHHHHHT---TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTH
T ss_pred             CCCCCCceeCcHHHHHHHHHHHHhcc---CCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHH
Confidence            33456778999999999999997532   23578999999999999999999998753  67789999999999999888


Q ss_pred             HHHHHHHHHhh---CCCCC------CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEE
Q 043252          262 RLTKSILLSIA---SDQNV------DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVT  332 (337)
Q Consensus       262 ~~~~~il~~~~---~~~~~------~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivT  332 (337)
                      .+...+...+.   .....      ...........+...|.++|||+||||||+.  ..|..+.      ..|||||||
T Consensus        92 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~--~~~~~~~------~~~srilvT  163 (277)
T d2a5yb3          92 TFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQE--ETIRWAQ------ELRLRCLVT  163 (277)
T ss_dssp             HHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCH--HHHHHHH------HTTCEEEEE
T ss_pred             HHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHH--hhhhhhc------ccCceEEEE
Confidence            77666654432   21110      1122334455688889999999999999986  4555432      247999999


Q ss_pred             ecCC
Q 043252          333 TRNQ  336 (337)
Q Consensus       333 TR~~  336 (337)
                      ||++
T Consensus       164 TR~~  167 (277)
T d2a5yb3         164 TRDV  167 (277)
T ss_dssp             ESBG
T ss_pred             eehH
Confidence            9975

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.88  E-value=1.9e-08  Score=85.69  Aligned_cols=121  Identities=17%  Similarity=0.100  Sum_probs=85.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~i  267 (337)
                      ..++||+.++++|.++|...-.........+.|+|++|+||||+|+.+++..  ...+. ..+|+..........++..+
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY--KDKTTARFVYINGFIYRNFTAIIGEI   93 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHH--TTSCCCEEEEEETTTCCSHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHH--hcccCCcEEEecchhhhhhhhhhhhh
Confidence            4689999999999999864210012345689999999999999999998753  22222 24577777778888888888


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHc--CCCeEEEEEeCCCCCChh
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQL--FGKKFLLVLDDVWNENYT  311 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~~~~  311 (337)
                      .................+...+.+.+  .....++++|++++....
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~  139 (276)
T d1fnna2          94 ARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPD  139 (276)
T ss_dssp             HHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHH
T ss_pred             HHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhh
Confidence            88877665545556666666666655  345777888888765433

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.65  E-value=1.2e-07  Score=81.00  Aligned_cols=119  Identities=18%  Similarity=0.172  Sum_probs=81.0

Q ss_pred             cccccccchhHHHHHHHHHhc----CCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccc----cccccceEEEEeCCCC
Q 043252          187 EEAKVYGRETEKKEIVELLLK----DDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQV----EDHFDLKAWTCVSDDF  258 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~----~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~----~~~F~~~~wv~v~~~~  258 (337)
                      .+..++||+.++++|.++|..    ... ......++.|+|++|+|||++++.+++.-..    ........++.+....
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~~-~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   92 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGAG-LSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAP   92 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSC-BCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCCC-CCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeecccccc
Confidence            346789999999999887642    221 1222345677899999999999999875211    1111345677777777


Q ss_pred             CHHHHHHHHHHHhhCCCCCCCCCHHHHHHHHHHHc--CCCeEEEEEeCCC
Q 043252          259 DVIRLTKSILLSIASDQNVDNHDLNKLQEELKKQL--FGKKFLLVLDDVW  306 (337)
Q Consensus       259 ~~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~  306 (337)
                      .....+..+...+.............+...+.+..  .+...++++|.+.
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          93 NLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             SHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             chhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEE
Confidence            88888888888877665544556666666666555  3567788888773

>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=98.63  E-value=4.1e-08  Score=81.62  Aligned_cols=125  Identities=14%  Similarity=0.103  Sum_probs=75.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.++.++.|..|+....      ...+.++|++|+||||+|+.+++.-..........-.+.+...+.......+.
T Consensus        14 ~divg~~~~~~~L~~~i~~~~------~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~   87 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGK------LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIK   87 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC------CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC------CCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchh
Confidence            569999999999999997544      23467999999999999999987522111112222233333333332222222


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      .......                ...+++-++|+|++.......-..+...+......++++++|..
T Consensus        88 ~~~~~~~----------------~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~  138 (227)
T d1sxjc2          88 DFASTRQ----------------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANY  138 (227)
T ss_dssp             HHHHBCC----------------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             hcccccc----------------ccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCc
Confidence            1111111                11234458889999776555556666666655667777777754

>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=98.61  E-value=6.3e-08  Score=80.37  Aligned_cols=126  Identities=15%  Similarity=0.124  Sum_probs=76.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.++.+++|..|+....      ..-+.++|++|+||||+|+.+.+.-.....-....-++.+...+...+...+.
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~~------~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~   88 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDGN------MPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIK   88 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCC------CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHH
T ss_pred             HHhcCCHHHHHHHHHHHHcCC------CCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHH
Confidence            568999999999999997554      23477999999999999998876421111101133344454444444333332


Q ss_pred             HHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ........ .              ..++.-++|+|++..........+...+......+++++||.+
T Consensus        89 ~~~~~~~~-~--------------~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~  140 (224)
T d1sxjb2          89 HFAQKKLH-L--------------PPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQ  140 (224)
T ss_dssp             HHHHBCCC-C--------------CTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHhhcc-C--------------CCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCc
Confidence            22222111 0              0235568889999876655555665555555556677777654

>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=98.58  E-value=6.4e-08  Score=82.38  Aligned_cols=42  Identities=19%  Similarity=0.415  Sum_probs=35.6

Q ss_pred             ccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          188 EAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       188 ~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+||++++++|.+..          .+++.|+|++|+|||+|++++.+.
T Consensus        11 ~~~f~GR~~el~~l~~~~----------~~~i~i~G~~G~GKTsLl~~~~~~   52 (283)
T d2fnaa2          11 RKDFFDREKEIEKLKGLR----------APITLVLGLRRTGKSSIIKIGINE   52 (283)
T ss_dssp             GGGSCCCHHHHHHHHHTC----------SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhhCCChHHHHHHHHhcc----------CCEEEEEcCCCCcHHHHHHHHHHH
Confidence            578999999999987631          248899999999999999998864

>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=98.54  E-value=9.5e-08  Score=79.71  Aligned_cols=135  Identities=10%  Similarity=0.035  Sum_probs=78.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccc-cccceEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVED-HFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      .+++|.++.++.|..|+....      ...+.++|++|+||||+|+.+++.-.... .......++.+.......+...+
T Consensus        12 ~diig~~~~~~~l~~~i~~~~------~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (237)
T d1sxjd2          12 DEVTAQDHAVTVLKKTLKSAN------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKV   85 (237)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTT------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC------CCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHH
Confidence            458999999999999996443      33478999999999999999987521111 11223444555554544333332


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      -........ .. ..    ..+.....++.-+||||++.......+..+...+......+++|+||..
T Consensus        86 ~~~~~~~~~-~~-~~----~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~  147 (237)
T d1sxjd2          86 KNFARLTVS-KP-SK----HDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNY  147 (237)
T ss_dssp             HHHHHSCCC-CC-CT----THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHHhhhhhh-hh-hH----HHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccc
Confidence            222211111 11 11    1122233444447999999776656666665555544555667666543

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.51  E-value=4.9e-07  Score=75.63  Aligned_cols=135  Identities=17%  Similarity=0.200  Sum_probs=74.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .+++|.+..++.|..++.....     ...+.|+|+.|+||||+|+.+.+.-.......       ..+.........+.
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~~-----~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~-------~~~~~~~~~~~~i~   79 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGRI-----HHAYLFSGTRGVGKTSIARLLAKGLNCETGIT-------ATPCGVCDNCREIE   79 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTCC-----CSEEEEECSTTSSHHHHHHHHHHHHHCTTCSC-------SSCCSCSHHHHHHH
T ss_pred             HHccChHHHHHHHHHHHHcCCC-----CeeEEEECCCCCcHHHHHHHHHHHhcCccccc-------cCccccchHHHHHH
Confidence            5789999999999999975432     34688999999999999998865311110000       00000001111111


Q ss_pred             HHhhCC----CCCCCCCHHHHHHHHHHH----cCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          269 LSIASD----QNVDNHDLNKLQEELKKQ----LFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       269 ~~~~~~----~~~~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..-...    ........+.+...+...    ..+++-++|||++.......-..|+..+......+++|++|.+
T Consensus        80 ~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~  154 (239)
T d1njfa_          80 QGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTD  154 (239)
T ss_dssp             HTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESC
T ss_pred             cCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCC
Confidence            110000    000111122222211111    1245568999999876656666677776655567788888764

>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=98.50  E-value=7.9e-08  Score=80.07  Aligned_cols=123  Identities=14%  Similarity=0.105  Sum_probs=72.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccc-eEEEEeCCCCCHHHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDL-KAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~v~~~~~~~~~~~~i  267 (337)
                      .+++|.++.++.|..|+....      .+.+.++|++|+||||+|+.+.+... ...+.. .+-++.+...+...+ ...
T Consensus        24 ~diig~~~~~~~l~~~i~~~~------~~~lll~Gp~G~GKTtla~~iak~l~-~~~~~~~~~e~n~s~~~~~~~~-~~~   95 (231)
T d1iqpa2          24 DDIVGQEHIVKRLKHYVKTGS------MPHLLFAGPPGVGKTTAALALARELF-GENWRHNFLELNASDERGINVI-REK   95 (231)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC------CCEEEEESCTTSSHHHHHHHHHHHHH-GGGHHHHEEEEETTCHHHHHTT-HHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC------CCeEEEECCCCCcHHHHHHHHHHHHH-hcccCCCeeEEecCcccchhHH-HHH
Confidence            569999999999999997543      34588999999999999999987421 112221 222333332111111 111


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                      ........               .....++.++++|++.......+..+...+........+|.||.
T Consensus        96 ~~~~~~~~---------------~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n  147 (231)
T d1iqpa2          96 VKEFARTK---------------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCN  147 (231)
T ss_dssp             HHHHHHSC---------------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             HHHHHhhh---------------hccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccC
Confidence            11111100               01124667899999977666677777666654444455666654

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.48  E-value=2.9e-08  Score=83.83  Aligned_cols=46  Identities=15%  Similarity=0.148  Sum_probs=36.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.++..+.|..++....     ...-+.|+|++|+||||+|+.+++.
T Consensus        11 ~diig~~~~~~~L~~~~~~~~-----~~~~lll~Gp~G~GKTt~~~~la~~   56 (252)
T d1sxje2          11 NALSHNEELTNFLKSLSDQPR-----DLPHLLLYGPNGTGKKTRCMALLES   56 (252)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTT-----CCCCEEEECSTTSSHHHHHHTHHHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC-----CCCeEEEECCCCCCHHHHHHHHHHh
Confidence            469999888888888775433     2334779999999999999999874

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.36  E-value=5.6e-06  Score=69.85  Aligned_cols=123  Identities=21%  Similarity=0.302  Sum_probs=72.1

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc---ccccc-ccceEEE-EeCCCCCHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK---QVEDH-FDLKAWT-CVSDDFDVIRLT  264 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~---~~~~~-F~~~~wv-~v~~~~~~~~~~  264 (337)
                      .++||++++++++..|.....      .-+.+||++|+|||+|+..+...-   .+... ....+|. +++.        
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~k------~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~--------   84 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRRK------NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS--------   84 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSS------CEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---------
T ss_pred             cccChHHHHHHHHHHHhcCcc------CCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeech--------
Confidence            478999999999999975432      356799999999999997776531   22222 2345553 2221        


Q ss_pred             HHHHHHhhCCCCCCCCCHHHHHHHHHHHc-CCCeEEEEEeCCCCC--------ChhcHHHhhccCCCCCCCcEEEEEec
Q 043252          265 KSILLSIASDQNVDNHDLNKLQEELKKQL-FGKKFLLVLDDVWNE--------NYTDWVHLSLPFQAGAQGSKIIVTTR  334 (337)
Q Consensus       265 ~~il~~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVlDdv~~~--------~~~~~~~l~~~l~~~~~gs~iivTTR  334 (337)
                            +..... ....++.....+.+.+ .....++++|++..-        ...+...+..|+... ..-++|.||.
T Consensus        85 ------liag~~-~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~r-g~i~vIgatT  155 (268)
T d1r6bx2          85 ------LLAGTK-YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS-GKIRVIGSTT  155 (268)
T ss_dssp             --------CCCC-CSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS-CCCEEEEEEC
T ss_pred             ------HhccCc-cchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhC-CCCeEEEeCC
Confidence                  111111 2345555555555555 456789999998553        112334444444332 2346776664

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.32  E-value=2.5e-06  Score=68.22  Aligned_cols=43  Identities=26%  Similarity=0.446  Sum_probs=36.0

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++||++++++++..|.....      .-+.++|.+|+|||+++..+..
T Consensus        23 ~~igRd~Ei~~l~~iL~r~~k------~n~lLvG~pGVGKTalv~~LA~   65 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRRTK------NNPVLIGEPGVGKTAIVEGLAQ   65 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSS------CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcCcHHHHHHHHHHHhccCC------CCeEEEecCCcccHHHHHHHHH
Confidence            478999999999999975442      3568999999999999977765

>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=98.10  E-value=1e-05  Score=65.78  Aligned_cols=130  Identities=11%  Similarity=0.107  Sum_probs=71.7

Q ss_pred             cchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhh
Q 043252          193 GRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIA  272 (337)
Q Consensus       193 Gr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~  272 (337)
                      +-+...+++.+.+....     -...+.++|+.|+||||+|+.+.+.--......   +-.+....+    ...+.....
T Consensus         6 w~~~~~~~l~~~~~~~~-----l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~---~~~~~~~~~----~~~i~~~~~   73 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGR-----GHHALLIQALPGMGDDALIYALSRYLLCQQPQG---HKSCGHCRG----CQLMQAGTH   73 (207)
T ss_dssp             GGHHHHHHHHHHHHTTC-----CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT---TBCCSCSHH----HHHHHHTCC
T ss_pred             ccHHHHHHHHHHHHcCC-----cCeEEEEECCCCCcHHHHHHHHHHhcccccccc---cccccccch----hhhhhhccc
Confidence            34556788888887544     245799999999999999998765310000000   000000000    001111100


Q ss_pred             CC-------CCCCCCCHHHHHHHHHHHc-----CCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          273 SD-------QNVDNHDLNKLQEELKKQL-----FGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       273 ~~-------~~~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ..       ........+... .+.+.+     .+++-++|+|++..........++..+......+.+|+||.+
T Consensus        74 ~~~~~~~~~~~~~~i~~~~ir-~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~  147 (207)
T d1a5ta2          74 PDYYTLAPEKGKNTLGVDAVR-EVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATRE  147 (207)
T ss_dssp             TTEEEECCCTTCSSBCHHHHH-HHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESC
T ss_pred             cccchhhhhhcccccccchhh-HHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecC
Confidence            00       000112222222 222222     355669999999887777888888888776778888888875

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.09  E-value=6e-06  Score=69.09  Aligned_cols=109  Identities=23%  Similarity=0.229  Sum_probs=63.4

Q ss_pred             cccccchhHHHHHHHHHhcC-----------CCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCC
Q 043252          189 AKVYGRETEKKEIVELLLKD-----------DSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDD  257 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~  257 (337)
                      .+++|.+..+++|.+||...           ...+....+.+.++|++|+||||+|+.+++...     -...++..+..
T Consensus        14 ~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~-----~~~~~~~~~~~   88 (253)
T d1sxja2          14 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG-----YDILEQNASDV   88 (253)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT-----CEEEEECTTSC
T ss_pred             HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHH-----hhhhccccccc
Confidence            67899999999999998541           111233456899999999999999999997521     12445666655


Q ss_pred             CCHHHHHHHHHHHhhCCCCC-CCCCHHHHHHHHHHHcCCCeEEEEEeCCCC
Q 043252          258 FDVIRLTKSILLSIASDQNV-DNHDLNKLQEELKKQLFGKKFLLVLDDVWN  307 (337)
Q Consensus       258 ~~~~~~~~~il~~~~~~~~~-~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  307 (337)
                      .+...+.. .+......... .....    ........++..++++|++..
T Consensus        89 ~~~~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~vi~ide~~~  134 (253)
T d1sxja2          89 RSKTLLNA-GVKNALDNMSVVGYFKH----NEEAQNLNGKHFVIIMDEVDG  134 (253)
T ss_dssp             CCHHHHHH-TGGGGTTBCCSTTTTTC--------CCSSTTSEEEEECSGGG
T ss_pred             hhhHHHHH-HHHHHhhcchhhhhhhh----hhhcccccccceEEEeeeccc
Confidence            54443322 22222211110 00000    011122345677899999854

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.00  E-value=1.6e-05  Score=70.71  Aligned_cols=97  Identities=16%  Similarity=0.290  Sum_probs=54.3

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc---cccc-ccccceEEE-EeCCCCCHHHHH
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND---KQVE-DHFDLKAWT-CVSDDFDVIRLT  264 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~---~~~~-~~F~~~~wv-~v~~~~~~~~~~  264 (337)
                      .++||+.++++++..|.....      .-+.+||.+|+|||+|+..+...   ..+- .-.+.++|. +++.-       
T Consensus        23 ~~~gr~~ei~~~~~~L~r~~k------~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l-------   89 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLRRTK------NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSL-------   89 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHCSSC------CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC----------
T ss_pred             CCcCcHHHHHHHHHHHhcCCC------CCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhh-------
Confidence            378999999999999986542      23467899999999988555432   1222 223455553 32221       


Q ss_pred             HHHHHHhhCCCCCCCCCHHHHHHHHHHHc-C-CCeEEEEEeCCCC
Q 043252          265 KSILLSIASDQNVDNHDLNKLQEELKKQL-F-GKKFLLVLDDVWN  307 (337)
Q Consensus       265 ~~il~~~~~~~~~~~~~~~~~~~~l~~~L-~-~kr~LlVlDdv~~  307 (337)
                         +...   .  ....++.....+...+ . ...++|++|++..
T Consensus        90 ---~ag~---~--~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~  126 (387)
T d1qvra2          90 ---LAGA---K--YRGEFEERLKAVIQEVVQSQGEVILFIDELHT  126 (387)
T ss_dssp             ----------------CHHHHHHHHHHHHHTTCSSEEEEECCC--
T ss_pred             ---hccc---C--cchhHHHHHHHHHHHhccCCCceEEEeccHHH
Confidence               1000   0  1223444444443333 3 3479999999965

>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=97.87  E-value=1.7e-05  Score=64.71  Aligned_cols=123  Identities=20%  Similarity=0.165  Sum_probs=67.7

Q ss_pred             ccccchhHH--HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHH
Q 043252          190 KVYGRETEK--KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       190 ~~vGr~~~~--~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      -++|...+.  ..+.++...+.    .....+.|+|+.|+|||.|++.+++..  .......++++      ..++...+
T Consensus        12 F~vg~~N~~a~~~~~~~~~~~~----~~~n~l~l~G~~G~GKTHLl~A~~~~~--~~~~~~~~~~~------~~~~~~~~   79 (213)
T d1l8qa2          12 FIVGEGNRLAYEVVKEALENLG----SLYNPIFIYGSVGTGKTHLLQAAGNEA--KKRGYRVIYSS------ADDFAQAM   79 (213)
T ss_dssp             CCCCTTTHHHHHHHHHHHHTTT----TSCSSEEEECSSSSSHHHHHHHHHHHH--HHTTCCEEEEE------HHHHHHHH
T ss_pred             ccCCCcHHHHHHHHHHHHhCcC----CCCCcEEEECCCCCcHHHHHHHHHHHh--ccCccceEEec------hHHHHHHH
Confidence            355654333  33444443322    123347899999999999999999863  22333445553      34455555


Q ss_pred             HHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCC-hhcHHH-hhccCCC-CCCCcEEEEEecC
Q 043252          268 LLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNEN-YTDWVH-LSLPFQA-GAQGSKIIVTTRN  335 (337)
Q Consensus       268 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~-~~~~~~-l~~~l~~-~~~gs~iivTTR~  335 (337)
                      ...+...      ......+.+.     .--+|+|||+.... ...|.. +...+-. ...|.+||+||+.
T Consensus        80 ~~~~~~~------~~~~~~~~~~-----~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~  139 (213)
T d1l8qa2          80 VEHLKKG------TINEFRNMYK-----SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDR  139 (213)
T ss_dssp             HHHHHHT------CHHHHHHHHH-----TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             HHHHHcc------chhhHHHHHh-----hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCC
Confidence            5555322      1222222221     34589999996431 234544 2222221 2457789999875

>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=97.80  E-value=6.7e-06  Score=68.29  Aligned_cols=50  Identities=26%  Similarity=0.400  Sum_probs=38.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++||.+.-+++|..++..... ....++-+.++|++|+||||+|+.+++.
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~-~~~~~~~~Ll~GPpG~GKTtla~~la~~   58 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKA-RKEPLEHLLLFGPPGLGKTTLAHVIAHE   58 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTT-SSSCCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHh-cCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999998888764322 1233556779999999999999999875

>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=97.80  E-value=2.1e-05  Score=65.65  Aligned_cols=48  Identities=15%  Similarity=0.118  Sum_probs=33.9

Q ss_pred             cccccchhHHHHHHHHHh-------cCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLL-------KDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~-------~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|....++.+++-+.       ...   ....+-|.++|++|+|||++|+.+++.
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~---~~p~~~vLL~GppGtGKT~la~alA~~   63 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSD---RTPLVSVLLEGPPHSGKTALAAKIAEE   63 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCS---SCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccC---CCCCeEEEEECcCCCCHHHHHHHHhhc
Confidence            347777766665544432       222   234677899999999999999999875

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.76  E-value=7.3e-05  Score=60.05  Aligned_cols=114  Identities=9%  Similarity=-0.015  Sum_probs=71.6

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhccc--ccccccceEEEEeCC-CCCHHHHHHHHHHHhhC
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQ--VEDHFDLKAWTCVSD-DFDVIRLTKSILLSIAS  273 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~v~~-~~~~~~~~~~il~~~~~  273 (337)
                      +++.+..++...      ....+.++|++|+||||+|..+.+...  ...|.| ..++.-.+ ...++++ +++...+..
T Consensus         2 ~~~~l~~~i~~~------~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~~~~~~I~Id~I-R~i~~~~~~   73 (198)
T d2gnoa2           2 QLETLKRIIEKS------EGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNY   73 (198)
T ss_dssp             HHHHHHHHHHTC------SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTS
T ss_pred             HHHHHHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEeCCcCCCCHHHH-HHHHHHHhh
Confidence            345555555432      467999999999999999998876421  122222 33443221 2233332 234444432


Q ss_pred             CCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCCCCCCCcEEEEEecC
Q 043252          274 DQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQAGAQGSKIIVTTRN  335 (337)
Q Consensus       274 ~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~~~~~gs~iivTTR~  335 (337)
                      ...                 .+++=++|+|++...+...+..|+..+..-+..+.+|++|.+
T Consensus        74 ~~~-----------------~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~  118 (198)
T d2gnoa2          74 SPE-----------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRR  118 (198)
T ss_dssp             CCS-----------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESC
T ss_pred             Ccc-----------------cCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCC
Confidence            211                 244558999999888888899998888766677888888765

>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=97.73  E-value=5e-06  Score=69.02  Aligned_cols=50  Identities=28%  Similarity=0.389  Sum_probs=38.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+..+++|..|+..... .+...+-+.++|++|+||||+|+.+.+.
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~-~~~~~~~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKM-RGEVLDHVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHH-HTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHcCChHHHHHHHHHHHHHHHh-cCCCCCeEEEECCCCCcHHHHHHHHHhc
Confidence            5689999999999988853211 1123445789999999999999999874

>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=97.63  E-value=7.5e-05  Score=62.50  Aligned_cols=97  Identities=18%  Similarity=0.163  Sum_probs=57.1

Q ss_pred             cccccchhHHHHHHH---HHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHH
Q 043252          189 AKVYGRETEKKEIVE---LLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~---~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~  262 (337)
                      .+++|.++.+++|.+   ++..+..   -+....+.+.++|++|+|||+||+.+.+..  ..+   .+-+..+.-.+   
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~--~~~---~~~i~~~~l~~---   83 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA--KVP---FFTISGSDFVE---   83 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH--TCC---EEEECSCSSTT---
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc--CCC---EEEEEhHHhhh---
Confidence            678999888777654   4433221   012234678899999999999999998742  212   12233332111   


Q ss_pred             HHHHHHHHhhCCCCCCCCCHHHHHHHHHHHcCCCeEEEEEeCCC
Q 043252          263 LTKSILLSIASDQNVDNHDLNKLQEELKKQLFGKKFLLVLDDVW  306 (337)
Q Consensus       263 ~~~~il~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~  306 (337)
                                 . . .......+...+...-+..+++|+|||+.
T Consensus        84 -----------~-~-~g~~~~~l~~~f~~A~~~~P~il~iDeiD  114 (256)
T d1lv7a_          84 -----------M-F-VGVGASRVRDMFEQAKKAAPCIIFIDEID  114 (256)
T ss_dssp             -----------S-C-CCCCHHHHHHHHHHHHTTCSEEEEETTHH
T ss_pred             -----------c-c-hhHHHHHHHHHHHHHHHcCCEEEEEEChh
Confidence                       0 0 12333444444555546678899999993

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.54  E-value=6.7e-05  Score=64.81  Aligned_cols=123  Identities=12%  Similarity=0.190  Sum_probs=65.4

Q ss_pred             cccccchhHHHHHHHHHhcCC---CCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKDD---SRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.+..++.+...+....   ...+....++.++|+.|+|||.||+.+...  +-..-...+-++++.-.+... . 
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~--l~~~~~~~~~~~~~~~~~~~~-~-   98 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTEYMEKHA-V-   98 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH--HHSSGGGEEEECTTTCCSSGG-G-
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHH--hcCCCcceEEEeccccccchh-h-
Confidence            347788888888766654210   112334568899999999999999988763  111111222333333222111 0 


Q ss_pred             HHHHHhhCCCC--CCCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCC
Q 043252          266 SILLSIASDQN--VDNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQ  321 (337)
Q Consensus       266 ~il~~~~~~~~--~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~  321 (337)
                         ..+.+..+  ........+.+.+++   ....+|+||++...+...+..|...+.
T Consensus        99 ---~~L~g~~~gyvG~~~~~~l~~~~~~---~p~~Vvl~DEieK~~~~v~~~ll~~l~  150 (315)
T d1qvra3          99 ---SRLIGAPPGYVGYEEGGQLTEAVRR---RPYSVILFDEIEKAHPDVFNILLQILD  150 (315)
T ss_dssp             ---GGC--------------CHHHHHHH---CSSEEEEESSGGGSCHHHHHHHHHHHT
T ss_pred             ---hhhcCCCCCCcCcccCChHHHHHHh---CCCcEEEEehHhhcCHHHHHHHHHHhc
Confidence               01111110  011111234444443   357899999998877777777766554

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.46  E-value=9.2e-05  Score=63.96  Aligned_cols=119  Identities=12%  Similarity=0.073  Sum_probs=67.3

Q ss_pred             cccccchhHHHHHHHHHhcC---CCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHH
Q 043252          189 AKVYGRETEKKEIVELLLKD---DSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTK  265 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~~---~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~  265 (337)
                      ..++|.++.++.+...+...   -...+....++.++|+.|+|||.||+.+..-  +   +...+-++++.-.+...   
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~--l---~~~~i~~d~s~~~~~~~---   93 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA--L---GIELLRFDMSEYMERHT---   93 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH--H---TCEEEEEEGGGCSSSSC---
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhh--c---cCCeeEeccccccchhh---
Confidence            45789998888887666311   0112345668899999999999999999763  2   22333444443211000   


Q ss_pred             HHHHHhhCCCCCCCCC---HHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccCC
Q 043252          266 SILLSIASDQNVDNHD---LNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPFQ  321 (337)
Q Consensus       266 ~il~~~~~~~~~~~~~---~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l~  321 (337)
                        +..+.+... ....   ...+...+.   +....+++||++...+.+.|..+...|.
T Consensus        94 --~~~l~g~~~-gy~g~~~~~~l~~~~~---~~~~~vvl~DeieKa~~~V~~~lLqild  146 (315)
T d1r6bx3          94 --VSRLIGAPP-GYVGFDQGGLLTDAVI---KHPHAVLLLDEIEKAHPDVFNILLQVMD  146 (315)
T ss_dssp             --CSSSCCCCS-CSHHHHHTTHHHHHHH---HCSSEEEEEETGGGSCHHHHHHHHHHHH
T ss_pred             --hhhhcccCC-CccccccCChhhHHHH---hCccchhhhcccccccchHhhhhHHhhc
Confidence              001111111 0000   011222222   3456799999998888888887776663

>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=97.42  E-value=8.2e-05  Score=61.95  Aligned_cols=51  Identities=29%  Similarity=0.357  Sum_probs=34.9

Q ss_pred             cccccchhHHHHHHH---HHhcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVE---LLLKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~---~L~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.++.+++|.+   .+..+..   -+....+-|.++|++|+|||+||+.+.+.
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~   65 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   65 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHH
Confidence            468999887766544   3332110   01123457899999999999999999974

>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=97.35  E-value=5.7e-05  Score=63.41  Aligned_cols=51  Identities=25%  Similarity=0.212  Sum_probs=36.7

Q ss_pred             cccccchhHHHHHHHHH----hcCCC---CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELL----LKDDS---RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L----~~~~~---~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.+..+++|.+.+    ..++.   .+-...+-+.++|++|+|||+||+.+.+.
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~   61 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE   61 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHH
Confidence            45889998888887764    32110   01123457899999999999999999874

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.30  E-value=8.2e-05  Score=58.04  Aligned_cols=26  Identities=19%  Similarity=0.096  Sum_probs=22.7

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....+|.|+|++|+||||+|+.+...
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La~~   29 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQVT   29 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999999863

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.27  E-value=0.00052  Score=57.48  Aligned_cols=86  Identities=17%  Similarity=0.130  Sum_probs=60.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~  290 (337)
                      .-++.-|+|++|+||||||..++......+  ..++|+.....++..     +++.++.+...    ...+.++..+.+.
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~  128 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  128 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHH
Confidence            456999999999999999988876533222  357899999989875     55666554321    3456677666666


Q ss_pred             HHcCC-CeEEEEEeCCCC
Q 043252          291 KQLFG-KKFLLVLDDVWN  307 (337)
Q Consensus       291 ~~L~~-kr~LlVlDdv~~  307 (337)
                      ..+.. +.-|||+|.+-.
T Consensus       129 ~l~~~~~~~liIiDSi~a  146 (268)
T d1xp8a1         129 LLVRSGAIDVVVVDSVAA  146 (268)
T ss_dssp             HHHTTTCCSEEEEECTTT
T ss_pred             HHHhcCCCcEEEEecccc
Confidence            66643 456999999944

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=97.25  E-value=0.00018  Score=60.24  Aligned_cols=44  Identities=20%  Similarity=0.323  Sum_probs=31.4

Q ss_pred             hhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       195 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +..+.+.+..|..... .....+.|.++|++|+||||||+.+++.
T Consensus        12 ~~~~~~~~~~~~~~~~-~~~~P~~ilL~GpPGtGKT~la~~la~~   55 (273)
T d1gvnb_          12 ENRLNDNLEELIQGKK-AVESPTAFLLGGQPGSGKTSLRSAIFEE   55 (273)
T ss_dssp             HHHHHHHHHHHHTTCC-CCSSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccc-CCCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3344444555544432 3456778999999999999999999874

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.24  E-value=0.00074  Score=56.51  Aligned_cols=88  Identities=20%  Similarity=0.138  Sum_probs=61.1

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEEL  289 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l  289 (337)
                      +.-++.-|+|+.|+||||||-.++......+  ...+|+.....++.+.     +++++.+...    .....++..+.+
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~  130 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIA  130 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHH
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHH
Confidence            3457999999999999999987776533333  3589999999998764     4455443221    345566666666


Q ss_pred             HHHcC-CCeEEEEEeCCCCC
Q 043252          290 KKQLF-GKKFLLVLDDVWNE  308 (337)
Q Consensus       290 ~~~L~-~kr~LlVlDdv~~~  308 (337)
                      ...+. ++.-|||+|.+-..
T Consensus       131 ~~l~~~~~~~liIiDSi~al  150 (269)
T d1mo6a1         131 DMLIRSGALDIVVIDSVAAL  150 (269)
T ss_dssp             HHHHHTTCEEEEEEECSTTC
T ss_pred             HHHHhcCCCCEEEEeccccc
Confidence            55553 55779999999543

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.19  E-value=8.7e-05  Score=57.42  Aligned_cols=24  Identities=25%  Similarity=0.398  Sum_probs=21.4

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|+.|+|+.|+|||||++.+.+.
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~   25 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPA   25 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            469999999999999999999763

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.17  E-value=9.2e-05  Score=58.04  Aligned_cols=25  Identities=20%  Similarity=0.186  Sum_probs=22.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.+.|.|.|+.|+||||||+.+...
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999763

>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=97.15  E-value=5.1e-05  Score=63.95  Aligned_cols=51  Identities=29%  Similarity=0.318  Sum_probs=34.2

Q ss_pred             cccccchhHHHHHHHHHh----cCC---CCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLL----KDD---SRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~----~~~---~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+++|.++.+++|.+.+.    .++   ..+-...+.|.++|++|.|||+||+.+++.
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~   64 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   64 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHH
Confidence            457787776666655442    110   001223567889999999999999999885

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.15  E-value=0.00011  Score=55.75  Aligned_cols=22  Identities=36%  Similarity=0.459  Sum_probs=19.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++|.|.|++|+||||||+.+..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4788999999999999998865

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.14  E-value=8.3e-05  Score=56.99  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+|+.+...
T Consensus         4 ~I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            6788899999999999999864

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.13  E-value=0.00029  Score=55.71  Aligned_cols=40  Identities=28%  Similarity=0.292  Sum_probs=29.5

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -++.|.+....-.   ..+.-+|+|.|..|+||||||+.+...
T Consensus         6 ~~~~~~~~~~~~~---~~~~~iIgI~G~~GSGKSTla~~L~~~   45 (198)
T d1rz3a_           6 RIDFLCKTILAIK---TAGRLVLGIDGLSRSGKTTLANQLSQT   45 (198)
T ss_dssp             HHHHHHHHHHTSC---CSSSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcc---CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3455555554433   235679999999999999999998763

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.11  E-value=0.00013  Score=56.39  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++|.|.|++|+||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999875

>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=96.99  E-value=0.00024  Score=56.42  Aligned_cols=26  Identities=27%  Similarity=0.321  Sum_probs=22.9

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.+|.|+|++|+||||+|+.+...
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999999864

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=96.97  E-value=0.00083  Score=56.07  Aligned_cols=85  Identities=22%  Similarity=0.143  Sum_probs=57.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCCC----CCCCHHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQNV----DNHDLNKLQEELK  290 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~~----~~~~~~~~~~~l~  290 (337)
                      .-+++-|+|++|+|||||+-.++.......  ...+|++....++...     ++.++.+...    ...+.++..+.+.
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~~-----a~~~Gvd~d~v~~~~~~~~E~~~~~i~  125 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD  125 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHHH-----HHHhCCCHHHEEEecCCCHHHHHHHHH
Confidence            346999999999999999988876543222  3578999998888653     4455443211    3445666666555


Q ss_pred             HHcC-CCeEEEEEeCCC
Q 043252          291 KQLF-GKKFLLVLDDVW  306 (337)
Q Consensus       291 ~~L~-~kr~LlVlDdv~  306 (337)
                      ...+ ++.-|||+|.+-
T Consensus       126 ~l~~~~~~~liViDSi~  142 (263)
T d1u94a1         126 ALARSGAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHHTCCSEEEEECGG
T ss_pred             HHHhcCCCCEEEEECcc
Confidence            5554 344599999994

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.97  E-value=0.00015  Score=56.09  Aligned_cols=23  Identities=35%  Similarity=0.492  Sum_probs=19.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|.|++|+||||+|+.+...
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~   27 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASK   27 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            45779999999999999999753

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.96  E-value=0.00027  Score=54.63  Aligned_cols=27  Identities=22%  Similarity=0.450  Sum_probs=23.2

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +...+++.|.|++|+||||+|+.+...
T Consensus         3 ~~~~~iivl~G~~GsGKsT~a~~La~~   29 (171)
T d1knqa_           3 NHDHHIYVLMGVSGSGKSAVASEVAHQ   29 (171)
T ss_dssp             CTTSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            345789999999999999999998763

>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=96.94  E-value=0.0018  Score=51.94  Aligned_cols=45  Identities=22%  Similarity=0.271  Sum_probs=29.2

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCH
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDV  260 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~  260 (337)
                      .....||.++|+.|+||||.+-++.....   .....+.+-..+.+.+
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~---~~g~kV~lit~Dt~R~   50 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFE---QQGKSVMLAAGDTFRA   50 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHH---TTTCCEEEECCCTTCH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH---HCCCcEEEEecccccc
Confidence            34578999999999999998866664322   1223445544455544

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.94  E-value=0.00016  Score=56.46  Aligned_cols=23  Identities=30%  Similarity=0.343  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.|.|+|++|+|||||++.+...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            36899999999999999999754

>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=96.93  E-value=0.00072  Score=55.98  Aligned_cols=46  Identities=26%  Similarity=0.282  Sum_probs=34.7

Q ss_pred             ccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          190 KVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       190 ~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|||....++.+.+.+..-..    .-.-|.|.|..|+|||++|+.++..
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~----~~~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISC----AECPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTT----CCSCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhC----CCCCEEEECCCCcCHHHHHHHHHHh
Confidence            378888888888777765322    1124689999999999999999763

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.93  E-value=0.00028  Score=56.14  Aligned_cols=26  Identities=35%  Similarity=0.433  Sum_probs=23.5

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +..++|.|.|++|+||||+|+.++..
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999999999874

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.91  E-value=0.0005  Score=56.16  Aligned_cols=22  Identities=27%  Similarity=0.570  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        27 ei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            4999999999999999999963

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.87  E-value=0.00011  Score=63.17  Aligned_cols=51  Identities=24%  Similarity=0.300  Sum_probs=35.0

Q ss_pred             cccccchhHHHHHHHHHhc----CCC----CCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLLK----DDS----RNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~~----~~~----~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..++|.++.++.|...+..    ...    ......+.+.++||+|+|||.||+.+.+.
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~   72 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   72 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhc
Confidence            4578998888887665521    110    00112456778999999999999999874

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.81  E-value=0.00032  Score=54.33  Aligned_cols=24  Identities=17%  Similarity=0.203  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|.|.|++|+||||+|+.+.+.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~   26 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999999763

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=0.00023  Score=56.23  Aligned_cols=24  Identities=25%  Similarity=0.347  Sum_probs=21.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ...+|.++|++|+||||+|+.+..
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~   41 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEE   41 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999999975

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.81  E-value=0.00037  Score=53.88  Aligned_cols=25  Identities=32%  Similarity=0.418  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|.|.|++|+||||+|+.+...
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            4457899999999999999999763

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.78  E-value=0.00044  Score=53.52  Aligned_cols=23  Identities=30%  Similarity=0.456  Sum_probs=21.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .++|.|.|++|+||||+|+.+..
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999875

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.77  E-value=0.00037  Score=55.84  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.+|.++|.+|+||||||+++...
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~   25 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRY   25 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999999863

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.76  E-value=0.00033  Score=54.72  Aligned_cols=23  Identities=35%  Similarity=0.638  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|.|.|+.|+||||+++.+...
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~   24 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDN   24 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998763

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.76  E-value=0.0049  Score=49.19  Aligned_cols=25  Identities=28%  Similarity=0.356  Sum_probs=20.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.++|.++|+.|+||||.+-++...
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~   29 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRY   29 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999988766653

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.70  E-value=0.00045  Score=53.90  Aligned_cols=25  Identities=28%  Similarity=0.333  Sum_probs=21.8

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +...+|.++|++|+||||+|+.+..
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999998865

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.68  E-value=0.00043  Score=53.40  Aligned_cols=23  Identities=30%  Similarity=0.345  Sum_probs=20.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++++|+|..|+|||||+..+...
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~   24 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAA   24 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH
Confidence            58999999999999999988764

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.67  E-value=0.00041  Score=53.95  Aligned_cols=21  Identities=43%  Similarity=0.589  Sum_probs=19.3

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |+|+|+.|+|||||++.+...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~   23 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhc
Confidence            789999999999999999863

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.64  E-value=0.00045  Score=53.21  Aligned_cols=21  Identities=48%  Similarity=0.667  Sum_probs=18.9

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|++|+||||+++.+...
T Consensus         3 I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            677899999999999999874

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.61  E-value=0.0057  Score=51.94  Aligned_cols=80  Identities=14%  Similarity=0.087  Sum_probs=43.4

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhccccccccc--ceEEEEeCCCCCHHHHHHHHHHHhhCC-CCCCCCCHHHHHHHH
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD--LKAWTCVSDDFDVIRLTKSILLSIASD-QNVDNHDLNKLQEEL  289 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~v~~~~~~~~~~~~il~~~~~~-~~~~~~~~~~~~~~l  289 (337)
                      ....-+|+|.|..|+||||+|+.+..-  ....+.  .+.-++..+-+-....+..  ..+... ..+.+.+.+.+.+.|
T Consensus        77 ~k~P~iIGIaG~sgSGKSTla~~L~~l--L~~~~~~~~v~~Is~D~F~~~~~~l~~--~~~~~~~g~Pes~D~~~L~~~L  152 (308)
T d1sq5a_          77 QRIPYIISIAGSVAVGKSTTARVLQAL--LSRWPEHRRVELITTDGFLHPNQVLKE--RGLMKKKGFPESYDMHRLVKFV  152 (308)
T ss_dssp             CCCCEEEEEEECTTSSHHHHHHHHHHH--HTTSTTCCCEEEEEGGGGBCCHHHHHH--HTCTTCTTSGGGBCHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCCCcHHHHHHHHH--HhhhcCCCceEEEeeeeeECCchHHHH--hcCCccCCchHhhhHHHHHHHH
Confidence            346789999999999999999998753  222221  1223333332222222211  111111 112456677777777


Q ss_pred             HHHcCCC
Q 043252          290 KKQLFGK  296 (337)
Q Consensus       290 ~~~L~~k  296 (337)
                      .....++
T Consensus       153 ~~lk~g~  159 (308)
T d1sq5a_         153 SDLKSGV  159 (308)
T ss_dssp             HHHTTTC
T ss_pred             HHHHcCC
Confidence            7666543

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.59  E-value=0.00051  Score=53.01  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=17.7

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|++|+||||+++.+...
T Consensus         4 IvliG~~G~GKSTig~~La~~   24 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKA   24 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            345599999999999999864

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=96.52  E-value=0.0004  Score=57.17  Aligned_cols=22  Identities=32%  Similarity=0.573  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||.+.+..
T Consensus        29 ei~glvG~nGaGKSTLl~~l~G   50 (238)
T d1vpla_          29 EIFGLIGPNGAGKTTTLRIIST   50 (238)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4999999999999999999964

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=96.52  E-value=0.0005  Score=53.33  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.++|++|+||||+|+.+.+.
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~   25 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARA   25 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4668899999999999999764

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.51  E-value=0.0018  Score=52.97  Aligned_cols=86  Identities=17%  Similarity=0.161  Sum_probs=52.8

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCC--------------CCCCCC
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASD--------------QNVDNH  280 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~--------------~~~~~~  280 (337)
                      .-.++.|+|.+|+|||+|+..+..+  ...+....+|++...+  ...+.... ..+...              ......
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEES--RAQLLRNA-YSWGMDFEEMERQNLLKIVCAYPESA   99 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSSC--HHHHHHHH-HTTSCCHHHHHHTTSEEECCCCGGGS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccCC--HHHHHHHH-HHcCCChHHHhhcCceEEEEeecchh
Confidence            3569999999999999999888765  3445566778876543  33333322 222111              011234


Q ss_pred             CHHHHHHHHHHHcC-CCeEEEEEeCC
Q 043252          281 DLNKLQEELKKQLF-GKKFLLVLDDV  305 (337)
Q Consensus       281 ~~~~~~~~l~~~L~-~kr~LlVlDdv  305 (337)
                      ........+...+. .+--++|+|.+
T Consensus       100 ~~~~~~~~i~~~i~~~~~~~vviDs~  125 (242)
T d1tf7a2         100 GLEDHLQIIKSEINDFKPARIAIDSL  125 (242)
T ss_dssp             CHHHHHHHHHHHHHTTCCSEEEEECH
T ss_pred             hHHHHHHHHHHHHHhcCCceeeeecc
Confidence            45566666666553 45558899987

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.50  E-value=0.00074  Score=53.40  Aligned_cols=23  Identities=26%  Similarity=0.356  Sum_probs=21.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|.|++|+||||+|+.+++.
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999864

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.44  E-value=0.00084  Score=52.51  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=20.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|.|.|+.|+||||+++.+...
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~   24 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68899999999999999999764

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.40  E-value=0.0042  Score=49.79  Aligned_cols=26  Identities=31%  Similarity=0.304  Sum_probs=21.3

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....||.++|+.|+||||.+-++...
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~   34 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKM   34 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999987666543

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.39  E-value=0.00078  Score=54.32  Aligned_cols=23  Identities=39%  Similarity=0.495  Sum_probs=21.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +||+|.|++|+||||+|+.+.+.
T Consensus         4 piI~I~GppGSGKgT~ak~La~~   26 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEA   26 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            49999999999999999999764

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.23  E-value=0.013  Score=46.69  Aligned_cols=24  Identities=29%  Similarity=0.321  Sum_probs=20.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +.+||.++|+.|+||||.+-++..
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~   32 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLAL   32 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999988866654

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.15  E-value=0.0042  Score=49.75  Aligned_cols=25  Identities=32%  Similarity=0.284  Sum_probs=16.7

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....||.++|+.|+||||.+-++..
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~   34 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAY   34 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999998765554

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=96.15  E-value=0.0011  Score=52.11  Aligned_cols=23  Identities=26%  Similarity=0.286  Sum_probs=20.0

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|.|.|++|+||||+|+.+.+.
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35779999999999999998764

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.14  E-value=0.0016  Score=52.25  Aligned_cols=24  Identities=17%  Similarity=0.152  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +-+|+|.|..|+||||||+.+...
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999988764

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=96.14  E-value=0.0017  Score=51.09  Aligned_cols=23  Identities=30%  Similarity=0.485  Sum_probs=19.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +.++| |+|++|+||||+|+.+..
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHH
Confidence            45666 789999999999999876

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.11  E-value=0.012  Score=48.96  Aligned_cols=100  Identities=20%  Similarity=0.231  Sum_probs=59.5

Q ss_pred             HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCC-CHHHHHHHHHHHhhCC--C-
Q 043252          200 EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDF-DVIRLTKSILLSIASD--Q-  275 (337)
Q Consensus       200 ~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~-~~~~~~~~il~~~~~~--~-  275 (337)
                      +.++.|..-.     .-.-++|.|..|+|||+|+..+.++. .+.+=+.++++-+.+.. ...++..++.+.-...  . 
T Consensus        57 raID~l~pig-----kGQr~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~  130 (276)
T d2jdid3          57 KVVDLLAPYA-----KGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDA  130 (276)
T ss_dssp             HHHHHHSCEE-----TTCEEEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSS
T ss_pred             eeeeeecccc-----CCCEEEeeCCCCCCHHHHHHHHHHHH-HhhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccc
Confidence            4566665322     12368999999999999998887652 22233456777777653 4556777776642111  0 


Q ss_pred             -CC-------CCCCH-H-----HHHHHHHHHc---CCCeEEEEEeCC
Q 043252          276 -NV-------DNHDL-N-----KLQEELKKQL---FGKKFLLVLDDV  305 (337)
Q Consensus       276 -~~-------~~~~~-~-----~~~~~l~~~L---~~kr~LlVlDdv  305 (337)
                       ..       ...+. .     ...-.+.+++   +++..||++||+
T Consensus       131 ~~~tvvv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsl  177 (276)
T d2jdid3         131 TSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNI  177 (276)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECT
T ss_pred             cceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcch
Confidence             00       11111 1     1222345555   389999999999

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.11  E-value=0.0014  Score=52.82  Aligned_cols=23  Identities=35%  Similarity=0.478  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -+|+|-|++|+||||+|+.+...
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~   26 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKD   26 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            36899999999999999999764

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.09  E-value=0.0014  Score=50.99  Aligned_cols=22  Identities=27%  Similarity=0.460  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+|+.+...
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3779999999999999998763

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.07  E-value=0.002  Score=51.72  Aligned_cols=24  Identities=29%  Similarity=0.242  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +..+|-+.|++|+||||||+.+..
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~   46 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEH   46 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999875

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=96.05  E-value=0.0017  Score=51.38  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|.|.|++|+||||+|+.+...
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999999999763

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=96.04  E-value=0.0019  Score=50.76  Aligned_cols=23  Identities=39%  Similarity=0.408  Sum_probs=20.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      ...+|+|.|..|+||||+|..+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            45799999999999999998773

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.00  E-value=0.0017  Score=50.79  Aligned_cols=23  Identities=22%  Similarity=0.417  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++|.|+|+.|+|||||++.+...
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            47889999999999999998754

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=95.97  E-value=0.0021  Score=50.71  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=20.0

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|.|++|+||||+|+.+...
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHH
Confidence            445667899999999999999863

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=95.97  E-value=0.0017  Score=50.66  Aligned_cols=22  Identities=32%  Similarity=0.495  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+|+.++..
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4779999999999999999874

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.97  E-value=0.0018  Score=50.56  Aligned_cols=22  Identities=27%  Similarity=0.332  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|.|++|+||||+|+.++..
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4778899999999999999864

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=95.94  E-value=0.002  Score=53.64  Aligned_cols=23  Identities=35%  Similarity=0.579  Sum_probs=19.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.|+|+|-||+||||+|-.+...
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~   24 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSG   24 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCcCCHHHHHHHHHHH
Confidence            68999999999999999777543

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.88  E-value=0.016  Score=48.47  Aligned_cols=83  Identities=17%  Similarity=0.111  Sum_probs=46.0

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhccccccccc-ceEEEEeCCCCCHHHHHHHHHHHhhCC------CCCCCCCHHHH
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFD-LKAWTCVSDDFDVIRLTKSILLSIASD------QNVDNHDLNKL  285 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~v~~~~~~~~~~~~il~~~~~~------~~~~~~~~~~~  285 (337)
                      +...-+|+|.|..|+|||||+..+...-..+..+. .++-++..+-+-...=...+......+      ..+...+.+.+
T Consensus        24 ~~~P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~ll  103 (286)
T d1odfa_          24 NKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLL  103 (286)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHHH
T ss_pred             CCCCEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhHHHH
Confidence            34567999999999999999988865311111122 233444444332222222333332111      12367788877


Q ss_pred             HHHHHHHcCC
Q 043252          286 QEELKKQLFG  295 (337)
Q Consensus       286 ~~~l~~~L~~  295 (337)
                      .+.|....++
T Consensus       104 ~~~l~~l~~~  113 (286)
T d1odfa_         104 QEVLNTIFNN  113 (286)
T ss_dssp             HHHHHHHTC-
T ss_pred             HHHHHHHHhh
Confidence            7777777654

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.88  E-value=0.0017  Score=51.30  Aligned_cols=22  Identities=27%  Similarity=0.558  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|+|+.|+|||||++.+...
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHh
Confidence            3679999999999999998753

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.86  E-value=0.0036  Score=53.75  Aligned_cols=37  Identities=16%  Similarity=0.237  Sum_probs=27.1

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++...+...    .++..+|+|.|++|+|||||...+...
T Consensus        41 ~~ll~~~~~~----~~~~~~IgitG~pGaGKSTLi~~l~~~   77 (327)
T d2p67a1          41 TQLLDAIMPY----CGNTLRLGVTGTPGAGKSTFLEAFGML   77 (327)
T ss_dssp             HHHHHHHGGG----CSCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             HHHHHHhhhc----cCCceEEEeeCCCCCCHHHHHHHHHHH
Confidence            3455555432    235789999999999999999887653

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.83  E-value=0.0018  Score=50.94  Aligned_cols=22  Identities=36%  Similarity=0.573  Sum_probs=19.5

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|+|+.|+|||||++.+...
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHh
Confidence            4789999999999999998764

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.76  E-value=0.0025  Score=50.23  Aligned_cols=27  Identities=26%  Similarity=0.073  Sum_probs=22.8

Q ss_pred             CCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          213 DGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       213 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.+..+|+|-|.-|+||||+++.+...
T Consensus         6 ~~kp~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1           6 GTQPFTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            345679999999999999999988653

>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=95.73  E-value=0.01  Score=50.45  Aligned_cols=23  Identities=26%  Similarity=0.436  Sum_probs=19.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.++|++|+|||.||+.+...
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~  146 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEA  146 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHHH
Confidence            35667899999999999999874

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=95.72  E-value=0.0045  Score=53.09  Aligned_cols=37  Identities=22%  Similarity=0.422  Sum_probs=27.1

Q ss_pred             HHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          198 KKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       198 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+|.+.+...    ..+..+|+|.|++|+|||||.-.+..
T Consensus        37 ~~~~~~~~~~~----~~~~~~igitG~pGaGKSTli~~l~~   73 (323)
T d2qm8a1          37 VRDLIDAVLPQ----TGRAIRVGITGVPGVGKSTTIDALGS   73 (323)
T ss_dssp             HHHHHHHHGGG----CCCSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHHHHhhhc----cCCceEEeeeCCCCCCHHHHHHHHHH
Confidence            34445555432    23578999999999999999988764

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.68  E-value=0.0027  Score=49.31  Aligned_cols=22  Identities=32%  Similarity=0.392  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|.|.|++|+||||+|+.++..
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3678999999999999999864

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.62  E-value=0.003  Score=49.22  Aligned_cols=21  Identities=33%  Similarity=0.398  Sum_probs=18.0

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|.|++|+||||+|+.+...
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            447799999999999999764

>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=95.59  E-value=0.0044  Score=51.70  Aligned_cols=35  Identities=29%  Similarity=0.531  Sum_probs=26.0

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHH
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      ++..+.+.+..      +..++|.+.|-||+||||+|-.+.
T Consensus         7 ~~~~~~~~~~~------~~~~iii~sGKGGVGKTT~a~nLA   41 (279)
T d1ihua2           7 SLSALVDDIAR------NEHGLIMLMGKGGVGKTTMAAAIA   41 (279)
T ss_dssp             CHHHHHHHHHT------TSCEEEEEECSTTSSHHHHHHHHH
T ss_pred             cHHHHHHHhhc------CCCEEEEEECCCCCCHHHHHHHHH
Confidence            34556666643      346899999999999999876664

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.59  E-value=0.0031  Score=49.14  Aligned_cols=23  Identities=13%  Similarity=0.469  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.|.|+|+.|+|||||++.+...
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHh
Confidence            47899999999999999988753

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=95.52  E-value=0.0035  Score=54.02  Aligned_cols=45  Identities=18%  Similarity=0.251  Sum_probs=32.7

Q ss_pred             cccccccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHH
Q 043252          187 EEAKVYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       187 ~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      +-+.++|.+..+..|.-.+....      ..-+.|+|.+|+||||||+.+.
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~~------~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDPG------IGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGG------GCCEEEECCGGGCTTHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhccC------CCeEEEECCCCccHHHHHHHHH
Confidence            34678999887776554443221      2357999999999999999885

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.46  E-value=0.0055  Score=49.71  Aligned_cols=22  Identities=27%  Similarity=0.540  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          32 EFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCcchhhHhccC
Confidence            4999999999999999998864

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.42  E-value=0.0031  Score=50.18  Aligned_cols=22  Identities=36%  Similarity=0.588  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.++.
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            4899999999999999999975

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.41  E-value=0.0038  Score=50.74  Aligned_cols=21  Identities=33%  Similarity=0.501  Sum_probs=19.4

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ||.|.|+.|+|||||...+..
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~   22 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGR   22 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHH
Confidence            899999999999999988864

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=95.40  E-value=0.0041  Score=50.79  Aligned_cols=22  Identities=27%  Similarity=0.507  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||++.++.
T Consensus        30 e~~~liG~sGaGKSTll~~i~g   51 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAG   51 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            4999999999999999999964

>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=95.38  E-value=0.0052  Score=51.51  Aligned_cols=98  Identities=16%  Similarity=0.109  Sum_probs=52.6

Q ss_pred             HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHhhCCCC--C
Q 043252          200 EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSIASDQN--V  277 (337)
Q Consensus       200 ~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~~~~~~--~  277 (337)
                      ++++.|..-.     .-.-++|.|..|+|||+|+..+.+... .++-++++.+.+-... .++ ..++.+.....--  .
T Consensus        32 r~ID~l~Pig-----rGQr~~I~g~~g~GKT~l~~~i~~~~~-~~~~~~v~~~~~iger-~~e-v~~~~~~~~~~vv~~t  103 (289)
T d1xpua3          32 RVLDLASPIG-----RGQRGLIVAPPKAGKTMLLQNIAQSIA-YNHPDCVLMVLLIDER-PEE-VTEMQRLVKGEVVAST  103 (289)
T ss_dssp             HHHHHHSCCB-----TTCEEEEEECSSSSHHHHHHHHHHHHH-HHCTTSEEEEEEEEEC-HHH-HHHHHHHCSSEEEEEE
T ss_pred             eeeeeccccc-----CCCeeeEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEEEeecee-HHH-HHhHHhhcceEEEecc
Confidence            5777776433     234889999999999999999887532 2333444444332221 122 2233333211100  0


Q ss_pred             CCCCH------HHHHHHHHHHc--CCCeEEEEEeCC
Q 043252          278 DNHDL------NKLQEELKKQL--FGKKFLLVLDDV  305 (337)
Q Consensus       278 ~~~~~------~~~~~~l~~~L--~~kr~LlVlDdv  305 (337)
                      ...+.      ....-.+.+++  +++..||++||+
T Consensus       104 ~d~~~~~r~~~~~~a~~iAEyfrd~G~dVLli~Dsl  139 (289)
T d1xpua3         104 FDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSI  139 (289)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEESCH
T ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhccCceeecCcH
Confidence            11111      11222333343  589999999999

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.37  E-value=0.0066  Score=49.43  Aligned_cols=21  Identities=24%  Similarity=0.464  Sum_probs=19.5

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +++|+|+.|+|||||.+.++.
T Consensus        26 ~~~liGpnGaGKSTll~~i~G   46 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCChHHHHHHHHHc
Confidence            788999999999999999975

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=95.35  E-value=0.0046  Score=52.03  Aligned_cols=23  Identities=35%  Similarity=0.534  Sum_probs=19.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+.|+|+|-||+||||+|-.+..
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~   24 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVA   24 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHH
Confidence            46788999999999999877643

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=95.33  E-value=0.0043  Score=46.68  Aligned_cols=21  Identities=29%  Similarity=0.406  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|.+|+|||||.+.+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            569999999999999988754

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=95.31  E-value=0.017  Score=50.10  Aligned_cols=64  Identities=23%  Similarity=0.159  Sum_probs=37.2

Q ss_pred             hhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcc-cccccccceEEEEeCCCCCHHHHHHHH
Q 043252          195 ETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDK-QVEDHFDLKAWTCVSDDFDVIRLTKSI  267 (337)
Q Consensus       195 ~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~-~~~~~F~~~~wv~v~~~~~~~~~~~~i  267 (337)
                      +..+..+...|.         -++..|.|++|.||||++..+...- +....-...+.+..+..-....+...+
T Consensus       151 ~~Q~~A~~~al~---------~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         151 NWQKVAAAVALT---------RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             CHHHHHHHHHHT---------BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHc---------CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            345555555552         2488999999999999986554321 111112346777766654444444443

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=95.29  E-value=0.0045  Score=46.88  Aligned_cols=21  Identities=38%  Similarity=0.539  Sum_probs=19.1

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |+|+|.+|+|||||.+.+.++
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            779999999999999988765

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=95.27  E-value=0.0045  Score=50.58  Aligned_cols=22  Identities=36%  Similarity=0.543  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||++.++.
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHcC
Confidence            4899999999999999999964

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.26  E-value=0.009  Score=48.30  Aligned_cols=48  Identities=17%  Similarity=0.101  Sum_probs=33.0

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhccccccc----ccceEEEEeCCCCCHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDH----FDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~v~~~~~~~~  262 (337)
                      .-+++.|+|++|+|||||+..+.........    -...+|+.....++...
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   84 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVR   84 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGG
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHH
Confidence            3469999999999999999877654222111    23577888777665443

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=95.23  E-value=0.0056  Score=50.15  Aligned_cols=23  Identities=35%  Similarity=0.456  Sum_probs=20.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -..++|+|+.|+|||||++.+..
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45999999999999999999964

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.22  E-value=0.0049  Score=50.85  Aligned_cols=22  Identities=32%  Similarity=0.665  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||++.+..
T Consensus        42 e~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            4899999999999999999964

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=95.21  E-value=0.0047  Score=50.55  Aligned_cols=22  Identities=45%  Similarity=0.735  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++|+|+.|.|||||++.+..
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            4899999999999999999965

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=95.20  E-value=0.006  Score=47.92  Aligned_cols=25  Identities=28%  Similarity=0.601  Sum_probs=22.1

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHh
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++.|+|+|.+|+|||||...+.+
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcC
Confidence            3567899999999999999999975

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.19  E-value=0.0053  Score=50.06  Aligned_cols=22  Identities=27%  Similarity=0.523  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        33 e~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHHc
Confidence            4899999999999999999964

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.18  E-value=0.005  Score=49.12  Aligned_cols=23  Identities=22%  Similarity=0.368  Sum_probs=20.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+|.|+|+.|+|||||.+.+...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            47889999999999999988763

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.13  E-value=0.022  Score=46.11  Aligned_cols=49  Identities=22%  Similarity=0.245  Sum_probs=34.4

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhccccc----ccccceEEEEeCCCCCHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVE----DHFDLKAWTCVSDDFDVIRL  263 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~v~~~~~~~~~  263 (337)
                      .-+++.|+|++|+||||+|.++.......    ......+|+......+...+
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            45799999999999999998776532111    12345778888777765543

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.12  E-value=0.0051  Score=50.87  Aligned_cols=22  Identities=41%  Similarity=0.601  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||++.+..
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHHc
Confidence            4999999999999999999964

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.07  E-value=0.0058  Score=50.34  Aligned_cols=22  Identities=41%  Similarity=0.667  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++|+|+.|+|||||++.+..
T Consensus        41 e~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            4999999999999999999964

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=95.05  E-value=0.011  Score=51.29  Aligned_cols=25  Identities=28%  Similarity=0.073  Sum_probs=22.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.+.++|++|+|||++|+.+.+.
T Consensus       153 ~~~~~~~~g~~~~gk~~~~~~~~~~  177 (362)
T d1svma_         153 KKRYWLFKGPIDSGKTTLAAALLEL  177 (362)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CcCeEEEECCCCCCHHHHHHHHHHH
Confidence            4569999999999999999999875

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.02  E-value=0.0065  Score=50.94  Aligned_cols=22  Identities=36%  Similarity=0.607  Sum_probs=20.5

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||++.++.
T Consensus        63 e~vaivG~nGsGKSTLl~~i~G   84 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILG   84 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHhC
Confidence            5899999999999999999975

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=95.02  E-value=0.0063  Score=51.04  Aligned_cols=24  Identities=25%  Similarity=0.275  Sum_probs=19.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++|.+.|-||+||||+|-.+..
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~   30 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAI   30 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHHH
Confidence            356899999999999998866643

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.84  E-value=0.0074  Score=45.89  Aligned_cols=22  Identities=32%  Similarity=0.379  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||+..+.++
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999888764

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=94.82  E-value=0.0055  Score=49.61  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        27 e~~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            4999999999999999999964

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.79  E-value=0.0076  Score=46.34  Aligned_cols=22  Identities=32%  Similarity=0.383  Sum_probs=19.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||+..+.++
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3679999999999999987654

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=94.76  E-value=0.021  Score=47.42  Aligned_cols=86  Identities=15%  Similarity=0.122  Sum_probs=47.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCC-HHHHHHHHHHHhhCC-------CCCCC--CC--HHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFD-VIRLTKSILLSIASD-------QNVDN--HD--LNKL  285 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~-~~~~~~~il~~~~~~-------~~~~~--~~--~~~~  285 (337)
                      -++|+|..|+|||+|+......  ...+-..++++.+..... ..++..++...-...       ...+.  ..  ....
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~  146 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYT  146 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHH
T ss_pred             eEeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHHH
Confidence            5789999999999999876543  223334567777666432 223333333221000       00010  00  1122


Q ss_pred             HHHHHHHc--CCCeEEEEEeCC
Q 043252          286 QEELKKQL--FGKKFLLVLDDV  305 (337)
Q Consensus       286 ~~~l~~~L--~~kr~LlVlDdv  305 (337)
                      .-.+.+++  ++++.||++||+
T Consensus       147 a~tiAEyfrd~G~~Vlll~Dsl  168 (276)
T d1fx0a3         147 GAALAEYFMYRERHTLIIYDDL  168 (276)
T ss_dssp             HHHHHHHHHHTTCEEEEEEECH
T ss_pred             HHHHHHHHHHcCCceeEEeecc
Confidence            23334444  589999999999

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.76  E-value=0.0054  Score=49.76  Aligned_cols=24  Identities=25%  Similarity=0.281  Sum_probs=21.5

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .+.|+|-|+-|+||||+++.+...
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999988764

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.75  E-value=0.0091  Score=45.40  Aligned_cols=21  Identities=24%  Similarity=0.553  Sum_probs=18.2

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||||+..+.++
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999877653

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.70  E-value=0.0098  Score=48.27  Aligned_cols=24  Identities=25%  Similarity=0.318  Sum_probs=21.7

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ++.|+|-|.-|+||||+++.+.+.
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH
Confidence            579999999999999999999764

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.69  E-value=0.0084  Score=45.69  Aligned_cols=22  Identities=32%  Similarity=0.369  Sum_probs=18.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||+|++.+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999887653

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=94.67  E-value=0.0052  Score=51.51  Aligned_cols=24  Identities=21%  Similarity=0.421  Sum_probs=17.9

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +..+|+|.|..|+||||+++.+.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHH
Confidence            345999999999999999988765

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=94.66  E-value=0.0082  Score=49.06  Aligned_cols=22  Identities=32%  Similarity=0.570  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||.+.+..
T Consensus        33 ei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4999999999999999999964

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=94.66  E-value=0.0081  Score=45.63  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=18.7

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|.+|+|||||.+.+.++
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            679999999999999998654

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.65  E-value=0.0088  Score=45.75  Aligned_cols=21  Identities=29%  Similarity=0.657  Sum_probs=18.3

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999887764

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=94.62  E-value=0.018  Score=51.42  Aligned_cols=51  Identities=24%  Similarity=0.331  Sum_probs=34.1

Q ss_pred             cccccchhHHHHHHHHHh--------cCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          189 AKVYGRETEKKEIVELLL--------KDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       189 ~~~vGr~~~~~~l~~~L~--------~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+||.++.+..|--.+.        ....+..-..+-|.++||.|+|||.||+.+...
T Consensus        14 ~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~   72 (443)
T d1g41a_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   72 (443)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHH
Confidence            357788877776654442        111111222457999999999999999999863

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.60  E-value=0.01  Score=47.34  Aligned_cols=23  Identities=22%  Similarity=0.368  Sum_probs=20.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..|+|-|+-|+||||+++.+.+.
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~   26 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEA   26 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999998874

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.59  E-value=0.0091  Score=45.50  Aligned_cols=22  Identities=27%  Similarity=0.587  Sum_probs=19.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||...+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999888764

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.57  E-value=0.0094  Score=45.24  Aligned_cols=21  Identities=29%  Similarity=0.455  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|.+|+|||||++.+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999988653

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.55  E-value=0.037  Score=44.72  Aligned_cols=49  Identities=16%  Similarity=0.072  Sum_probs=35.2

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhccc----ccccccceEEEEeCCCCCHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYNDKQ----VEDHFDLKAWTCVSDDFDVIR  262 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~----~~~~F~~~~wv~v~~~~~~~~  262 (337)
                      +.-+++.|+|.+|+|||++|.++.....    ....+....|+.....+....
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDR   87 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHH
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHH
Confidence            3467999999999999999988865321    223445678888777766443

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.53  E-value=0.0096  Score=45.52  Aligned_cols=22  Identities=36%  Similarity=0.431  Sum_probs=19.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||...+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            4789999999999999987653

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.53  E-value=0.0096  Score=45.60  Aligned_cols=22  Identities=36%  Similarity=0.528  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||.+.+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988753

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.52  E-value=0.0098  Score=45.36  Aligned_cols=21  Identities=24%  Similarity=0.494  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|.+|+|||||.+.+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999888754

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.52  E-value=0.0097  Score=45.36  Aligned_cols=22  Identities=27%  Similarity=0.483  Sum_probs=18.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||+|+..+.++
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4689999999999999987653

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.48  E-value=0.0094  Score=49.13  Aligned_cols=22  Identities=41%  Similarity=0.594  Sum_probs=20.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||++.++.
T Consensus        31 ei~~liG~nGaGKSTLl~~i~G   52 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITG   52 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHHC
Confidence            4899999999999999999975

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.44  E-value=0.012  Score=47.39  Aligned_cols=37  Identities=22%  Similarity=0.148  Sum_probs=25.8

Q ss_pred             EEEEEE-ccCCCchHHHHHHHHhcccccccccceEEEEeC
Q 043252          217 SVIPII-GMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVS  255 (337)
Q Consensus       217 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~  255 (337)
                      ++|+|+ |-||+||||+|..+...-  ...-..++.|.+.
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~l--a~~g~~VlliD~D   39 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVAL--AQLGHDVTIVDAD   39 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHH--HHTTCCEEEEECC
T ss_pred             EEEEEECCCCCChHHHHHHHHHHHH--HhCCCCEEEEeCC
Confidence            688888 889999999998876542  2222246666653

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.44  E-value=0.011  Score=45.25  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=18.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|..|+|||||++.+.+.
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCcCHHHHHHHHhCC
Confidence            3679999999999999988653

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.43  E-value=0.01  Score=45.47  Aligned_cols=22  Identities=41%  Similarity=0.613  Sum_probs=19.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||...+.++
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            4789999999999999887653

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.42  E-value=0.01  Score=46.12  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||+..+.++
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            4779999999999999888754

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.41  E-value=0.011  Score=45.12  Aligned_cols=21  Identities=29%  Similarity=0.461  Sum_probs=19.3

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .|+|+|..|+|||||.+.+..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            689999999999999998864

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.38  E-value=0.011  Score=45.18  Aligned_cols=21  Identities=29%  Similarity=0.561  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||+|.+.+.++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999888764

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.38  E-value=0.011  Score=44.98  Aligned_cols=22  Identities=36%  Similarity=0.511  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||...+.++
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4779999999999999988764

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=94.36  E-value=0.073  Score=43.78  Aligned_cols=49  Identities=14%  Similarity=0.099  Sum_probs=29.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSIL  268 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il  268 (337)
                      .++.|.|.+|+||||++..+..+.-....+ .+++++..  .+...+...++
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s~E--~~~~~~~~r~~   84 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAMLE--ESVEETAEDLI   84 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEESS--SCHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhccc-ceeEeeec--cchhhHHhHHH
Confidence            488899999999999997776432122222 24444433  34444444443

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.35  E-value=0.012  Score=47.35  Aligned_cols=25  Identities=36%  Similarity=0.523  Sum_probs=22.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++|..|.|+-|.|||||.+.+...
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            4789999999999999999998764

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.35  E-value=0.011  Score=46.53  Aligned_cols=24  Identities=21%  Similarity=0.176  Sum_probs=20.8

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.++.|.|++|+|||+||..+..+
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHH
Confidence            459999999999999999877654

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=94.27  E-value=0.021  Score=49.52  Aligned_cols=24  Identities=42%  Similarity=0.434  Sum_probs=20.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ....+..+|+.|+|||.||+.+..
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcceeeeCCCCccHHHHHHHHHh
Confidence            355688899999999999998865

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.27  E-value=0.012  Score=45.00  Aligned_cols=22  Identities=18%  Similarity=0.383  Sum_probs=18.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||+..+.++
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3689999999999999887643

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.26  E-value=0.012  Score=44.02  Aligned_cols=22  Identities=36%  Similarity=0.623  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||...+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999888754

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.24  E-value=0.013  Score=46.32  Aligned_cols=22  Identities=36%  Similarity=0.560  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|+|-|.-|+||||+++.+.+.
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~   23 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGA   23 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999988753

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.23  E-value=0.012  Score=44.99  Aligned_cols=22  Identities=27%  Similarity=0.560  Sum_probs=18.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||...+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999887654

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.22  E-value=0.012  Score=44.70  Aligned_cols=21  Identities=29%  Similarity=0.716  Sum_probs=18.7

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999888764

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.20  E-value=0.012  Score=44.69  Aligned_cols=23  Identities=26%  Similarity=0.446  Sum_probs=19.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|..|+|||||...+.++
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            35778999999999999887654

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.20  E-value=0.012  Score=45.04  Aligned_cols=21  Identities=29%  Similarity=0.442  Sum_probs=18.4

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|.++|.+|+|||||+..+..
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999988764

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.20  E-value=0.012  Score=45.14  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|..|+|||||+..+.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999887653

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=94.19  E-value=0.0072  Score=49.30  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|+|||||.+.+..
T Consensus        32 e~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHHc
Confidence            4999999999999999999964

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.18  E-value=0.019  Score=43.94  Aligned_cols=23  Identities=26%  Similarity=0.537  Sum_probs=19.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|.+|+|||+|...+.++
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34679999999999999887654

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.17  E-value=0.011  Score=45.41  Aligned_cols=23  Identities=30%  Similarity=0.489  Sum_probs=19.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      --|.|+|.+|+|||||...+...
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34779999999999999988654

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.15  E-value=0.013  Score=44.60  Aligned_cols=21  Identities=29%  Similarity=0.640  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|..|+|||+|...+..+
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            679999999999999887654

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.15  E-value=0.013  Score=46.16  Aligned_cols=22  Identities=41%  Similarity=0.468  Sum_probs=20.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|+|+|.+|+|||||...+.+.
T Consensus         5 ~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           5 SIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            7899999999999999988754

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=94.14  E-value=0.016  Score=44.47  Aligned_cols=24  Identities=29%  Similarity=0.531  Sum_probs=19.9

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-|.|+|.+|+|||||...+...
T Consensus        13 ~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          13 TGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            345779999999999999888653

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.13  E-value=0.016  Score=44.53  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ...|+|+|..|+|||||...+...
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999864

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=94.11  E-value=0.013  Score=46.55  Aligned_cols=20  Identities=30%  Similarity=0.454  Sum_probs=18.2

Q ss_pred             EEEEEccCCCchHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~  237 (337)
                      +|+|+|..|+||||+|+.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998763

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.11  E-value=0.016  Score=44.36  Aligned_cols=25  Identities=28%  Similarity=0.413  Sum_probs=21.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ....|+|+|.+|+|||||...+.+.
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cccEEEEECCCCCCHHHHHHHHhCC
Confidence            3567999999999999999999853

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.01  E-value=0.014  Score=44.86  Aligned_cols=22  Identities=36%  Similarity=0.478  Sum_probs=18.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||+|...+.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678899999999999887654

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.01  E-value=0.022  Score=45.69  Aligned_cols=34  Identities=24%  Similarity=0.440  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++.|.++|..         ++..++|..|+|||||...+..+
T Consensus        85 g~~~L~~~l~~---------kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          85 GIEELKEYLKG---------KISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             THHHHHHHHSS---------SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             hHhhHHHHhcC---------CeEEEECCCCCCHHHHHHhhcch
Confidence            46777777731         37789999999999999998754

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.00  E-value=0.016  Score=45.39  Aligned_cols=22  Identities=32%  Similarity=0.511  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||...+.++
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            4789999999999999988754

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.96  E-value=0.015  Score=45.95  Aligned_cols=22  Identities=23%  Similarity=0.332  Sum_probs=19.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||||...+.+.
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6899999999999999888754

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.96  E-value=0.0086  Score=49.37  Aligned_cols=22  Identities=36%  Similarity=0.655  Sum_probs=19.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..++|+|+.|+|||||++.+..
T Consensus        45 e~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTT
T ss_pred             CEEEEECCCCCcHHHHHHHHHh
Confidence            4899999999999999998853

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=93.94  E-value=0.11  Score=37.50  Aligned_cols=51  Identities=16%  Similarity=0.122  Sum_probs=33.2

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLSI  271 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~~  271 (337)
                      ...+..|+++-|.|||+++-.++..      ....+.+.+....-..+....+...+
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~------~~~~vli~~P~~~l~~q~~~~~~~~~   57 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAH   57 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHT------TTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH------cCCcEEEEcChHHHHHHHHHHHHHHh
Confidence            4678899999999999998766542      23356666665444444444444443

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=93.93  E-value=0.011  Score=47.92  Aligned_cols=22  Identities=27%  Similarity=0.530  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+++|+|+.|.|||||.+.+..
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4999999999999999998864

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=93.93  E-value=0.015  Score=46.05  Aligned_cols=21  Identities=38%  Similarity=0.491  Sum_probs=18.9

Q ss_pred             EEEEEEccCCCchHHHHHHHH
Q 043252          217 SVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      -+|+|.|..|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            589999999999999998763

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.92  E-value=0.015  Score=44.29  Aligned_cols=21  Identities=14%  Similarity=0.445  Sum_probs=18.0

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.|+|..|+|||+|...+..+
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999887653

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.88  E-value=0.016  Score=44.25  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999887653

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.85  E-value=0.016  Score=44.85  Aligned_cols=22  Identities=23%  Similarity=0.357  Sum_probs=18.5

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||+|.+.+..+
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3679999999999999887554

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=93.84  E-value=0.051  Score=43.55  Aligned_cols=24  Identities=29%  Similarity=0.308  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.++.|.|.+|+|||++|..+..+
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            469999999999999999888653

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.82  E-value=0.016  Score=44.81  Aligned_cols=22  Identities=27%  Similarity=0.371  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||+|...+..+
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999887654

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.81  E-value=0.016  Score=44.97  Aligned_cols=22  Identities=36%  Similarity=0.468  Sum_probs=19.2

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|+|.+|+|||+|.+.+.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4789999999999999887754

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=93.79  E-value=0.024  Score=43.27  Aligned_cols=23  Identities=26%  Similarity=0.374  Sum_probs=19.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .-|.|+|.+|+|||||...+..+
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35679999999999999887654

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.76  E-value=0.01  Score=45.78  Aligned_cols=20  Identities=20%  Similarity=0.428  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHh
Q 043252          219 IPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~  238 (337)
                      |+|+|.+|+|||||...+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999864

>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=93.72  E-value=0.027  Score=42.49  Aligned_cols=25  Identities=28%  Similarity=0.254  Sum_probs=22.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhcc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYNDK  240 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~~  240 (337)
                      ..+|.+.|.=|+||||++|.+.+.-
T Consensus        33 g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          33 AIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEecCCCccHHHHHHHHHhhc
Confidence            4599999999999999999998753

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.71  E-value=0.017  Score=44.50  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=19.8

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999763

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=93.70  E-value=0.018  Score=43.63  Aligned_cols=21  Identities=24%  Similarity=0.515  Sum_probs=18.0

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||||...+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            568899999999999887654

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=93.66  E-value=0.021  Score=43.55  Aligned_cols=24  Identities=29%  Similarity=0.596  Sum_probs=20.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.-|.|+|.+|+|||||.+.+.++
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCcCHHHHHHHHHhC
Confidence            446789999999999999887653

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.64  E-value=0.02  Score=45.93  Aligned_cols=23  Identities=39%  Similarity=0.622  Sum_probs=19.6

Q ss_pred             EEEEEE-ccCCCchHHHHHHHHhc
Q 043252          217 SVIPII-GMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~-G~gGiGKTtLa~~v~~~  239 (337)
                      ++|+|+ +-||+||||+|..+...
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~   26 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVA   26 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHH
Confidence            689999 67999999999888653

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.60  E-value=0.019  Score=44.46  Aligned_cols=22  Identities=36%  Similarity=0.551  Sum_probs=19.0

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||+..+.+.
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3679999999999999888753

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.57  E-value=0.022  Score=45.48  Aligned_cols=24  Identities=33%  Similarity=0.487  Sum_probs=21.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -+.|+|-|+-|+||||+++.+.+.
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~   26 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKK   26 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHH
Confidence            458999999999999999999864

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.55  E-value=0.022  Score=43.45  Aligned_cols=21  Identities=29%  Similarity=0.718  Sum_probs=18.2

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|..|+|||||...+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            567899999999999988764

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.55  E-value=0.019  Score=43.95  Aligned_cols=22  Identities=36%  Similarity=0.579  Sum_probs=18.8

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      --|.++|.+|+|||+|.+.+..
T Consensus         4 ~Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           4 YRVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3477999999999999988764

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.54  E-value=0.02  Score=44.06  Aligned_cols=21  Identities=43%  Similarity=0.635  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||||.+.+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999987653

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.50  E-value=0.018  Score=44.90  Aligned_cols=19  Identities=32%  Similarity=0.550  Sum_probs=17.1

Q ss_pred             EEEEEccCCCchHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLV  236 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v  236 (337)
                      -|.|+|.+|+|||||...+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4679999999999999887

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.48  E-value=0.02  Score=43.78  Aligned_cols=22  Identities=27%  Similarity=0.502  Sum_probs=18.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      --|.++|.+|+|||||...+.+
T Consensus         7 ~KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           7 FKVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            3478999999999999977754

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.47  E-value=0.15  Score=40.99  Aligned_cols=23  Identities=22%  Similarity=0.093  Sum_probs=20.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -+++.|.|+...||||+.|.+.-
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l   63 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTAL   63 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHH
Confidence            36899999999999999998854

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.35  E-value=0.022  Score=43.98  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=18.3

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|..|+|||+|++.+.++
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999888664

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.33  E-value=0.021  Score=44.42  Aligned_cols=22  Identities=23%  Similarity=0.338  Sum_probs=18.7

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||+|.+.+..+
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3679999999999999888654

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.29  E-value=0.023  Score=45.05  Aligned_cols=23  Identities=39%  Similarity=0.511  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.|+|-|+-|+||||+++.+.+.
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~   25 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVET   25 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            47889999999999999998763

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=93.25  E-value=0.017  Score=44.75  Aligned_cols=21  Identities=29%  Similarity=0.545  Sum_probs=19.0

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|+|+|.+++|||||...+.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999864

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=93.24  E-value=0.016  Score=44.37  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=20.1

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++ |.++|.+|+|||||.+.+.++
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcC
Confidence            455 568999999999999998754

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.22  E-value=0.013  Score=44.77  Aligned_cols=21  Identities=33%  Similarity=0.591  Sum_probs=17.1

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999877553

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=93.15  E-value=0.025  Score=42.42  Aligned_cols=21  Identities=24%  Similarity=0.325  Sum_probs=18.5

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|+|+|.+|+|||||...+..
T Consensus         3 kI~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            367999999999999998874

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.15  E-value=0.024  Score=44.13  Aligned_cols=21  Identities=29%  Similarity=0.415  Sum_probs=17.8

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.++|.+|+|||+|...+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668899999999999877653

>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=93.08  E-value=0.13  Score=42.71  Aligned_cols=35  Identities=26%  Similarity=0.126  Sum_probs=24.7

Q ss_pred             HHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          200 EIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       200 ~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.++.|..-.     .-.-++|.|.+|+|||+|+..+...
T Consensus        57 raID~l~pig-----~GQr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          57 KAVDSLVPIG-----RGQRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             HHHHHHSCCB-----TTCBCEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEecccCcc-----CCCEEEeecCCCCChHHHHHHHHHh
Confidence            4566665332     2236789999999999999777653

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.07  E-value=0.025  Score=43.46  Aligned_cols=22  Identities=18%  Similarity=0.332  Sum_probs=18.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.++|.+|+|||||...+.++
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5789999999999999877653

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=93.00  E-value=0.017  Score=44.62  Aligned_cols=24  Identities=33%  Similarity=0.477  Sum_probs=19.5

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      .++ |.++|.+|+|||||...+...
T Consensus        17 ~~K-I~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          17 ELR-ILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTCCS
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcC
Confidence            344 569999999999999988643

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=92.97  E-value=0.03  Score=45.21  Aligned_cols=22  Identities=27%  Similarity=0.413  Sum_probs=20.1

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+|+|.|..|+||||+|+.+.+
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999998865

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=92.97  E-value=0.027  Score=43.41  Aligned_cols=22  Identities=32%  Similarity=0.557  Sum_probs=19.3

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|+|+|..|+|||||...+.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4789999999999999888753

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=92.43  E-value=0.025  Score=43.31  Aligned_cols=24  Identities=17%  Similarity=0.163  Sum_probs=20.7

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHh
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +..-|+|+|.+++|||||.+.+..
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhC
Confidence            456799999999999999988754

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=92.41  E-value=0.033  Score=44.53  Aligned_cols=22  Identities=23%  Similarity=0.412  Sum_probs=18.9

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .-|.++|.+|+|||||.+.+..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999988754

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.37  E-value=0.02  Score=43.80  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=8.7

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|.|+|.+|+|||||...+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            377999999999999977664

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=92.29  E-value=0.042  Score=43.34  Aligned_cols=23  Identities=17%  Similarity=0.205  Sum_probs=19.4

Q ss_pred             EEEEEEccC-CCchHHHHHHHHhc
Q 043252          217 SVIPIIGMG-GLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~g-GiGKTtLa~~v~~~  239 (337)
                      +.+.|.|-| |+||||++-.+..-
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~a   25 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQA   25 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHH
Confidence            468899998 99999999777653

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=91.70  E-value=0.06  Score=41.33  Aligned_cols=22  Identities=27%  Similarity=0.312  Sum_probs=19.3

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .-|.|.|.+|+||||||..+..
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            4688999999999999988764

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=91.54  E-value=0.048  Score=43.40  Aligned_cols=23  Identities=22%  Similarity=0.146  Sum_probs=19.3

Q ss_pred             CcEEEEEEccCCCchHHHHHHHH
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .-.++.|.|.+|+|||+||..+.
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~   47 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFL   47 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHH
Confidence            34699999999999999996653

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=91.39  E-value=0.13  Score=42.01  Aligned_cols=40  Identities=25%  Similarity=0.419  Sum_probs=28.4

Q ss_pred             hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          196 TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       196 ~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..+.++...|....    ..--.|.|+|..|+|||||...++..
T Consensus        16 ~~l~e~~~~l~~~~----~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          16 TKLLELLGNLKQED----VNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHHTT----CCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhhcC----CCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            44455555555432    23456789999999999999999864

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=91.31  E-value=0.068  Score=41.02  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=19.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .-|.|.|.+|+||||||..+..
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH
Confidence            4688999999999999988764

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=91.12  E-value=0.26  Score=39.22  Aligned_cols=21  Identities=24%  Similarity=0.243  Sum_probs=18.8

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++.|.|+...||||+.+.+.-
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l   57 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTAL   57 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHH
T ss_pred             EEEEECCCccccchhhhhhHH
Confidence            788999999999999998853

>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=91.09  E-value=0.06  Score=44.16  Aligned_cols=22  Identities=32%  Similarity=0.452  Sum_probs=18.7

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .+..|+|.+|+|||||+..++-
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            3778999999999999977654

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.09  E-value=0.019  Score=43.10  Aligned_cols=21  Identities=33%  Similarity=0.588  Sum_probs=18.9

Q ss_pred             EEEEccCCCchHHHHHHHHhc
Q 043252          219 IPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       219 i~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |+++|.+|+|||||...+...
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998754

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=90.98  E-value=0.084  Score=44.80  Aligned_cols=22  Identities=27%  Similarity=0.297  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|.|.|..|+||||+.+.+...
T Consensus       168 nili~G~tgSGKTT~l~al~~~  189 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEF  189 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGG
T ss_pred             CEEEEeeccccchHHHHHHhhh
Confidence            4789999999999999999863

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=90.81  E-value=0.082  Score=40.25  Aligned_cols=22  Identities=27%  Similarity=0.351  Sum_probs=19.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      .-|.|.|..|+||||||-.+..
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~   37 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIK   37 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            4788999999999999987765

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=90.71  E-value=0.067  Score=44.29  Aligned_cols=24  Identities=25%  Similarity=0.188  Sum_probs=20.8

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHH
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      .+++-|+|+|.+|.|||||+-.+.
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll   27 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERIL   27 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHH
Confidence            357889999999999999997664

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=89.64  E-value=0.1  Score=42.94  Aligned_cols=21  Identities=33%  Similarity=0.668  Sum_probs=19.0

Q ss_pred             cEEEEEEccCCCchHHHHHHH
Q 043252          216 FSVIPIIGMGGLGKTTLAQLV  236 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v  236 (337)
                      ++-|+|+|..|.|||||+..+
T Consensus         2 iRNv~iiGh~~~GKTtL~e~l   22 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEAL   22 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHH
Confidence            478999999999999999776

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=89.58  E-value=0.15  Score=39.71  Aligned_cols=37  Identities=11%  Similarity=0.056  Sum_probs=28.3

Q ss_pred             HHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          197 EKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       197 ~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -+..+..+|..     .++...+.|+|+++.|||++|..+.+
T Consensus        39 Fl~~l~~~l~~-----~PKkn~i~~~GP~~TGKS~f~~sl~~   75 (205)
T d1tuea_          39 FLGALKSFLKG-----TPKKNCLVFCGPANTGKSYFGMSFIH   75 (205)
T ss_dssp             HHHHHHHHHHT-----CTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHHcC-----CCCceEEEEECCCCccHHHHHHHHHH
Confidence            35566677743     23567999999999999999988765

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=89.37  E-value=0.14  Score=43.52  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=21.1

Q ss_pred             cEEEEEEccCCCchHHHHHHHHhc
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +-.|.|=|.-|+||||+++.+.+.
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~   29 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASA   29 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSG
T ss_pred             eEEEEEECCccCCHHHHHHHHHHH
Confidence            457888899999999999999875

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=89.09  E-value=0.11  Score=41.63  Aligned_cols=22  Identities=27%  Similarity=0.477  Sum_probs=19.4

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ++|+|+|-...|||||+..+..
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~   27 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRG   27 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHh
Confidence            4799999999999999987754

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=89.01  E-value=0.11  Score=39.61  Aligned_cols=21  Identities=33%  Similarity=0.430  Sum_probs=19.1

Q ss_pred             EEEEEccCCCchHHHHHHHHh
Q 043252          218 VIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      -|+|+|...+|||||...+..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            589999999999999998864

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=88.47  E-value=0.1  Score=44.25  Aligned_cols=23  Identities=39%  Similarity=0.457  Sum_probs=20.3

Q ss_pred             cEEEEEEccCCCchHHHHHHHHh
Q 043252          216 FSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       216 ~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      +..|+|=|.-|+||||+++.+.+
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~   26 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVA   26 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC
T ss_pred             ceEEEEECCcCCCHHHHHHHHHH
Confidence            45689999999999999999865

>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=88.36  E-value=0.31  Score=42.43  Aligned_cols=40  Identities=20%  Similarity=0.311  Sum_probs=29.2

Q ss_pred             cch-hHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          193 GRE-TEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       193 Gr~-~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      |.. ...+.+..++..+       -..|.|.|+.|.||||....+.+.
T Consensus       141 G~~~~~~~~l~~l~~~~-------~GliLvtGpTGSGKSTTl~~~l~~  181 (401)
T d1p9ra_         141 GMTAHNHDNFRRLIKRP-------HGIILVTGPTGSGKSTTLYAGLQE  181 (401)
T ss_dssp             CCCHHHHHHHHHHHTSS-------SEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHhhh-------hceEEEEcCCCCCccHHHHHHhhh
Confidence            543 4455666665433       369999999999999999888763

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.39  E-value=0.31  Score=40.13  Aligned_cols=26  Identities=23%  Similarity=0.345  Sum_probs=23.3

Q ss_pred             CCcEEEEEEccCCCchHHHHHHHHhc
Q 043252          214 GGFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       214 ~~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +.+.||+|+|+-+.|||||...++..
T Consensus        30 ~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          30 QPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             SBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            35899999999999999999999863

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=87.28  E-value=0.058  Score=43.35  Aligned_cols=22  Identities=23%  Similarity=0.460  Sum_probs=18.4

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      +..++|..|+|||||...+..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            5568899999999999998754

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=86.54  E-value=0.058  Score=41.61  Aligned_cols=20  Identities=30%  Similarity=0.371  Sum_probs=17.1

Q ss_pred             EEEEEccCCCchHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~  237 (337)
                      +..|+|+.|+||||+..+++
T Consensus        26 ~tvi~G~NGsGKStil~Ai~   45 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFV   45 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            44578999999999998885

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=86.39  E-value=0.17  Score=42.96  Aligned_cols=23  Identities=35%  Similarity=0.345  Sum_probs=20.2

Q ss_pred             EEEEEEccCCCchHHHHHHHHhc
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -.|+|=|.-|+||||+++.+.+.
T Consensus         6 lrI~IEG~iGsGKSTl~~~L~~~   28 (331)
T d1osna_           6 LRIYLDGAYGIGKTTAAEEFLHH   28 (331)
T ss_dssp             EEEEEEESSSSCTTHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35888899999999999999774

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=85.95  E-value=0.45  Score=38.84  Aligned_cols=36  Identities=22%  Similarity=0.234  Sum_probs=26.7

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHh
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      ..+..+|....    +.-..+.++|+|+.|||+++..+..
T Consensus        91 ~~l~~~L~~~~----~k~n~~~l~G~~~tGKS~f~~~i~~  126 (267)
T d1u0ja_          91 SVFLGWATKKF----GKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHHTTCS----TTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHcCCC----CccEEEEEEcCCCCCHHHHHHHHHH
Confidence            44555664332    3456899999999999999988865

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.56  E-value=0.25  Score=41.98  Aligned_cols=34  Identities=21%  Similarity=0.247  Sum_probs=25.9

Q ss_pred             HHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHH
Q 043252          199 KEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       199 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~  237 (337)
                      +.+.+++...     ++++-|+|+|..|.|||||+-.+.
T Consensus         5 ~~~~~lm~~~-----~~IRNI~iiGhvd~GKTTL~d~Ll   38 (341)
T d1n0ua2           5 DQMRSLMDKV-----TNVRNMSVIAHVDHGKSTLTDSLV   38 (341)
T ss_dssp             HHHHHHHHCG-----GGEEEEEEECCGGGTHHHHHHHHH
T ss_pred             HHHHHHhcCc-----ccCcEEEEEeCCCCcHHHHHHHHH
Confidence            4455555432     358889999999999999997664

>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=84.37  E-value=4.9  Score=30.65  Aligned_cols=110  Identities=16%  Similarity=0.167  Sum_probs=55.5

Q ss_pred             cccchhHHHHHHHHHhcCCCCCCCCcEEEEEEccCCCchHHHHHHHHhcccccccccceEEEEeCCCCCHHHHHHHHHHH
Q 043252          191 VYGRETEKKEIVELLLKDDSRNDGGFSVIPIIGMGGLGKTTLAQLVYNDKQVEDHFDLKAWTCVSDDFDVIRLTKSILLS  270 (337)
Q Consensus       191 ~vGr~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v~~~~~~~~~~~~il~~  270 (337)
                      +--|+-..+.+..++..        -+. .|+++.|.|||.+|-.+...      +...+.|-+...    .+..+..+.
T Consensus        69 ~~Lr~yQ~eav~~~~~~--------~~~-ll~~~tG~GKT~~a~~~~~~------~~~~~Liv~p~~----~L~~q~~~~  129 (206)
T d2fz4a1          69 ISLRDYQEKALERWLVD--------KRG-CIVLPTGSGKTHVAMAAINE------LSTPTLIVVPTL----ALAEQWKER  129 (206)
T ss_dssp             CCCCHHHHHHHHHHTTT--------SEE-EEEESSSTTHHHHHHHHHHH------SCSCEEEEESSH----HHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHhC--------CCc-EEEeCCCCCceehHHhHHHH------hcCceeEEEccc----chHHHHHHH
Confidence            34466666666655521        123 46789999999998777653      222333333321    223333333


Q ss_pred             hhC---CC--------C-C---CCCCHHHHHHHHHHHcCCCeEEEEEeCCCCCChhcHHHhhccC
Q 043252          271 IAS---DQ--------N-V---DNHDLNKLQEELKKQLFGKKFLLVLDDVWNENYTDWVHLSLPF  320 (337)
Q Consensus       271 ~~~---~~--------~-~---~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~~l  320 (337)
                      +..   ..        . .   .....+.+..... .+.++--+||+|++.+.....|..+...+
T Consensus       130 ~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~-~~~~~~~lvIiDEaH~~~a~~~~~i~~~~  193 (206)
T d2fz4a1         130 LGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAE-KLGNRFMLLIFDEVHHLPAESYVQIAQMS  193 (206)
T ss_dssp             HGGGCGGGEEEESSSCBCCCSEEEEEHHHHHHTHH-HHTTTCSEEEEECSSCCCTTTHHHHHHTC
T ss_pred             HHhhcccchhhcccccccccccccceehhhhhhhH-hhCCcCCEEEEECCeeCCcHHHHHHHhcc
Confidence            321   10        0 0   0112333333222 23333339999999876546777666544

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=84.28  E-value=0.27  Score=38.42  Aligned_cols=20  Identities=35%  Similarity=0.348  Sum_probs=17.6

Q ss_pred             EEEEEccCCCchHHHHHHHH
Q 043252          218 VIPIIGMGGLGKTTLAQLVY  237 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~  237 (337)
                      -|+|+|-.+.|||||+.++.
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll   24 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALT   24 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHH
Confidence            48899999999999997763

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=84.01  E-value=0.19  Score=41.53  Aligned_cols=16  Identities=25%  Similarity=0.331  Sum_probs=13.6

Q ss_pred             EEEEEccCCCchHHHH
Q 043252          218 VIPIIGMGGLGKTTLA  233 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa  233 (337)
                      .+.|.|.+|.||||.+
T Consensus        16 ~~lI~g~aGTGKTt~l   31 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVI   31 (306)
T ss_dssp             EEEECCCTTSCHHHHH
T ss_pred             CEEEEeeCCccHHHHH
Confidence            4678899999999865

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=83.21  E-value=0.28  Score=40.85  Aligned_cols=15  Identities=33%  Similarity=0.483  Sum_probs=13.2

Q ss_pred             EEEEccCCCchHHHH
Q 043252          219 IPIIGMGGLGKTTLA  233 (337)
Q Consensus       219 i~I~G~gGiGKTtLa  233 (337)
                      +.|.|.+|.||||.+
T Consensus        27 ~lV~g~aGSGKTt~l   41 (318)
T d1pjra1          27 LLIMAGAGSGKTRVL   41 (318)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEEecCCccHHHHH
Confidence            668899999999876

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=82.95  E-value=0.34  Score=39.74  Aligned_cols=22  Identities=27%  Similarity=0.427  Sum_probs=19.6

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|+|+|.+.+|||||-..+-+.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHCC
Confidence            5899999999999999988653

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.50  E-value=0.33  Score=42.20  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=19.6

Q ss_pred             EEEEEEccCCCchHHHHHHHHh
Q 043252          217 SVIPIIGMGGLGKTTLAQLVYN  238 (337)
Q Consensus       217 ~vi~I~G~gGiGKTtLa~~v~~  238 (337)
                      --|+|+|.+|+|||||...+..
T Consensus        57 l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          57 LNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            3589999999999999999874

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=80.99  E-value=1.3  Score=36.04  Aligned_cols=25  Identities=28%  Similarity=0.320  Sum_probs=21.6

Q ss_pred             CcEEEEEEccCCCchHHHHHHHHhc
Q 043252          215 GFSVIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       215 ~~~vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      ..-.|+|+|++.+|||||+..+...
T Consensus       111 ~~~~v~vvG~PNvGKSsliN~L~~~  135 (273)
T d1puja_         111 RAIRALIIGIPNVGKSTLINRLAKK  135 (273)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CceEEEEEecCccchhhhhhhhhcc
Confidence            3456899999999999999999864

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=80.28  E-value=0.43  Score=39.52  Aligned_cols=22  Identities=27%  Similarity=0.471  Sum_probs=19.9

Q ss_pred             EEEEEccCCCchHHHHHHHHhc
Q 043252          218 VIPIIGMGGLGKTTLAQLVYND  239 (337)
Q Consensus       218 vi~I~G~gGiGKTtLa~~v~~~  239 (337)
                      -|+|+|.+.+|||||-..+-+.
T Consensus        12 kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          12 KTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            5999999999999999999754